Starting phenix.real_space_refine on Fri Jun 27 15:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpi_44778/06_2025/9bpi_44778.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpi_44778/06_2025/9bpi_44778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpi_44778/06_2025/9bpi_44778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpi_44778/06_2025/9bpi_44778.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpi_44778/06_2025/9bpi_44778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpi_44778/06_2025/9bpi_44778.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 21000 2.51 5 N 5760 2.21 5 O 6312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 241 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33192 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "D" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "H" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "J" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "L" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "N" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "P" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "R" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "T" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "V" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "X" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Time building chain proxies: 18.85, per 1000 atoms: 0.57 Number of scatterers: 33192 At special positions: 0 Unit cell: (135.96, 134.93, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 6312 8.00 N 5760 7.00 C 21000 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: 10.97 Conformation dependent library (CDL) restraints added in 5.3 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 13 through 41 Processing helix chain 'A' and resid 48 through 76 removed outlier: 3.653A pdb=" N ARG A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 158 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'C' and resid 13 through 43 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'D' and resid 13 through 41 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 158 Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 43 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 157 Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'F' and resid 13 through 41 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 125 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 175 Processing helix chain 'G' and resid 13 through 43 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 138 through 157 Processing helix chain 'G' and resid 162 through 174 Processing helix chain 'H' and resid 13 through 43 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 158 Processing helix chain 'H' and resid 163 through 175 Processing helix chain 'I' and resid 13 through 41 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 158 Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'J' and resid 13 through 43 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 158 Processing helix chain 'J' and resid 163 through 175 Processing helix chain 'K' and resid 13 through 41 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 158 Processing helix chain 'K' and resid 163 through 175 Processing helix chain 'L' and resid 13 through 41 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 125 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 158 Processing helix chain 'L' and resid 164 through 174 Processing helix chain 'M' and resid 13 through 41 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 125 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 158 Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'N' and resid 13 through 41 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 41 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 125 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 125 Processing helix chain 'P' and resid 126 through 137 removed outlier: 3.733A pdb=" N HIS P 136 " --> pdb=" O PHE P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 175 Processing helix chain 'Q' and resid 13 through 41 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 158 Processing helix chain 'Q' and resid 159 through 161 No H-bonds generated for 'chain 'Q' and resid 159 through 161' Processing helix chain 'Q' and resid 162 through 174 Processing helix chain 'R' and resid 13 through 43 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 41 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 158 Processing helix chain 'S' and resid 162 through 174 Processing helix chain 'T' and resid 13 through 43 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 125 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 158 Processing helix chain 'T' and resid 163 through 175 Processing helix chain 'U' and resid 13 through 41 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 160 removed outlier: 4.076A pdb=" N GLY U 160 " --> pdb=" O HIS U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 175 Processing helix chain 'V' and resid 13 through 41 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 158 Processing helix chain 'V' and resid 162 through 174 removed outlier: 3.509A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 43 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 158 Processing helix chain 'W' and resid 162 through 174 Processing helix chain 'X' and resid 13 through 41 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 162 through 174 2679 hydrogen bonds defined for protein. 8037 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: 10.98 Time building geometry restraints manager: 12.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10039 1.33 - 1.45: 5545 1.45 - 1.58: 18016 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 33816 Sorted by residual: bond pdb=" CZ ARG D 76 " pdb=" NH2 ARG D 76 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" CZ ARG A 157 " pdb=" NH2 ARG A 157 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.07e+01 bond pdb=" CZ ARG R 76 " pdb=" NH2 ARG R 76 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG Q 76 " pdb=" NH2 ARG Q 76 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" CZ ARG K 63 " pdb=" NH2 ARG K 63 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.92e+00 ... (remaining 33811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 31747 1.71 - 3.41: 11126 3.41 - 5.12: 2316 5.12 - 6.83: 255 6.83 - 8.53: 36 Bond angle restraints: 45480 Sorted by residual: angle pdb=" N ASP W 98 " pdb=" CA ASP W 98 " pdb=" C ASP W 98 " ideal model delta sigma weight residual 111.71 119.99 -8.28 1.15e+00 7.56e-01 5.18e+01 angle pdb=" CA ASP X 126 " pdb=" CB ASP X 126 " pdb=" CG ASP X 126 " ideal model delta sigma weight residual 112.60 106.78 5.82 1.00e+00 1.00e+00 3.39e+01 angle pdb=" CB HIS K 156 " pdb=" CG HIS K 156 " pdb=" CD2 HIS K 156 " ideal model delta sigma weight residual 131.20 124.20 7.00 1.30e+00 5.92e-01 2.90e+01 angle pdb=" CB HIS D 156 " pdb=" CG HIS D 156 " pdb=" CD2 HIS D 156 " ideal model delta sigma weight residual 131.20 124.21 6.99 1.30e+00 5.92e-01 2.89e+01 angle pdb=" CA PHE W 170 " pdb=" CB PHE W 170 " pdb=" CG PHE W 170 " ideal model delta sigma weight residual 113.80 108.47 5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 45475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 18352 17.74 - 35.48: 1528 35.48 - 53.22: 377 53.22 - 70.96: 116 70.96 - 88.69: 51 Dihedral angle restraints: 20424 sinusoidal: 8472 harmonic: 11952 Sorted by residual: dihedral pdb=" N ASP W 98 " pdb=" C ASP W 98 " pdb=" CA ASP W 98 " pdb=" CB ASP W 98 " ideal model delta harmonic sigma weight residual 122.80 139.08 -16.28 0 2.50e+00 1.60e-01 4.24e+01 dihedral pdb=" C ASN K 11 " pdb=" N ASN K 11 " pdb=" CA ASN K 11 " pdb=" CB ASN K 11 " ideal model delta harmonic sigma weight residual -122.60 -137.80 15.20 0 2.50e+00 1.60e-01 3.69e+01 dihedral pdb=" C ARG U 68 " pdb=" N ARG U 68 " pdb=" CA ARG U 68 " pdb=" CB ARG U 68 " ideal model delta harmonic sigma weight residual -122.60 -137.61 15.01 0 2.50e+00 1.60e-01 3.60e+01 ... (remaining 20421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3999 0.133 - 0.265: 806 0.265 - 0.397: 54 0.397 - 0.530: 9 0.530 - 0.662: 4 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA ASP W 98 " pdb=" N ASP W 98 " pdb=" C ASP W 98 " pdb=" CB ASP W 98 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ARG U 68 " pdb=" N ARG U 68 " pdb=" C ARG U 68 " pdb=" CB ARG U 68 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.95e+00 chirality pdb=" CA ASN K 11 " pdb=" N ASN K 11 " pdb=" C ASN K 11 " pdb=" CB ASN K 11 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.42e+00 ... (remaining 4869 not shown) Planarity restraints: 5952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 34 " 0.189 2.00e-02 2.50e+03 1.06e-01 2.27e+02 pdb=" CG TYR D 34 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR D 34 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR D 34 " -0.082 2.00e-02 2.50e+03 pdb=" CE1 TYR D 34 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR D 34 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR D 34 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR D 34 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 66 " 0.167 2.00e-02 2.50e+03 9.17e-02 1.68e+02 pdb=" CG TYR O 66 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR O 66 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR O 66 " -0.081 2.00e-02 2.50e+03 pdb=" CE1 TYR O 66 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR O 66 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR O 66 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR O 66 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 12 " -0.152 2.00e-02 2.50e+03 8.43e-02 1.42e+02 pdb=" CG TYR G 12 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR G 12 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR G 12 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR G 12 " 0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR G 12 " 0.051 2.00e-02 2.50e+03 pdb=" CZ TYR G 12 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR G 12 " -0.134 2.00e-02 2.50e+03 ... (remaining 5949 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 16909 2.98 - 3.46: 41041 3.46 - 3.94: 62376 3.94 - 4.42: 73108 4.42 - 4.90: 115582 Nonbonded interactions: 309016 Sorted by model distance: nonbonded pdb=" OH TYR R 27 " pdb=" OE2 GLU R 141 " model vdw 2.506 3.040 nonbonded pdb=" OH TYR L 27 " pdb=" OE2 GLU L 141 " model vdw 2.506 3.040 nonbonded pdb=" OH TYR K 27 " pdb=" OE2 GLU K 141 " model vdw 2.510 3.040 nonbonded pdb=" OD2 ASP B 44 " pdb=" OG SER W 6 " model vdw 2.511 3.040 nonbonded pdb=" OD2 ASP C 44 " pdb=" OG SER X 6 " model vdw 2.515 3.040 ... (remaining 309011 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: 0.01 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 78.010 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.210 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.011 0.045 33816 Z= 0.701 Angle : 1.746 8.532 45480 Z= 1.180 Chirality : 0.100 0.662 4872 Planarity : 0.020 0.351 5952 Dihedral : 15.487 88.694 12744 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.76 % Allowed : 4.49 % Favored : 94.75 % Rotamer: Outliers : 4.31 % Allowed : 7.01 % Favored : 88.68 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.12), residues: 4080 helix: 0.71 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -2.58 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.016 TRP P 93 HIS 0.023 0.005 HIS P 136 PHE 0.103 0.020 PHE M 41 TYR 0.189 0.032 TYR D 34 ARG 0.018 0.002 ARG O 9 Details of bonding type rmsd hydrogen bonds : bond 0.10667 ( 2679) hydrogen bonds : angle 6.21598 ( 8037) covalent geometry : bond 0.01121 (33816) covalent geometry : angle 1.74574 (45480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1973 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1823 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7008 (p0) cc_final: 0.6777 (p0) REVERT: B 60 GLU cc_start: 0.5324 (tp30) cc_final: 0.5122 (tp30) REVERT: B 87 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7277 (ptmm) REVERT: B 145 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7848 (mt) REVERT: E 107 GLU cc_start: 0.5048 (tp30) cc_final: 0.4697 (tp30) REVERT: G 34 TYR cc_start: 0.7156 (m-80) cc_final: 0.6857 (m-10) REVERT: G 44 ASP cc_start: 0.6910 (p0) cc_final: 0.6478 (p0) REVERT: G 107 GLU cc_start: 0.4897 (mm-30) cc_final: 0.4234 (mm-30) REVERT: G 162 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.5241 (pm20) REVERT: J 111 ASN cc_start: 0.6494 (t0) cc_final: 0.5981 (t0) REVERT: K 27 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.6219 (t80) REVERT: K 107 GLU cc_start: 0.5401 (tp30) cc_final: 0.5201 (tp30) REVERT: L 34 TYR cc_start: 0.6680 (m-80) cc_final: 0.6410 (m-10) REVERT: M 53 HIS cc_start: 0.6077 (t-90) cc_final: 0.5488 (t-90) REVERT: M 75 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6742 (mp10) REVERT: M 144 LEU cc_start: 0.7463 (tp) cc_final: 0.6930 (tp) REVERT: N 34 TYR cc_start: 0.7076 (m-80) cc_final: 0.6802 (m-10) REVERT: N 74 ASN cc_start: 0.6599 (m-40) cc_final: 0.6393 (m-40) REVERT: N 107 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5047 (mm-30) REVERT: N 116 ASP cc_start: 0.5600 (m-30) cc_final: 0.5314 (m-30) REVERT: P 8 ILE cc_start: 0.8125 (pt) cc_final: 0.7766 (pt) REVERT: P 52 SER cc_start: 0.5820 (t) cc_final: 0.5537 (p) REVERT: P 53 HIS cc_start: 0.6300 (t-170) cc_final: 0.5994 (t70) REVERT: Q 53 HIS cc_start: 0.5858 (t-170) cc_final: 0.5572 (t-90) REVERT: Q 136 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.6323 (p-80) REVERT: R 46 VAL cc_start: 0.7615 (t) cc_final: 0.7323 (t) REVERT: R 125 THR cc_start: 0.6977 (m) cc_final: 0.6720 (p) REVERT: R 131 ASP cc_start: 0.6309 (t70) cc_final: 0.6048 (t0) REVERT: U 11 ASN cc_start: 0.6911 (OUTLIER) cc_final: 0.6602 (p0) REVERT: U 144 LEU cc_start: 0.7271 (tp) cc_final: 0.6942 (tp) REVERT: V 63 ARG cc_start: 0.5264 (ttp-170) cc_final: 0.4909 (ttm-80) REVERT: V 112 GLN cc_start: 0.7038 (tp40) cc_final: 0.6741 (mm-40) REVERT: V 148 MET cc_start: 0.6296 (mmt) cc_final: 0.5615 (mmm) REVERT: X 112 GLN cc_start: 0.6723 (tp40) cc_final: 0.6273 (tp-100) REVERT: X 131 ASP cc_start: 0.5692 (t70) cc_final: 0.5356 (t0) outliers start: 150 outliers final: 42 residues processed: 1896 average time/residue: 0.7348 time to fit residues: 2105.5211 Evaluate side-chains 1132 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1082 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 136 HIS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 136 HIS Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain V residue 15 ASP Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 95 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 136 HIS B 74 ASN B 136 HIS C 29 GLN C 74 ASN C 83 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS D 53 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN E 74 ASN F 74 ASN F 156 HIS G 29 GLN G 53 HIS G 74 ASN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN H 11 ASN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN K 151 HIS L 29 GLN L 53 HIS L 73 GLN M 25 ASN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN O 151 HIS P 10 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** S 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 156 HIS ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 HIS V 83 GLN W 73 GLN W 75 GLN ** W 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.060430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053221 restraints weight = 120209.699| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.07 r_work: 0.2828 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33816 Z= 0.246 Angle : 0.772 9.843 45480 Z= 0.406 Chirality : 0.045 0.221 4872 Planarity : 0.005 0.068 5952 Dihedral : 6.860 73.891 4643 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.60 % Favored : 97.13 % Rotamer: Outliers : 5.26 % Allowed : 17.73 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 4080 helix: 1.94 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -2.71 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 93 HIS 0.013 0.002 HIS V 128 PHE 0.025 0.003 PHE T 132 TYR 0.054 0.003 TYR B 66 ARG 0.008 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 2679) hydrogen bonds : angle 4.31314 ( 8037) covalent geometry : bond 0.00519 (33816) covalent geometry : angle 0.77203 (45480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1242 time to evaluate : 4.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.9315 (p0) cc_final: 0.8872 (p0) REVERT: A 16 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9042 (t) REVERT: A 29 GLN cc_start: 0.9105 (tp40) cc_final: 0.8859 (tp40) REVERT: A 42 ASP cc_start: 0.9233 (t0) cc_final: 0.8913 (t0) REVERT: A 107 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8396 (mm-30) REVERT: A 112 GLN cc_start: 0.9344 (tp40) cc_final: 0.8797 (tp-100) REVERT: A 124 ARG cc_start: 0.9189 (mmt-90) cc_final: 0.8897 (mmt-90) REVERT: A 141 GLU cc_start: 0.8843 (tp30) cc_final: 0.8367 (tp30) REVERT: A 152 LEU cc_start: 0.9519 (mt) cc_final: 0.9293 (mt) REVERT: A 171 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8998 (tm-30) REVERT: B 12 TYR cc_start: 0.8627 (t80) cc_final: 0.8376 (t80) REVERT: B 15 ASP cc_start: 0.9310 (m-30) cc_final: 0.8970 (p0) REVERT: B 17 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8979 (tt0) REVERT: B 22 SER cc_start: 0.9677 (m) cc_final: 0.9430 (p) REVERT: B 53 HIS cc_start: 0.9093 (t70) cc_final: 0.8517 (t70) REVERT: B 79 ARG cc_start: 0.7526 (mmp80) cc_final: 0.7323 (mmp80) REVERT: B 81 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8994 (mm) REVERT: B 98 ASP cc_start: 0.9519 (t0) cc_final: 0.9188 (m-30) REVERT: B 104 MET cc_start: 0.9466 (ttp) cc_final: 0.9110 (ttm) REVERT: B 111 ASN cc_start: 0.9593 (t0) cc_final: 0.9374 (t0) REVERT: B 124 ARG cc_start: 0.9427 (tpp-160) cc_final: 0.8806 (mmm-85) REVERT: B 126 ASP cc_start: 0.8769 (t0) cc_final: 0.8485 (t0) REVERT: B 136 HIS cc_start: 0.9088 (OUTLIER) cc_final: 0.8014 (p-80) REVERT: B 139 ASP cc_start: 0.9076 (p0) cc_final: 0.8673 (p0) REVERT: B 148 MET cc_start: 0.9640 (mtt) cc_final: 0.9415 (mtp) REVERT: B 153 THR cc_start: 0.9464 (m) cc_final: 0.9192 (p) REVERT: C 12 TYR cc_start: 0.8529 (t80) cc_final: 0.8293 (t80) REVERT: C 64 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9144 (mm-30) REVERT: C 74 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8872 (m110) REVERT: C 126 ASP cc_start: 0.9136 (t0) cc_final: 0.8516 (t0) REVERT: C 132 PHE cc_start: 0.9387 (t80) cc_final: 0.9089 (t80) REVERT: C 168 TYR cc_start: 0.9141 (t80) cc_final: 0.8941 (t80) REVERT: D 52 SER cc_start: 0.9542 (t) cc_final: 0.9338 (t) REVERT: D 61 GLU cc_start: 0.9561 (OUTLIER) cc_final: 0.9001 (tm-30) REVERT: D 66 TYR cc_start: 0.9505 (p90) cc_final: 0.9185 (p90) REVERT: D 68 ARG cc_start: 0.9241 (ttm-80) cc_final: 0.8722 (ttm-80) REVERT: D 72 MET cc_start: 0.9622 (tmm) cc_final: 0.9363 (tmm) REVERT: D 74 ASN cc_start: 0.9061 (m-40) cc_final: 0.8756 (m-40) REVERT: D 112 GLN cc_start: 0.9354 (tp40) cc_final: 0.8855 (tp40) REVERT: D 116 ASP cc_start: 0.9381 (m-30) cc_final: 0.8898 (m-30) REVERT: D 124 ARG cc_start: 0.9313 (mmp80) cc_final: 0.9041 (mmt-90) REVERT: D 126 ASP cc_start: 0.9149 (t0) cc_final: 0.8808 (t70) REVERT: D 135 THR cc_start: 0.8452 (m) cc_final: 0.8183 (p) REVERT: D 136 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.8494 (p90) REVERT: D 172 ARG cc_start: 0.9344 (mmp-170) cc_final: 0.8892 (mmp80) REVERT: E 10 GLN cc_start: 0.8135 (tt0) cc_final: 0.7879 (tt0) REVERT: E 12 TYR cc_start: 0.9230 (t80) cc_final: 0.8604 (t80) REVERT: E 42 ASP cc_start: 0.9415 (t0) cc_final: 0.9101 (t0) REVERT: E 44 ASP cc_start: 0.9241 (p0) cc_final: 0.8997 (p0) REVERT: E 57 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8990 (tp30) REVERT: E 62 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9136 (mptt) REVERT: E 72 MET cc_start: 0.9482 (tmm) cc_final: 0.9278 (tmm) REVERT: E 86 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8986 (mmmm) REVERT: E 111 ASN cc_start: 0.9299 (t0) cc_final: 0.8803 (t0) REVERT: E 112 GLN cc_start: 0.9183 (tp40) cc_final: 0.8795 (tp40) REVERT: E 116 ASP cc_start: 0.8992 (m-30) cc_final: 0.8643 (m-30) REVERT: E 136 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8340 (p90) REVERT: E 141 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8122 (mt-10) REVERT: E 143 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9134 (mtmm) REVERT: E 168 TYR cc_start: 0.9192 (t80) cc_final: 0.8908 (t80) REVERT: F 17 GLU cc_start: 0.9145 (tt0) cc_final: 0.8705 (tt0) REVERT: F 42 ASP cc_start: 0.9133 (t70) cc_final: 0.8928 (t70) REVERT: F 44 ASP cc_start: 0.7999 (p0) cc_final: 0.7395 (p0) REVERT: F 52 SER cc_start: 0.9536 (t) cc_final: 0.9115 (m) REVERT: F 53 HIS cc_start: 0.9098 (t-170) cc_final: 0.8837 (t-90) REVERT: F 56 ARG cc_start: 0.9156 (tpp80) cc_final: 0.8855 (tpp80) REVERT: F 57 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8838 (mm-30) REVERT: F 90 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8566 (tp30) REVERT: F 104 MET cc_start: 0.9107 (ttp) cc_final: 0.8843 (ttm) REVERT: F 107 GLU cc_start: 0.9042 (tp30) cc_final: 0.8344 (tp30) REVERT: F 112 GLN cc_start: 0.9274 (tp40) cc_final: 0.8581 (tp-100) REVERT: F 140 GLU cc_start: 0.9547 (tp30) cc_final: 0.9343 (tp30) REVERT: F 145 ILE cc_start: 0.9630 (mt) cc_final: 0.9405 (mm) REVERT: F 170 PHE cc_start: 0.9490 (t80) cc_final: 0.9163 (t80) REVERT: G 34 TYR cc_start: 0.9267 (m-80) cc_final: 0.8898 (m-80) REVERT: G 53 HIS cc_start: 0.8757 (t-90) cc_final: 0.8487 (t70) REVERT: G 60 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8595 (tm-30) REVERT: G 61 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8980 (tt0) REVERT: G 64 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8160 (mp0) REVERT: G 68 ARG cc_start: 0.9223 (ttp-110) cc_final: 0.8878 (ttp-110) REVERT: G 126 ASP cc_start: 0.8982 (t0) cc_final: 0.8665 (t0) REVERT: G 131 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8971 (t0) REVERT: G 139 ASP cc_start: 0.9178 (p0) cc_final: 0.8831 (p0) REVERT: G 140 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8565 (mp0) REVERT: G 162 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: G 169 LEU cc_start: 0.9667 (mt) cc_final: 0.9427 (mt) REVERT: G 172 ARG cc_start: 0.9091 (mmm160) cc_final: 0.8840 (mmp80) REVERT: H 35 LEU cc_start: 0.9610 (tp) cc_final: 0.9402 (tp) REVERT: H 53 HIS cc_start: 0.9141 (t70) cc_final: 0.8817 (t70) REVERT: H 61 GLU cc_start: 0.9483 (mt-10) cc_final: 0.9182 (tm-30) REVERT: H 62 LYS cc_start: 0.9546 (mmtm) cc_final: 0.8807 (mmtt) REVERT: H 101 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8560 (mtmt) REVERT: H 111 ASN cc_start: 0.9634 (t0) cc_final: 0.9434 (t0) REVERT: H 124 ARG cc_start: 0.9455 (tpp-160) cc_final: 0.9150 (mmt-90) REVERT: H 141 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8575 (mm-30) REVERT: I 42 ASP cc_start: 0.9240 (t70) cc_final: 0.9008 (t70) REVERT: I 60 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8827 (tp30) REVERT: I 61 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8930 (tm-30) REVERT: I 124 ARG cc_start: 0.9310 (mmp80) cc_final: 0.9052 (mmp80) REVERT: I 126 ASP cc_start: 0.9281 (t0) cc_final: 0.8954 (t0) REVERT: I 140 GLU cc_start: 0.8777 (mp0) cc_final: 0.8522 (mp0) REVERT: I 168 TYR cc_start: 0.9422 (t80) cc_final: 0.9085 (t80) REVERT: J 10 GLN cc_start: 0.8354 (tt0) cc_final: 0.7871 (tt0) REVERT: J 44 ASP cc_start: 0.8444 (p0) cc_final: 0.7995 (p0) REVERT: J 46 VAL cc_start: 0.9391 (t) cc_final: 0.9064 (p) REVERT: J 60 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8370 (tm-30) REVERT: J 64 GLU cc_start: 0.9465 (mm-30) cc_final: 0.8920 (mm-30) REVERT: J 66 TYR cc_start: 0.9506 (p90) cc_final: 0.9193 (p90) REVERT: K 7 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: K 42 ASP cc_start: 0.9267 (t70) cc_final: 0.8924 (t70) REVERT: K 56 ARG cc_start: 0.9070 (ttm-80) cc_final: 0.8453 (ttm-80) REVERT: K 72 MET cc_start: 0.9655 (tmm) cc_final: 0.9450 (ppp) REVERT: K 81 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8541 (tt) REVERT: K 83 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8888 (mm110) REVERT: K 126 ASP cc_start: 0.9302 (t0) cc_final: 0.8933 (t0) REVERT: K 143 LYS cc_start: 0.9253 (mtmm) cc_final: 0.8979 (mtmm) REVERT: K 144 LEU cc_start: 0.9563 (tp) cc_final: 0.9313 (tt) REVERT: L 29 GLN cc_start: 0.9445 (tt0) cc_final: 0.8635 (tm-30) REVERT: L 34 TYR cc_start: 0.9345 (m-80) cc_final: 0.8850 (m-10) REVERT: L 56 ARG cc_start: 0.9003 (mmt90) cc_final: 0.8760 (mtt-85) REVERT: L 67 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8961 (tp30) REVERT: L 68 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8173 (ttp-170) REVERT: L 74 ASN cc_start: 0.9341 (m-40) cc_final: 0.8943 (m-40) REVERT: L 107 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8587 (mm-30) REVERT: L 112 GLN cc_start: 0.9222 (tp40) cc_final: 0.8797 (tp40) REVERT: L 126 ASP cc_start: 0.9090 (t70) cc_final: 0.8885 (t0) REVERT: L 131 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8930 (t0) REVERT: L 139 ASP cc_start: 0.9011 (t0) cc_final: 0.8757 (t0) REVERT: L 140 GLU cc_start: 0.8866 (mp0) cc_final: 0.8636 (mp0) REVERT: L 141 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: L 143 LYS cc_start: 0.9478 (mtpt) cc_final: 0.9173 (mtmm) REVERT: L 170 PHE cc_start: 0.9522 (t80) cc_final: 0.9299 (t80) REVERT: M 46 VAL cc_start: 0.9471 (t) cc_final: 0.9139 (m) REVERT: M 75 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.8694 (mp10) REVERT: N 42 ASP cc_start: 0.8995 (t0) cc_final: 0.8643 (t0) REVERT: N 44 ASP cc_start: 0.8412 (p0) cc_final: 0.7959 (p0) REVERT: N 52 SER cc_start: 0.9545 (t) cc_final: 0.9046 (m) REVERT: N 64 GLU cc_start: 0.9045 (mp0) cc_final: 0.8738 (mp0) REVERT: N 74 ASN cc_start: 0.9204 (m-40) cc_final: 0.8927 (m-40) REVERT: N 112 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8495 (tp40) REVERT: N 136 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8623 (p90) REVERT: N 139 ASP cc_start: 0.9254 (t0) cc_final: 0.9016 (t0) REVERT: N 142 VAL cc_start: 0.9503 (t) cc_final: 0.9198 (m) REVERT: N 147 LYS cc_start: 0.9079 (ptpp) cc_final: 0.8595 (ptpp) REVERT: O 39 PHE cc_start: 0.8908 (m-10) cc_final: 0.8191 (m-10) REVERT: O 42 ASP cc_start: 0.9330 (t0) cc_final: 0.8888 (t70) REVERT: O 44 ASP cc_start: 0.8551 (p0) cc_final: 0.8326 (p0) REVERT: O 52 SER cc_start: 0.9444 (t) cc_final: 0.9162 (p) REVERT: O 60 GLU cc_start: 0.9274 (tp30) cc_final: 0.8959 (tp30) REVERT: O 64 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9066 (mm-30) REVERT: O 66 TYR cc_start: 0.9379 (p90) cc_final: 0.9151 (p90) REVERT: O 68 ARG cc_start: 0.9201 (ttm-80) cc_final: 0.8977 (ttm-80) REVERT: O 71 LYS cc_start: 0.9469 (ttmm) cc_final: 0.9134 (tppp) REVERT: O 126 ASP cc_start: 0.8937 (t0) cc_final: 0.8673 (t0) REVERT: O 153 THR cc_start: 0.9224 (m) cc_final: 0.8964 (p) REVERT: O 167 GLU cc_start: 0.8816 (mp0) cc_final: 0.8471 (mp0) REVERT: O 172 ARG cc_start: 0.9278 (mmp-170) cc_final: 0.9015 (mmp80) REVERT: P 53 HIS cc_start: 0.9011 (t-170) cc_final: 0.8496 (t-90) REVERT: P 57 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8663 (mm-30) REVERT: P 61 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9028 (tm-30) REVERT: P 62 LYS cc_start: 0.9305 (mmpt) cc_final: 0.8977 (mmmt) REVERT: P 64 GLU cc_start: 0.9421 (tp30) cc_final: 0.8796 (tm-30) REVERT: P 74 ASN cc_start: 0.9051 (m-40) cc_final: 0.8826 (m-40) REVERT: P 87 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9165 (ptpp) REVERT: P 100 MET cc_start: 0.9375 (mmm) cc_final: 0.9040 (tpt) REVERT: P 107 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9025 (mm-30) REVERT: P 139 ASP cc_start: 0.8880 (t70) cc_final: 0.8219 (t70) REVERT: P 143 LYS cc_start: 0.9368 (mtmt) cc_final: 0.9082 (mtmm) REVERT: P 148 MET cc_start: 0.9624 (tpp) cc_final: 0.9065 (mmm) REVERT: Q 22 SER cc_start: 0.9467 (m) cc_final: 0.9261 (p) REVERT: Q 53 HIS cc_start: 0.9290 (t-170) cc_final: 0.8620 (t-90) REVERT: Q 57 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8878 (mm-30) REVERT: Q 104 MET cc_start: 0.9447 (ttt) cc_final: 0.9199 (ttm) REVERT: Q 107 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8892 (mm-30) REVERT: Q 140 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8582 (mp0) REVERT: Q 172 ARG cc_start: 0.9323 (mmp80) cc_final: 0.9115 (mmp80) REVERT: R 10 GLN cc_start: 0.8099 (tt0) cc_final: 0.7844 (tt0) REVERT: R 34 TYR cc_start: 0.9587 (m-10) cc_final: 0.9346 (m-10) REVERT: R 44 ASP cc_start: 0.8756 (p0) cc_final: 0.8467 (p0) REVERT: R 52 SER cc_start: 0.9443 (t) cc_final: 0.9221 (m) REVERT: R 53 HIS cc_start: 0.8902 (t-90) cc_final: 0.8408 (m-70) REVERT: R 68 ARG cc_start: 0.9126 (mtm-85) cc_final: 0.8836 (mtt-85) REVERT: R 104 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9040 (tpp) REVERT: S 68 ARG cc_start: 0.9183 (ptp-110) cc_final: 0.8943 (ptp90) REVERT: S 74 ASN cc_start: 0.9292 (m-40) cc_final: 0.9040 (m110) REVERT: S 104 MET cc_start: 0.9235 (ttp) cc_final: 0.8573 (ttm) REVERT: S 135 THR cc_start: 0.9398 (m) cc_final: 0.9123 (p) REVERT: S 144 LEU cc_start: 0.9532 (tp) cc_final: 0.9180 (tp) REVERT: S 145 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9332 (mp) REVERT: S 148 MET cc_start: 0.9289 (ttm) cc_final: 0.8598 (mtp) REVERT: T 7 GLN cc_start: 0.7673 (pm20) cc_final: 0.6947 (pm20) REVERT: T 12 TYR cc_start: 0.9004 (t80) cc_final: 0.8537 (t80) REVERT: T 17 GLU cc_start: 0.9269 (tt0) cc_final: 0.8935 (tt0) REVERT: T 53 HIS cc_start: 0.9116 (t-170) cc_final: 0.8722 (t-90) REVERT: T 64 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8893 (mm-30) REVERT: T 68 ARG cc_start: 0.9333 (ttp-170) cc_final: 0.8785 (ttp-170) REVERT: T 107 GLU cc_start: 0.9288 (tp30) cc_final: 0.9074 (tp30) REVERT: T 124 ARG cc_start: 0.9335 (mmp80) cc_final: 0.8936 (mmp80) REVERT: T 132 PHE cc_start: 0.9154 (t80) cc_final: 0.8745 (t80) REVERT: T 136 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.7687 (p-80) REVERT: T 144 LEU cc_start: 0.9619 (tp) cc_final: 0.9334 (tp) REVERT: T 168 TYR cc_start: 0.9259 (t80) cc_final: 0.9035 (t80) REVERT: T 172 ARG cc_start: 0.9337 (mmp80) cc_final: 0.8886 (tpp80) REVERT: U 27 TYR cc_start: 0.9355 (m-80) cc_final: 0.9047 (m-80) REVERT: U 29 GLN cc_start: 0.9156 (tp40) cc_final: 0.8866 (tp40) REVERT: U 42 ASP cc_start: 0.9239 (t0) cc_final: 0.8930 (t0) REVERT: U 111 ASN cc_start: 0.9560 (t0) cc_final: 0.9334 (t0) REVERT: U 112 GLN cc_start: 0.9535 (tp40) cc_final: 0.9161 (tp40) REVERT: U 171 GLU cc_start: 0.9358 (tm-30) cc_final: 0.8984 (tm-30) REVERT: V 12 TYR cc_start: 0.8096 (t80) cc_final: 0.7793 (t80) REVERT: V 34 TYR cc_start: 0.9279 (m-10) cc_final: 0.9035 (m-10) REVERT: V 39 PHE cc_start: 0.9131 (m-80) cc_final: 0.8884 (m-80) REVERT: V 46 VAL cc_start: 0.9545 (t) cc_final: 0.9319 (p) REVERT: V 49 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8694 (tm-30) REVERT: V 61 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9105 (mm-30) REVERT: V 68 ARG cc_start: 0.9144 (ttp-110) cc_final: 0.8857 (mtp85) REVERT: V 104 MET cc_start: 0.9294 (tpp) cc_final: 0.8904 (tpp) REVERT: V 112 GLN cc_start: 0.9310 (tp40) cc_final: 0.8912 (tp-100) REVERT: V 139 ASP cc_start: 0.9089 (t70) cc_final: 0.8685 (t0) REVERT: V 148 MET cc_start: 0.9653 (mmt) cc_final: 0.9371 (mmm) REVERT: V 171 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8673 (tm-30) REVERT: W 15 ASP cc_start: 0.9083 (t0) cc_final: 0.8817 (t0) REVERT: W 44 ASP cc_start: 0.9127 (p0) cc_final: 0.8469 (p0) REVERT: W 61 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8880 (tm-30) REVERT: W 67 GLU cc_start: 0.9586 (mt-10) cc_final: 0.9222 (mt-10) REVERT: W 126 ASP cc_start: 0.9366 (t0) cc_final: 0.8689 (t0) REVERT: W 137 PHE cc_start: 0.9127 (m-80) cc_final: 0.8845 (m-10) REVERT: W 153 THR cc_start: 0.9105 (m) cc_final: 0.8825 (p) REVERT: X 53 HIS cc_start: 0.9023 (t-90) cc_final: 0.8649 (t-90) REVERT: X 84 ASP cc_start: 0.9194 (m-30) cc_final: 0.8016 (m-30) REVERT: X 126 ASP cc_start: 0.8851 (t0) cc_final: 0.8561 (t0) REVERT: X 132 PHE cc_start: 0.9157 (t80) cc_final: 0.8623 (t80) outliers start: 183 outliers final: 93 residues processed: 1358 average time/residue: 0.5462 time to fit residues: 1165.6982 Evaluate side-chains 1120 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1007 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 136 HIS Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 136 HIS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain R residue 136 HIS Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 136 HIS Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 87 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 193 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 301 optimal weight: 8.9990 chunk 230 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 359 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 136 HIS C 29 GLN C 75 GLN C 83 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN G 29 GLN G 83 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 ASN N 21 ASN ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** R 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN T 75 GLN T 111 ASN U 75 GLN U 156 HIS V 29 GLN V 53 HIS V 75 GLN W 73 GLN ** W 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054071 restraints weight = 119480.814| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.07 r_work: 0.2849 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33816 Z= 0.187 Angle : 0.704 9.920 45480 Z= 0.369 Chirality : 0.042 0.205 4872 Planarity : 0.004 0.046 5952 Dihedral : 6.362 80.023 4600 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.97 % Favored : 96.84 % Rotamer: Outliers : 5.11 % Allowed : 20.43 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.13), residues: 4080 helix: 1.99 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -2.62 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 93 HIS 0.016 0.001 HIS B 136 PHE 0.028 0.003 PHE U 132 TYR 0.037 0.003 TYR H 66 ARG 0.015 0.001 ARG H 43 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 2679) hydrogen bonds : angle 4.17098 ( 8037) covalent geometry : bond 0.00410 (33816) covalent geometry : angle 0.70433 (45480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 1193 time to evaluate : 4.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.9341 (p0) cc_final: 0.9068 (p0) REVERT: A 16 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9024 (t) REVERT: A 29 GLN cc_start: 0.9123 (tp40) cc_final: 0.8840 (tp40) REVERT: A 42 ASP cc_start: 0.9267 (t0) cc_final: 0.8904 (t0) REVERT: A 52 SER cc_start: 0.9442 (t) cc_final: 0.9165 (m) REVERT: A 107 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 112 GLN cc_start: 0.9327 (tp40) cc_final: 0.8811 (tp-100) REVERT: A 124 ARG cc_start: 0.9235 (mmt-90) cc_final: 0.8983 (mmt-90) REVERT: A 141 GLU cc_start: 0.8866 (tp30) cc_final: 0.7904 (tp30) REVERT: A 171 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8938 (tm-30) REVERT: B 22 SER cc_start: 0.9683 (m) cc_final: 0.9439 (p) REVERT: B 53 HIS cc_start: 0.8975 (t70) cc_final: 0.8435 (t70) REVERT: B 57 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8721 (mm-30) REVERT: B 63 ARG cc_start: 0.9323 (ttp80) cc_final: 0.8961 (ttp80) REVERT: B 66 TYR cc_start: 0.9362 (p90) cc_final: 0.9135 (p90) REVERT: B 98 ASP cc_start: 0.9495 (t0) cc_final: 0.9209 (m-30) REVERT: B 104 MET cc_start: 0.9390 (ttp) cc_final: 0.9029 (ttm) REVERT: B 112 GLN cc_start: 0.9400 (tp40) cc_final: 0.8993 (tp-100) REVERT: B 140 GLU cc_start: 0.8471 (mp0) cc_final: 0.8204 (mp0) REVERT: B 148 MET cc_start: 0.9589 (mtt) cc_final: 0.9382 (mtp) REVERT: B 153 THR cc_start: 0.9393 (m) cc_final: 0.9146 (p) REVERT: C 42 ASP cc_start: 0.9309 (t70) cc_final: 0.9015 (t70) REVERT: C 44 ASP cc_start: 0.8785 (p0) cc_final: 0.8380 (p0) REVERT: C 58 LEU cc_start: 0.9533 (mp) cc_final: 0.9210 (tp) REVERT: C 63 ARG cc_start: 0.9111 (mtp85) cc_final: 0.8701 (mtp85) REVERT: C 68 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8681 (mtt180) REVERT: C 73 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8661 (tp40) REVERT: C 74 ASN cc_start: 0.9309 (m-40) cc_final: 0.8745 (t0) REVERT: C 132 PHE cc_start: 0.9251 (t80) cc_final: 0.8779 (t80) REVERT: C 136 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.8526 (p-80) REVERT: C 144 LEU cc_start: 0.9748 (tp) cc_final: 0.9491 (tt) REVERT: C 172 ARG cc_start: 0.9387 (tpp-160) cc_final: 0.9182 (tpp-160) REVERT: C 176 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7713 (ttmm) REVERT: D 11 ASN cc_start: 0.8873 (t0) cc_final: 0.8499 (t0) REVERT: D 61 GLU cc_start: 0.9547 (mt-10) cc_final: 0.9012 (tm-30) REVERT: D 68 ARG cc_start: 0.9296 (ttm-80) cc_final: 0.8979 (ttm-80) REVERT: D 72 MET cc_start: 0.9600 (tmm) cc_final: 0.9246 (tmm) REVERT: D 74 ASN cc_start: 0.9113 (m-40) cc_final: 0.8726 (m-40) REVERT: D 83 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8668 (mm110) REVERT: D 84 ASP cc_start: 0.8962 (m-30) cc_final: 0.8588 (t0) REVERT: D 112 GLN cc_start: 0.9305 (tp40) cc_final: 0.8705 (tp40) REVERT: D 116 ASP cc_start: 0.9344 (m-30) cc_final: 0.8753 (m-30) REVERT: D 124 ARG cc_start: 0.9298 (mmp80) cc_final: 0.9070 (mmt-90) REVERT: D 135 THR cc_start: 0.8429 (m) cc_final: 0.8079 (p) REVERT: D 136 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8658 (p90) REVERT: E 12 TYR cc_start: 0.9187 (t80) cc_final: 0.8554 (t80) REVERT: E 26 LEU cc_start: 0.9515 (tp) cc_final: 0.9248 (tp) REVERT: E 44 ASP cc_start: 0.9259 (p0) cc_final: 0.8884 (p0) REVERT: E 48 LEU cc_start: 0.9361 (mt) cc_final: 0.8985 (mt) REVERT: E 49 GLU cc_start: 0.8974 (pp20) cc_final: 0.8726 (pp20) REVERT: E 52 SER cc_start: 0.9377 (t) cc_final: 0.8985 (m) REVERT: E 68 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8661 (ttm110) REVERT: E 72 MET cc_start: 0.9503 (tmm) cc_final: 0.9229 (tmm) REVERT: E 112 GLN cc_start: 0.9211 (tp40) cc_final: 0.8717 (tp40) REVERT: E 116 ASP cc_start: 0.8933 (m-30) cc_final: 0.8529 (m-30) REVERT: E 125 THR cc_start: 0.9486 (m) cc_final: 0.8915 (p) REVERT: E 136 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8482 (p90) REVERT: E 140 GLU cc_start: 0.8521 (mp0) cc_final: 0.8046 (mp0) REVERT: E 168 TYR cc_start: 0.9093 (t80) cc_final: 0.8825 (t80) REVERT: E 171 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8551 (tm-30) REVERT: F 12 TYR cc_start: 0.8429 (t80) cc_final: 0.8126 (t80) REVERT: F 15 ASP cc_start: 0.9242 (p0) cc_final: 0.8886 (p0) REVERT: F 42 ASP cc_start: 0.9112 (t70) cc_final: 0.8845 (t0) REVERT: F 44 ASP cc_start: 0.8197 (p0) cc_final: 0.7595 (p0) REVERT: F 52 SER cc_start: 0.9439 (t) cc_final: 0.9083 (m) REVERT: F 56 ARG cc_start: 0.9157 (tpp80) cc_final: 0.8767 (tpp80) REVERT: F 57 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8988 (tm-30) REVERT: F 67 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8422 (mt-10) REVERT: F 79 ARG cc_start: 0.8930 (mmp80) cc_final: 0.8517 (mmp80) REVERT: F 81 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8942 (mt) REVERT: F 104 MET cc_start: 0.8949 (ttp) cc_final: 0.8685 (ttm) REVERT: F 112 GLN cc_start: 0.9286 (tp40) cc_final: 0.8535 (tp-100) REVERT: F 124 ARG cc_start: 0.9182 (mmm160) cc_final: 0.8902 (mmt90) REVERT: F 168 TYR cc_start: 0.9380 (t80) cc_final: 0.9179 (t80) REVERT: F 170 PHE cc_start: 0.9409 (t80) cc_final: 0.9158 (t80) REVERT: G 34 TYR cc_start: 0.9322 (m-80) cc_final: 0.9104 (m-80) REVERT: G 53 HIS cc_start: 0.8782 (t-90) cc_final: 0.8196 (t-90) REVERT: G 56 ARG cc_start: 0.9147 (tpp80) cc_final: 0.8896 (ttm-80) REVERT: G 57 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8525 (mt-10) REVERT: G 61 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9080 (tt0) REVERT: G 64 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8637 (mt-10) REVERT: G 73 GLN cc_start: 0.9260 (tp40) cc_final: 0.8927 (tm-30) REVERT: G 104 MET cc_start: 0.9136 (ttt) cc_final: 0.8777 (ttm) REVERT: G 131 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8915 (t0) REVERT: G 140 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8971 (mt-10) REVERT: G 169 LEU cc_start: 0.9660 (mt) cc_final: 0.9375 (mt) REVERT: H 35 LEU cc_start: 0.9640 (tp) cc_final: 0.9325 (tp) REVERT: H 67 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8970 (tp30) REVERT: H 101 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8526 (mtmt) REVERT: H 124 ARG cc_start: 0.9421 (tpp-160) cc_final: 0.9156 (mmt-90) REVERT: H 171 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9032 (tm-30) REVERT: I 42 ASP cc_start: 0.9197 (t70) cc_final: 0.8868 (t0) REVERT: I 60 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8893 (mm-30) REVERT: I 61 GLU cc_start: 0.9234 (mt-10) cc_final: 0.9005 (tm-30) REVERT: I 64 GLU cc_start: 0.9402 (mm-30) cc_final: 0.8968 (mp0) REVERT: I 68 ARG cc_start: 0.9138 (ttp-170) cc_final: 0.8221 (ttp80) REVERT: I 104 MET cc_start: 0.9236 (ttp) cc_final: 0.9022 (ttm) REVERT: I 126 ASP cc_start: 0.9231 (t0) cc_final: 0.8960 (t0) REVERT: I 140 GLU cc_start: 0.8792 (mp0) cc_final: 0.8520 (mp0) REVERT: I 148 MET cc_start: 0.9428 (ttm) cc_final: 0.9060 (ttm) REVERT: I 168 TYR cc_start: 0.9439 (t80) cc_final: 0.9043 (t80) REVERT: I 172 ARG cc_start: 0.9469 (mmp-170) cc_final: 0.9215 (tpp-160) REVERT: J 44 ASP cc_start: 0.8523 (p0) cc_final: 0.8093 (p0) REVERT: J 60 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8382 (tm-30) REVERT: J 64 GLU cc_start: 0.9482 (mm-30) cc_final: 0.8901 (mm-30) REVERT: J 68 ARG cc_start: 0.9245 (mtt90) cc_final: 0.8810 (mtm-85) REVERT: J 109 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9221 (ptpp) REVERT: J 126 ASP cc_start: 0.9088 (t0) cc_final: 0.8795 (t0) REVERT: J 140 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8412 (mt-10) REVERT: K 7 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: K 42 ASP cc_start: 0.9371 (t70) cc_final: 0.8865 (t70) REVERT: K 56 ARG cc_start: 0.9074 (ttm-80) cc_final: 0.8517 (ttm-80) REVERT: K 74 ASN cc_start: 0.9247 (m-40) cc_final: 0.8803 (m-40) REVERT: K 81 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8475 (mm) REVERT: K 126 ASP cc_start: 0.9300 (t0) cc_final: 0.8899 (t0) REVERT: K 136 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8651 (p-80) REVERT: K 143 LYS cc_start: 0.9318 (mtmm) cc_final: 0.9047 (mtmm) REVERT: L 29 GLN cc_start: 0.9423 (tt0) cc_final: 0.8759 (tm-30) REVERT: L 34 TYR cc_start: 0.9319 (m-80) cc_final: 0.8865 (m-10) REVERT: L 52 SER cc_start: 0.9495 (t) cc_final: 0.9114 (p) REVERT: L 56 ARG cc_start: 0.9041 (mmt90) cc_final: 0.8635 (mtt-85) REVERT: L 63 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8403 (ttp80) REVERT: L 67 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8973 (tp30) REVERT: L 74 ASN cc_start: 0.9319 (m-40) cc_final: 0.8761 (m-40) REVERT: L 107 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8490 (mm-30) REVERT: L 112 GLN cc_start: 0.9215 (tp40) cc_final: 0.8665 (tp40) REVERT: L 126 ASP cc_start: 0.9004 (t70) cc_final: 0.8781 (t0) REVERT: L 139 ASP cc_start: 0.9011 (t70) cc_final: 0.8636 (t0) REVERT: L 143 LYS cc_start: 0.9545 (mtpt) cc_final: 0.9201 (mtmm) REVERT: L 172 ARG cc_start: 0.9265 (mmp-170) cc_final: 0.8681 (mmp-170) REVERT: M 46 VAL cc_start: 0.9375 (t) cc_final: 0.9160 (m) REVERT: M 56 ARG cc_start: 0.9295 (tpp80) cc_final: 0.8816 (ttm-80) REVERT: M 68 ARG cc_start: 0.9035 (ttm110) cc_final: 0.8599 (ttm110) REVERT: M 144 LEU cc_start: 0.9658 (tp) cc_final: 0.9378 (tt) REVERT: N 34 TYR cc_start: 0.9528 (m-10) cc_final: 0.9325 (m-10) REVERT: N 42 ASP cc_start: 0.9030 (t70) cc_final: 0.8449 (t70) REVERT: N 44 ASP cc_start: 0.8208 (p0) cc_final: 0.7731 (p0) REVERT: N 52 SER cc_start: 0.9552 (t) cc_final: 0.9059 (m) REVERT: N 53 HIS cc_start: 0.9159 (t-170) cc_final: 0.8848 (t-170) REVERT: N 64 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8681 (mp0) REVERT: N 74 ASN cc_start: 0.9091 (m-40) cc_final: 0.8762 (m-40) REVERT: N 112 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8166 (tp40) REVERT: N 137 PHE cc_start: 0.8998 (m-80) cc_final: 0.8453 (m-80) REVERT: N 140 GLU cc_start: 0.8790 (mp0) cc_final: 0.8275 (mp0) REVERT: O 15 ASP cc_start: 0.9215 (p0) cc_final: 0.8841 (p0) REVERT: O 39 PHE cc_start: 0.8959 (m-10) cc_final: 0.8221 (m-10) REVERT: O 42 ASP cc_start: 0.9320 (t0) cc_final: 0.8664 (t70) REVERT: O 44 ASP cc_start: 0.8658 (p0) cc_final: 0.8228 (p0) REVERT: O 60 GLU cc_start: 0.9362 (tp30) cc_final: 0.8742 (tp30) REVERT: O 64 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8998 (mm-30) REVERT: O 68 ARG cc_start: 0.9250 (ttm-80) cc_final: 0.8745 (ttm110) REVERT: O 71 LYS cc_start: 0.9498 (ttmm) cc_final: 0.9080 (tppp) REVERT: O 124 ARG cc_start: 0.9160 (mmt-90) cc_final: 0.8873 (mmt-90) REVERT: O 126 ASP cc_start: 0.8890 (t0) cc_final: 0.8553 (t0) REVERT: O 132 PHE cc_start: 0.9292 (t80) cc_final: 0.9047 (t80) REVERT: O 136 HIS cc_start: 0.9127 (OUTLIER) cc_final: 0.8676 (p-80) REVERT: O 170 PHE cc_start: 0.9478 (t80) cc_final: 0.9227 (t80) REVERT: O 172 ARG cc_start: 0.9333 (mmp-170) cc_final: 0.9113 (tpp-160) REVERT: P 52 SER cc_start: 0.9520 (t) cc_final: 0.9222 (m) REVERT: P 53 HIS cc_start: 0.9077 (t-170) cc_final: 0.8498 (t-90) REVERT: P 57 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8617 (mm-30) REVERT: P 61 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9052 (tm-30) REVERT: P 62 LYS cc_start: 0.9306 (mmpt) cc_final: 0.9053 (mmmt) REVERT: P 64 GLU cc_start: 0.9460 (tp30) cc_final: 0.8815 (tm-30) REVERT: P 90 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: P 107 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8920 (mm-30) REVERT: P 131 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9244 (t0) REVERT: P 135 THR cc_start: 0.9133 (t) cc_final: 0.8727 (p) REVERT: P 139 ASP cc_start: 0.8920 (t70) cc_final: 0.8332 (p0) REVERT: P 140 GLU cc_start: 0.9224 (mm-30) cc_final: 0.7837 (mm-30) REVERT: P 170 PHE cc_start: 0.9203 (t80) cc_final: 0.8924 (t80) REVERT: Q 22 SER cc_start: 0.9469 (m) cc_final: 0.9243 (p) REVERT: Q 46 VAL cc_start: 0.9343 (t) cc_final: 0.9087 (p) REVERT: Q 53 HIS cc_start: 0.9225 (t-170) cc_final: 0.8449 (t-90) REVERT: Q 57 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8913 (mm-30) REVERT: Q 84 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8648 (m-30) REVERT: Q 104 MET cc_start: 0.9274 (ttt) cc_final: 0.9029 (ttm) REVERT: Q 107 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8646 (mm-30) REVERT: Q 136 HIS cc_start: 0.9196 (OUTLIER) cc_final: 0.8678 (p-80) REVERT: Q 172 ARG cc_start: 0.9386 (mmp80) cc_final: 0.9108 (mmp80) REVERT: R 44 ASP cc_start: 0.8699 (p0) cc_final: 0.8365 (p0) REVERT: R 49 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8558 (tm-30) REVERT: R 53 HIS cc_start: 0.9028 (t-90) cc_final: 0.8423 (m-70) REVERT: R 126 ASP cc_start: 0.9076 (t0) cc_final: 0.8825 (t0) REVERT: R 147 LYS cc_start: 0.9275 (ttmm) cc_final: 0.9062 (ttpt) REVERT: S 42 ASP cc_start: 0.9505 (t0) cc_final: 0.9066 (t0) REVERT: S 68 ARG cc_start: 0.9115 (ptp-110) cc_final: 0.8808 (ptp-170) REVERT: S 72 MET cc_start: 0.9560 (tmm) cc_final: 0.9347 (tmm) REVERT: S 104 MET cc_start: 0.9131 (ttp) cc_final: 0.8505 (ttm) REVERT: S 126 ASP cc_start: 0.8677 (t0) cc_final: 0.8045 (t0) REVERT: S 135 THR cc_start: 0.9395 (m) cc_final: 0.9156 (p) REVERT: S 136 HIS cc_start: 0.9084 (OUTLIER) cc_final: 0.8788 (p-80) REVERT: S 143 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8790 (mtmm) REVERT: S 148 MET cc_start: 0.9283 (ttm) cc_final: 0.8791 (mtp) REVERT: T 7 GLN cc_start: 0.7766 (pm20) cc_final: 0.7067 (pm20) REVERT: T 12 TYR cc_start: 0.8844 (t80) cc_final: 0.8541 (t80) REVERT: T 45 ASP cc_start: 0.9008 (p0) cc_final: 0.8745 (p0) REVERT: T 53 HIS cc_start: 0.9189 (t-170) cc_final: 0.8572 (t-90) REVERT: T 104 MET cc_start: 0.9108 (tpp) cc_final: 0.8432 (tpp) REVERT: T 107 GLU cc_start: 0.9083 (tp30) cc_final: 0.8683 (tm-30) REVERT: T 124 ARG cc_start: 0.9352 (mmp80) cc_final: 0.8988 (mmp80) REVERT: T 126 ASP cc_start: 0.9108 (t70) cc_final: 0.8854 (t0) REVERT: T 132 PHE cc_start: 0.9143 (t80) cc_final: 0.8846 (t80) REVERT: T 148 MET cc_start: 0.9410 (mtt) cc_final: 0.8117 (mtp) REVERT: T 168 TYR cc_start: 0.9285 (t80) cc_final: 0.8935 (t80) REVERT: T 172 ARG cc_start: 0.9382 (mmp80) cc_final: 0.8944 (tpp80) REVERT: U 29 GLN cc_start: 0.9185 (tp40) cc_final: 0.8906 (tp40) REVERT: U 42 ASP cc_start: 0.9189 (t0) cc_final: 0.8839 (t0) REVERT: U 52 SER cc_start: 0.9686 (t) cc_final: 0.9383 (m) REVERT: U 60 GLU cc_start: 0.9492 (tp30) cc_final: 0.9017 (tp30) REVERT: U 63 ARG cc_start: 0.9353 (ttp80) cc_final: 0.8847 (ttp80) REVERT: U 84 ASP cc_start: 0.8959 (m-30) cc_final: 0.8525 (m-30) REVERT: U 112 GLN cc_start: 0.9556 (tp40) cc_final: 0.9150 (tp-100) REVERT: U 139 ASP cc_start: 0.9312 (t70) cc_final: 0.9012 (t0) REVERT: U 156 HIS cc_start: 0.8975 (m90) cc_final: 0.8734 (m170) REVERT: U 171 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8915 (tm-30) REVERT: V 12 TYR cc_start: 0.8340 (t80) cc_final: 0.8071 (t80) REVERT: V 34 TYR cc_start: 0.9306 (m-10) cc_final: 0.9073 (m-10) REVERT: V 42 ASP cc_start: 0.9191 (t70) cc_final: 0.8599 (t0) REVERT: V 49 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8739 (tm-30) REVERT: V 53 HIS cc_start: 0.8654 (t70) cc_final: 0.8070 (t-90) REVERT: V 57 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8359 (mm-30) REVERT: V 61 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9036 (mm-30) REVERT: V 64 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: V 84 ASP cc_start: 0.9180 (m-30) cc_final: 0.8928 (m-30) REVERT: V 104 MET cc_start: 0.9129 (tpp) cc_final: 0.8914 (tpp) REVERT: V 112 GLN cc_start: 0.9325 (tp40) cc_final: 0.9088 (tm-30) REVERT: V 124 ARG cc_start: 0.9483 (mmp80) cc_final: 0.9209 (mmp80) REVERT: V 126 ASP cc_start: 0.9189 (t0) cc_final: 0.8802 (t0) REVERT: V 139 ASP cc_start: 0.9074 (t70) cc_final: 0.8848 (t70) REVERT: V 140 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8836 (mp0) REVERT: V 141 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8964 (tp30) REVERT: V 148 MET cc_start: 0.9546 (mmt) cc_final: 0.9286 (mmm) REVERT: V 171 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8771 (tm-30) REVERT: W 15 ASP cc_start: 0.9180 (t0) cc_final: 0.8923 (t0) REVERT: W 34 TYR cc_start: 0.9295 (m-80) cc_final: 0.9018 (m-80) REVERT: W 42 ASP cc_start: 0.9264 (t0) cc_final: 0.9046 (t70) REVERT: W 44 ASP cc_start: 0.9186 (p0) cc_final: 0.8645 (p0) REVERT: W 61 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8763 (tm-30) REVERT: W 67 GLU cc_start: 0.9588 (mt-10) cc_final: 0.9211 (mt-10) REVERT: W 136 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.8523 (p-80) REVERT: X 53 HIS cc_start: 0.9096 (t-90) cc_final: 0.8717 (t-90) REVERT: X 60 GLU cc_start: 0.9393 (tp30) cc_final: 0.8980 (tp30) REVERT: X 63 ARG cc_start: 0.9244 (ttp80) cc_final: 0.8916 (ttp80) REVERT: X 74 ASN cc_start: 0.9308 (m-40) cc_final: 0.8949 (m-40) REVERT: X 124 ARG cc_start: 0.9472 (mmt-90) cc_final: 0.9268 (mmt-90) REVERT: X 126 ASP cc_start: 0.8851 (t0) cc_final: 0.8469 (t0) outliers start: 178 outliers final: 106 residues processed: 1301 average time/residue: 0.5227 time to fit residues: 1059.6391 Evaluate side-chains 1182 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1054 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 136 HIS Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 136 HIS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 136 HIS Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 136 HIS Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 11 ASN Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 402 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 HIS C 75 GLN C 111 ASN D 53 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN G 75 GLN H 21 ASN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN K 156 HIS ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN P 10 GLN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 ASN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN ** R 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 ASN ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 HIS T 75 GLN U 11 ASN ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 GLN V 53 HIS V 75 GLN V 83 GLN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN W 75 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052304 restraints weight = 121124.537| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.12 r_work: 0.2810 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33816 Z= 0.247 Angle : 0.717 12.112 45480 Z= 0.372 Chirality : 0.043 0.234 4872 Planarity : 0.004 0.054 5952 Dihedral : 6.077 59.903 4588 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.67 % Favored : 97.13 % Rotamer: Outliers : 5.66 % Allowed : 21.58 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.13), residues: 4080 helix: 1.94 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -2.52 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 93 HIS 0.023 0.001 HIS D 53 PHE 0.035 0.003 PHE X 39 TYR 0.037 0.003 TYR O 66 ARG 0.011 0.001 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 2679) hydrogen bonds : angle 4.16453 ( 8037) covalent geometry : bond 0.00533 (33816) covalent geometry : angle 0.71658 (45480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1124 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.9432 (OUTLIER) cc_final: 0.9194 (p0) REVERT: A 29 GLN cc_start: 0.9123 (tp40) cc_final: 0.8824 (tp40) REVERT: A 52 SER cc_start: 0.9497 (t) cc_final: 0.9253 (m) REVERT: A 74 ASN cc_start: 0.9290 (m-40) cc_final: 0.8709 (m-40) REVERT: A 107 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8530 (mm-30) REVERT: A 112 GLN cc_start: 0.9319 (tp40) cc_final: 0.8863 (tp-100) REVERT: A 141 GLU cc_start: 0.8816 (tp30) cc_final: 0.8252 (tp30) REVERT: A 171 GLU cc_start: 0.9330 (tm-30) cc_final: 0.8978 (tm-30) REVERT: B 12 TYR cc_start: 0.8953 (t80) cc_final: 0.8522 (t80) REVERT: B 22 SER cc_start: 0.9671 (m) cc_final: 0.9443 (p) REVERT: B 53 HIS cc_start: 0.9045 (t70) cc_final: 0.8474 (t70) REVERT: B 57 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8728 (mm-30) REVERT: B 67 GLU cc_start: 0.8957 (pp20) cc_final: 0.8753 (pp20) REVERT: B 72 MET cc_start: 0.9650 (tmm) cc_final: 0.9133 (tmm) REVERT: B 104 MET cc_start: 0.9412 (ttp) cc_final: 0.9037 (ttm) REVERT: B 112 GLN cc_start: 0.9319 (tp40) cc_final: 0.8976 (tp-100) REVERT: B 126 ASP cc_start: 0.8792 (t0) cc_final: 0.8525 (t0) REVERT: B 148 MET cc_start: 0.9596 (mtt) cc_final: 0.9340 (mtp) REVERT: B 153 THR cc_start: 0.9407 (m) cc_final: 0.9187 (p) REVERT: C 42 ASP cc_start: 0.9297 (t70) cc_final: 0.9049 (t70) REVERT: C 58 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9294 (tp) REVERT: C 66 TYR cc_start: 0.9376 (p90) cc_final: 0.9164 (p90) REVERT: C 68 ARG cc_start: 0.8926 (mtt180) cc_final: 0.8690 (mtt180) REVERT: C 126 ASP cc_start: 0.9175 (t0) cc_final: 0.8564 (t0) REVERT: C 131 ASP cc_start: 0.9432 (t0) cc_final: 0.8807 (t0) REVERT: C 132 PHE cc_start: 0.9216 (t80) cc_final: 0.8669 (t80) REVERT: C 136 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8012 (p-80) REVERT: C 140 GLU cc_start: 0.8834 (mp0) cc_final: 0.8431 (mp0) REVERT: C 176 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7773 (ttmm) REVERT: D 11 ASN cc_start: 0.8925 (t0) cc_final: 0.8549 (t0) REVERT: D 61 GLU cc_start: 0.9533 (OUTLIER) cc_final: 0.9039 (tm-30) REVERT: D 72 MET cc_start: 0.9615 (tmm) cc_final: 0.9215 (tmm) REVERT: D 74 ASN cc_start: 0.9201 (m-40) cc_final: 0.8838 (m-40) REVERT: D 83 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.9005 (mm110) REVERT: D 112 GLN cc_start: 0.9272 (tp40) cc_final: 0.8692 (tp40) REVERT: D 116 ASP cc_start: 0.9327 (m-30) cc_final: 0.8708 (m-30) REVERT: D 126 ASP cc_start: 0.9224 (t0) cc_final: 0.8898 (t70) REVERT: D 135 THR cc_start: 0.8285 (m) cc_final: 0.8035 (p) REVERT: E 12 TYR cc_start: 0.9355 (t80) cc_final: 0.8719 (t80) REVERT: E 26 LEU cc_start: 0.9527 (tp) cc_final: 0.9258 (tp) REVERT: E 44 ASP cc_start: 0.9311 (p0) cc_final: 0.8957 (p0) REVERT: E 48 LEU cc_start: 0.9393 (mt) cc_final: 0.8979 (mt) REVERT: E 52 SER cc_start: 0.9382 (t) cc_final: 0.8758 (p) REVERT: E 57 GLU cc_start: 0.9141 (tp30) cc_final: 0.8776 (tp30) REVERT: E 68 ARG cc_start: 0.9187 (ttm110) cc_final: 0.8757 (ttm110) REVERT: E 112 GLN cc_start: 0.9222 (tp40) cc_final: 0.8837 (tp40) REVERT: E 116 ASP cc_start: 0.8966 (m-30) cc_final: 0.8698 (m-30) REVERT: E 136 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8264 (p90) REVERT: E 168 TYR cc_start: 0.9175 (t80) cc_final: 0.8884 (t80) REVERT: E 171 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: F 15 ASP cc_start: 0.9167 (p0) cc_final: 0.8756 (p0) REVERT: F 17 GLU cc_start: 0.9078 (tt0) cc_final: 0.8735 (tt0) REVERT: F 31 SER cc_start: 0.9557 (OUTLIER) cc_final: 0.9173 (m) REVERT: F 42 ASP cc_start: 0.9226 (t70) cc_final: 0.8856 (t0) REVERT: F 44 ASP cc_start: 0.8439 (p0) cc_final: 0.7729 (p0) REVERT: F 52 SER cc_start: 0.9469 (t) cc_final: 0.9153 (m) REVERT: F 56 ARG cc_start: 0.9046 (tpp80) cc_final: 0.8729 (tpp80) REVERT: F 67 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8325 (mt-10) REVERT: F 79 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8310 (mmp80) REVERT: F 84 ASP cc_start: 0.9143 (m-30) cc_final: 0.8753 (t0) REVERT: F 104 MET cc_start: 0.8865 (ttp) cc_final: 0.8532 (tpp) REVERT: F 112 GLN cc_start: 0.9272 (tp40) cc_final: 0.8574 (tp-100) REVERT: F 153 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8672 (p) REVERT: G 44 ASP cc_start: 0.9070 (p0) cc_final: 0.8697 (p0) REVERT: G 53 HIS cc_start: 0.8816 (t-90) cc_final: 0.8172 (t-90) REVERT: G 56 ARG cc_start: 0.9161 (tpp80) cc_final: 0.8737 (ttm-80) REVERT: G 57 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8395 (mt-10) REVERT: G 60 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8585 (tm-30) REVERT: G 64 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8432 (mt-10) REVERT: G 73 GLN cc_start: 0.9213 (tp40) cc_final: 0.8803 (tm-30) REVERT: G 75 GLN cc_start: 0.9410 (OUTLIER) cc_final: 0.9196 (mp-120) REVERT: G 104 MET cc_start: 0.9089 (ttt) cc_final: 0.8729 (ttm) REVERT: G 107 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8003 (mm-30) REVERT: G 140 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9036 (mt-10) REVERT: H 17 GLU cc_start: 0.9239 (tt0) cc_final: 0.9014 (tt0) REVERT: H 35 LEU cc_start: 0.9669 (tp) cc_final: 0.9320 (tp) REVERT: H 57 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8675 (mm-30) REVERT: H 67 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8699 (tp30) REVERT: H 90 GLU cc_start: 0.9106 (mp0) cc_final: 0.8885 (mp0) REVERT: H 141 GLU cc_start: 0.9168 (tp30) cc_final: 0.8853 (tp30) REVERT: H 171 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8984 (tm-30) REVERT: I 7 GLN cc_start: 0.8739 (pt0) cc_final: 0.8512 (pm20) REVERT: I 42 ASP cc_start: 0.9300 (t70) cc_final: 0.8931 (t0) REVERT: I 61 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8967 (mm-30) REVERT: I 104 MET cc_start: 0.9249 (ttp) cc_final: 0.9039 (ttm) REVERT: I 148 MET cc_start: 0.9392 (ttm) cc_final: 0.9121 (ttm) REVERT: I 168 TYR cc_start: 0.9488 (t80) cc_final: 0.8946 (t80) REVERT: J 44 ASP cc_start: 0.8594 (p0) cc_final: 0.8233 (p0) REVERT: J 64 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9185 (tm-30) REVERT: J 91 ASP cc_start: 0.9242 (p0) cc_final: 0.9008 (p0) REVERT: K 7 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: K 42 ASP cc_start: 0.9405 (t70) cc_final: 0.8826 (t70) REVERT: K 56 ARG cc_start: 0.9069 (ttm-80) cc_final: 0.8514 (ttm-80) REVERT: K 74 ASN cc_start: 0.9359 (m-40) cc_final: 0.8969 (m-40) REVERT: K 81 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8581 (mm) REVERT: K 83 GLN cc_start: 0.8937 (mm110) cc_final: 0.8719 (mm-40) REVERT: K 126 ASP cc_start: 0.9360 (t0) cc_final: 0.9007 (t0) REVERT: K 136 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.8584 (p-80) REVERT: K 143 LYS cc_start: 0.9312 (mtmm) cc_final: 0.9042 (mtmm) REVERT: L 29 GLN cc_start: 0.9440 (tt0) cc_final: 0.8843 (tm-30) REVERT: L 52 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9149 (p) REVERT: L 64 GLU cc_start: 0.9464 (mt-10) cc_final: 0.8857 (tm-30) REVERT: L 67 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8970 (tm-30) REVERT: L 74 ASN cc_start: 0.9412 (m-40) cc_final: 0.8991 (m-40) REVERT: L 112 GLN cc_start: 0.9139 (tp40) cc_final: 0.8568 (tp40) REVERT: L 126 ASP cc_start: 0.9031 (t70) cc_final: 0.8726 (t0) REVERT: L 139 ASP cc_start: 0.8944 (t70) cc_final: 0.8686 (t0) REVERT: L 143 LYS cc_start: 0.9513 (mtpt) cc_final: 0.9259 (mtmm) REVERT: L 168 TYR cc_start: 0.9179 (t80) cc_final: 0.8966 (t80) REVERT: M 11 ASN cc_start: 0.8870 (t0) cc_final: 0.8516 (t0) REVERT: M 46 VAL cc_start: 0.9431 (t) cc_final: 0.9178 (p) REVERT: M 56 ARG cc_start: 0.9304 (tpp80) cc_final: 0.8912 (ttm-80) REVERT: M 60 GLU cc_start: 0.9337 (tp30) cc_final: 0.8989 (tp30) REVERT: M 68 ARG cc_start: 0.9034 (ttm110) cc_final: 0.8534 (ttm110) REVERT: N 42 ASP cc_start: 0.9076 (t70) cc_final: 0.8322 (t70) REVERT: N 44 ASP cc_start: 0.8199 (p0) cc_final: 0.7937 (p0) REVERT: N 53 HIS cc_start: 0.9153 (t-170) cc_final: 0.8948 (t-170) REVERT: N 63 ARG cc_start: 0.9255 (mtp-110) cc_final: 0.8985 (mtp85) REVERT: N 64 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8726 (mp0) REVERT: N 74 ASN cc_start: 0.9096 (m-40) cc_final: 0.8623 (m-40) REVERT: N 112 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8266 (tp40) REVERT: N 126 ASP cc_start: 0.8991 (t0) cc_final: 0.8580 (t0) REVERT: N 140 GLU cc_start: 0.8814 (mp0) cc_final: 0.8319 (mp0) REVERT: O 15 ASP cc_start: 0.9274 (p0) cc_final: 0.8968 (p0) REVERT: O 39 PHE cc_start: 0.9142 (m-10) cc_final: 0.8842 (m-10) REVERT: O 42 ASP cc_start: 0.9429 (t0) cc_final: 0.8922 (t70) REVERT: O 44 ASP cc_start: 0.8616 (p0) cc_final: 0.7847 (p0) REVERT: O 60 GLU cc_start: 0.9215 (tp30) cc_final: 0.8854 (tp30) REVERT: O 64 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9027 (mm-30) REVERT: O 68 ARG cc_start: 0.9261 (ttm-80) cc_final: 0.8720 (ttm110) REVERT: O 71 LYS cc_start: 0.9502 (ttmm) cc_final: 0.9284 (tppt) REVERT: O 101 LYS cc_start: 0.9370 (mtmt) cc_final: 0.9087 (mtmt) REVERT: O 124 ARG cc_start: 0.9354 (mmt-90) cc_final: 0.9071 (mmt-90) REVERT: O 126 ASP cc_start: 0.8916 (t0) cc_final: 0.8590 (t0) REVERT: O 132 PHE cc_start: 0.9279 (t80) cc_final: 0.9077 (t80) REVERT: O 136 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8679 (p-80) REVERT: O 147 LYS cc_start: 0.9584 (ttpp) cc_final: 0.9333 (ttpp) REVERT: O 172 ARG cc_start: 0.9290 (mmp-170) cc_final: 0.8960 (mmp-170) REVERT: P 17 GLU cc_start: 0.9250 (tt0) cc_final: 0.8953 (tt0) REVERT: P 53 HIS cc_start: 0.9117 (t-170) cc_final: 0.8462 (t70) REVERT: P 57 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8541 (mm-30) REVERT: P 61 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9039 (tm-30) REVERT: P 64 GLU cc_start: 0.9477 (tp30) cc_final: 0.8890 (tm-30) REVERT: P 90 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8582 (tt0) REVERT: P 92 GLU cc_start: 0.9119 (tp30) cc_final: 0.8876 (mm-30) REVERT: P 126 ASP cc_start: 0.9171 (t0) cc_final: 0.8935 (t0) REVERT: P 131 ASP cc_start: 0.9453 (OUTLIER) cc_final: 0.9227 (t0) REVERT: P 148 MET cc_start: 0.9476 (mmm) cc_final: 0.9236 (mtp) REVERT: P 170 PHE cc_start: 0.9258 (t80) cc_final: 0.8953 (t80) REVERT: Q 22 SER cc_start: 0.9484 (m) cc_final: 0.9265 (p) REVERT: Q 53 HIS cc_start: 0.9190 (t-170) cc_final: 0.8429 (t-90) REVERT: Q 57 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8959 (mm-30) REVERT: Q 64 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9046 (mm-30) REVERT: Q 67 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8879 (mt-10) REVERT: Q 68 ARG cc_start: 0.9018 (ttm170) cc_final: 0.8609 (ttm110) REVERT: Q 104 MET cc_start: 0.9281 (ttt) cc_final: 0.9028 (ttm) REVERT: Q 107 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8709 (mm-30) REVERT: Q 112 GLN cc_start: 0.9159 (tp40) cc_final: 0.8914 (tp40) REVERT: R 44 ASP cc_start: 0.8762 (p0) cc_final: 0.8545 (p0) REVERT: R 46 VAL cc_start: 0.9266 (t) cc_final: 0.9028 (p) REVERT: R 49 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8765 (tm-30) REVERT: R 126 ASP cc_start: 0.9101 (t0) cc_final: 0.8753 (t0) REVERT: S 42 ASP cc_start: 0.9472 (t0) cc_final: 0.8632 (t0) REVERT: S 49 GLU cc_start: 0.9031 (tp30) cc_final: 0.8712 (tm-30) REVERT: S 68 ARG cc_start: 0.9173 (ptp-110) cc_final: 0.8960 (ptp90) REVERT: S 72 MET cc_start: 0.9620 (tmm) cc_final: 0.9392 (tmm) REVERT: S 126 ASP cc_start: 0.8796 (t0) cc_final: 0.8217 (t0) REVERT: S 136 HIS cc_start: 0.9141 (OUTLIER) cc_final: 0.8698 (p-80) REVERT: S 137 PHE cc_start: 0.9088 (m-80) cc_final: 0.8847 (m-80) REVERT: S 148 MET cc_start: 0.9313 (ttm) cc_final: 0.9032 (ttm) REVERT: T 7 GLN cc_start: 0.8009 (pm20) cc_final: 0.7431 (pm20) REVERT: T 29 GLN cc_start: 0.9023 (tt0) cc_final: 0.8799 (tt0) REVERT: T 53 HIS cc_start: 0.8969 (t70) cc_final: 0.8407 (t-170) REVERT: T 60 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8930 (mm-30) REVERT: T 61 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8759 (mm-30) REVERT: T 74 ASN cc_start: 0.8998 (m-40) cc_final: 0.8550 (t0) REVERT: T 90 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8924 (mm-30) REVERT: T 104 MET cc_start: 0.9117 (tpp) cc_final: 0.8444 (tpp) REVERT: T 124 ARG cc_start: 0.9409 (mmp80) cc_final: 0.9083 (mmp80) REVERT: T 136 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8392 (p-80) REVERT: T 148 MET cc_start: 0.9583 (mtt) cc_final: 0.8072 (mtp) REVERT: T 172 ARG cc_start: 0.9476 (mmp80) cc_final: 0.9136 (tpp80) REVERT: U 29 GLN cc_start: 0.9127 (tp40) cc_final: 0.8808 (tp40) REVERT: U 42 ASP cc_start: 0.9190 (t0) cc_final: 0.8692 (t0) REVERT: U 63 ARG cc_start: 0.9369 (ttp80) cc_final: 0.9144 (ttm-80) REVERT: U 100 MET cc_start: 0.9134 (mmm) cc_final: 0.8800 (mmt) REVERT: U 104 MET cc_start: 0.8638 (ttm) cc_final: 0.8349 (tpp) REVERT: U 112 GLN cc_start: 0.9489 (tp40) cc_final: 0.8705 (tp-100) REVERT: U 116 ASP cc_start: 0.9193 (m-30) cc_final: 0.8642 (m-30) REVERT: U 139 ASP cc_start: 0.9299 (t70) cc_final: 0.8923 (t0) REVERT: U 156 HIS cc_start: 0.9027 (m90) cc_final: 0.8598 (m90) REVERT: U 171 GLU cc_start: 0.9369 (tm-30) cc_final: 0.8964 (tm-30) REVERT: V 34 TYR cc_start: 0.9392 (m-10) cc_final: 0.9084 (m-10) REVERT: V 39 PHE cc_start: 0.9276 (m-80) cc_final: 0.9058 (m-80) REVERT: V 42 ASP cc_start: 0.9227 (t70) cc_final: 0.8671 (t0) REVERT: V 49 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8735 (tm-30) REVERT: V 56 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8674 (tpp80) REVERT: V 57 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8407 (mm-30) REVERT: V 64 GLU cc_start: 0.9174 (tt0) cc_final: 0.8871 (pp20) REVERT: V 68 ARG cc_start: 0.8863 (mtp180) cc_final: 0.8079 (mtm110) REVERT: V 84 ASP cc_start: 0.9185 (m-30) cc_final: 0.8920 (m-30) REVERT: V 112 GLN cc_start: 0.9397 (tp40) cc_final: 0.9097 (tm-30) REVERT: V 126 ASP cc_start: 0.9151 (t0) cc_final: 0.8684 (t0) REVERT: V 136 HIS cc_start: 0.9116 (OUTLIER) cc_final: 0.8156 (p-80) REVERT: V 139 ASP cc_start: 0.9063 (t70) cc_final: 0.8820 (t70) REVERT: V 140 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8795 (mp0) REVERT: V 141 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8968 (tp30) REVERT: V 171 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8894 (tm-30) REVERT: W 15 ASP cc_start: 0.9105 (t0) cc_final: 0.8893 (t0) REVERT: W 29 GLN cc_start: 0.9162 (tp40) cc_final: 0.8796 (mm110) REVERT: W 42 ASP cc_start: 0.9292 (t0) cc_final: 0.8981 (t70) REVERT: W 61 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8813 (tm-30) REVERT: W 67 GLU cc_start: 0.9559 (mt-10) cc_final: 0.9164 (mt-10) REVERT: W 126 ASP cc_start: 0.9407 (t0) cc_final: 0.8683 (t70) REVERT: W 136 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8584 (p-80) REVERT: X 12 TYR cc_start: 0.9365 (t80) cc_final: 0.8575 (t80) REVERT: X 53 HIS cc_start: 0.9095 (t-90) cc_final: 0.8720 (t-90) REVERT: X 57 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8924 (mm-30) REVERT: X 60 GLU cc_start: 0.9467 (tp30) cc_final: 0.9250 (tp30) REVERT: X 74 ASN cc_start: 0.9322 (m-40) cc_final: 0.8917 (m-40) REVERT: X 126 ASP cc_start: 0.8893 (t0) cc_final: 0.8608 (t0) outliers start: 197 outliers final: 115 residues processed: 1247 average time/residue: 0.5205 time to fit residues: 1006.2296 Evaluate side-chains 1168 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1029 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 79 ARG Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 136 HIS Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 136 HIS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 136 HIS Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 136 HIS Chi-restraints excluded: chain V residue 8 ILE Chi-restraints excluded: chain V residue 29 GLN Chi-restraints excluded: chain V residue 31 SER Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain W residue 174 THR Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 11 ASN Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 268 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN D 11 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN F 53 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN H 21 ASN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 HIS S 74 ASN S 111 ASN ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 83 GLN ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 HIS V 83 GLN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054558 restraints weight = 118573.407| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.11 r_work: 0.2865 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33816 Z= 0.167 Angle : 0.682 12.052 45480 Z= 0.358 Chirality : 0.042 0.235 4872 Planarity : 0.004 0.035 5952 Dihedral : 5.766 57.448 4580 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.94 % Rotamer: Outliers : 5.11 % Allowed : 23.25 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.13), residues: 4080 helix: 1.96 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -2.49 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 93 HIS 0.008 0.001 HIS W 128 PHE 0.034 0.002 PHE X 39 TYR 0.054 0.003 TYR B 66 ARG 0.009 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 2679) hydrogen bonds : angle 4.19070 ( 8037) covalent geometry : bond 0.00368 (33816) covalent geometry : angle 0.68193 (45480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 1162 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.9099 (p0) REVERT: A 12 TYR cc_start: 0.8493 (t80) cc_final: 0.8247 (t80) REVERT: A 29 GLN cc_start: 0.9149 (tp40) cc_final: 0.8872 (tp40) REVERT: A 42 ASP cc_start: 0.9329 (t0) cc_final: 0.8907 (t0) REVERT: A 52 SER cc_start: 0.9430 (t) cc_final: 0.9193 (m) REVERT: A 74 ASN cc_start: 0.9277 (m-40) cc_final: 0.8711 (m-40) REVERT: A 107 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8409 (mm-30) REVERT: A 112 GLN cc_start: 0.9292 (tp40) cc_final: 0.8715 (tp-100) REVERT: A 141 GLU cc_start: 0.8809 (tp30) cc_final: 0.8294 (tp30) REVERT: A 171 GLU cc_start: 0.9328 (tm-30) cc_final: 0.8993 (tm-30) REVERT: B 12 TYR cc_start: 0.8920 (t80) cc_final: 0.8615 (t80) REVERT: B 22 SER cc_start: 0.9654 (m) cc_final: 0.9433 (p) REVERT: B 56 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8716 (tpp80) REVERT: B 72 MET cc_start: 0.9680 (tmm) cc_final: 0.9273 (tmm) REVERT: B 98 ASP cc_start: 0.9485 (t0) cc_final: 0.9224 (m-30) REVERT: B 104 MET cc_start: 0.9350 (ttp) cc_final: 0.8962 (ttm) REVERT: B 112 GLN cc_start: 0.9348 (tp40) cc_final: 0.9070 (tp40) REVERT: B 126 ASP cc_start: 0.8774 (t0) cc_final: 0.8527 (t0) REVERT: B 148 MET cc_start: 0.9485 (mtm) cc_final: 0.9216 (mtp) REVERT: B 153 THR cc_start: 0.9379 (m) cc_final: 0.9179 (p) REVERT: C 42 ASP cc_start: 0.9299 (t70) cc_final: 0.9051 (t70) REVERT: C 58 LEU cc_start: 0.9599 (mp) cc_final: 0.9322 (tp) REVERT: C 68 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8557 (mtt180) REVERT: C 124 ARG cc_start: 0.9000 (mmp80) cc_final: 0.8651 (mmp80) REVERT: C 126 ASP cc_start: 0.9164 (t0) cc_final: 0.8503 (t0) REVERT: C 129 LEU cc_start: 0.9755 (tp) cc_final: 0.9518 (tp) REVERT: C 131 ASP cc_start: 0.9363 (t0) cc_final: 0.8721 (t0) REVERT: C 136 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.7727 (p-80) REVERT: C 176 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7718 (ttmm) REVERT: D 7 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: D 52 SER cc_start: 0.9308 (t) cc_final: 0.8869 (m) REVERT: D 61 GLU cc_start: 0.9507 (OUTLIER) cc_final: 0.9073 (tm-30) REVERT: D 66 TYR cc_start: 0.9524 (p90) cc_final: 0.9209 (p90) REVERT: D 72 MET cc_start: 0.9632 (tmm) cc_final: 0.9202 (tmm) REVERT: D 74 ASN cc_start: 0.9159 (m110) cc_final: 0.8879 (m-40) REVERT: D 112 GLN cc_start: 0.9279 (tp40) cc_final: 0.8626 (tp40) REVERT: D 116 ASP cc_start: 0.9290 (m-30) cc_final: 0.8813 (m-30) REVERT: D 126 ASP cc_start: 0.9141 (t0) cc_final: 0.8696 (t70) REVERT: D 132 PHE cc_start: 0.9052 (t80) cc_final: 0.8758 (t80) REVERT: D 167 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8511 (mp0) REVERT: E 12 TYR cc_start: 0.9221 (t80) cc_final: 0.8765 (t80) REVERT: E 26 LEU cc_start: 0.9492 (tp) cc_final: 0.9227 (tp) REVERT: E 40 TYR cc_start: 0.9193 (t80) cc_final: 0.8855 (t80) REVERT: E 44 ASP cc_start: 0.9311 (p0) cc_final: 0.8950 (p0) REVERT: E 48 LEU cc_start: 0.9365 (mt) cc_final: 0.8968 (mt) REVERT: E 49 GLU cc_start: 0.8996 (pp20) cc_final: 0.8723 (pp20) REVERT: E 52 SER cc_start: 0.9380 (t) cc_final: 0.8974 (m) REVERT: E 57 GLU cc_start: 0.9109 (tp30) cc_final: 0.8772 (tp30) REVERT: E 112 GLN cc_start: 0.9244 (tp40) cc_final: 0.8744 (tp40) REVERT: E 116 ASP cc_start: 0.8971 (m-30) cc_final: 0.8569 (m-30) REVERT: E 125 THR cc_start: 0.9448 (m) cc_final: 0.9157 (p) REVERT: E 168 TYR cc_start: 0.9079 (t80) cc_final: 0.8824 (t80) REVERT: E 171 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: F 31 SER cc_start: 0.9511 (OUTLIER) cc_final: 0.9151 (m) REVERT: F 42 ASP cc_start: 0.9170 (t70) cc_final: 0.8831 (t0) REVERT: F 44 ASP cc_start: 0.8312 (p0) cc_final: 0.7541 (p0) REVERT: F 52 SER cc_start: 0.9493 (t) cc_final: 0.9168 (m) REVERT: F 56 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8667 (tpp80) REVERT: F 67 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8275 (mt-10) REVERT: F 68 ARG cc_start: 0.8969 (mtm-85) cc_final: 0.8639 (mtm-85) REVERT: F 79 ARG cc_start: 0.8921 (mmp80) cc_final: 0.8286 (mmp80) REVERT: F 112 GLN cc_start: 0.9258 (tp40) cc_final: 0.8478 (tp-100) REVERT: F 136 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8104 (p-80) REVERT: F 153 THR cc_start: 0.8998 (m) cc_final: 0.8706 (p) REVERT: G 53 HIS cc_start: 0.8784 (t-90) cc_final: 0.8239 (t-90) REVERT: G 64 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8470 (mt-10) REVERT: G 68 ARG cc_start: 0.9155 (ttp-110) cc_final: 0.8856 (ttp-110) REVERT: G 73 GLN cc_start: 0.9139 (tp40) cc_final: 0.8805 (tm-30) REVERT: G 75 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.9237 (mp10) REVERT: G 104 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8651 (ttm) REVERT: G 124 ARG cc_start: 0.9215 (mmp80) cc_final: 0.8868 (mmp80) REVERT: G 140 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8982 (mt-10) REVERT: G 172 ARG cc_start: 0.9157 (mmp80) cc_final: 0.8899 (mmp80) REVERT: H 12 TYR cc_start: 0.9094 (t80) cc_final: 0.8516 (t80) REVERT: H 35 LEU cc_start: 0.9651 (tp) cc_final: 0.9336 (tp) REVERT: H 42 ASP cc_start: 0.9203 (t70) cc_final: 0.8795 (t0) REVERT: H 63 ARG cc_start: 0.9295 (ttp80) cc_final: 0.9069 (ttp80) REVERT: H 72 MET cc_start: 0.9644 (tmm) cc_final: 0.9232 (tmm) REVERT: H 74 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8743 (t0) REVERT: H 98 ASP cc_start: 0.9276 (m-30) cc_final: 0.9058 (m-30) REVERT: H 171 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8861 (tm-30) REVERT: I 42 ASP cc_start: 0.9335 (t70) cc_final: 0.9024 (t0) REVERT: I 61 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8940 (mm-30) REVERT: I 98 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.9006 (t0) REVERT: I 107 GLU cc_start: 0.9122 (tp30) cc_final: 0.8666 (tp30) REVERT: J 68 ARG cc_start: 0.9453 (mtt90) cc_final: 0.9047 (ttm170) REVERT: J 73 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8478 (tm-30) REVERT: J 109 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9185 (ptpp) REVERT: J 124 ARG cc_start: 0.9165 (mmt-90) cc_final: 0.8951 (mmt-90) REVERT: J 126 ASP cc_start: 0.9137 (t0) cc_final: 0.8825 (t0) REVERT: J 143 LYS cc_start: 0.9357 (mmtp) cc_final: 0.9138 (mmmm) REVERT: K 7 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: K 42 ASP cc_start: 0.9384 (t70) cc_final: 0.8764 (t70) REVERT: K 56 ARG cc_start: 0.9031 (ttm-80) cc_final: 0.8505 (ttm-80) REVERT: K 74 ASN cc_start: 0.9284 (m-40) cc_final: 0.8809 (m-40) REVERT: K 81 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8730 (mm) REVERT: K 87 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8627 (ptpp) REVERT: K 126 ASP cc_start: 0.9275 (t0) cc_final: 0.8931 (t0) REVERT: K 132 PHE cc_start: 0.9084 (t80) cc_final: 0.8759 (t80) REVERT: K 136 HIS cc_start: 0.8979 (OUTLIER) cc_final: 0.8229 (p-80) REVERT: K 143 LYS cc_start: 0.9337 (mtmm) cc_final: 0.9049 (mtmm) REVERT: L 29 GLN cc_start: 0.9421 (tt0) cc_final: 0.8774 (tm-30) REVERT: L 49 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8500 (tm-30) REVERT: L 52 SER cc_start: 0.9542 (t) cc_final: 0.9119 (p) REVERT: L 53 HIS cc_start: 0.9100 (t-90) cc_final: 0.8673 (t-90) REVERT: L 60 GLU cc_start: 0.9215 (tt0) cc_final: 0.8898 (tt0) REVERT: L 64 GLU cc_start: 0.9452 (mt-10) cc_final: 0.8844 (tm-30) REVERT: L 67 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8905 (tm-30) REVERT: L 74 ASN cc_start: 0.9352 (m-40) cc_final: 0.8903 (m-40) REVERT: L 112 GLN cc_start: 0.9156 (tp40) cc_final: 0.8699 (tp40) REVERT: L 126 ASP cc_start: 0.8971 (t70) cc_final: 0.8667 (t0) REVERT: L 143 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9289 (mttm) REVERT: M 11 ASN cc_start: 0.8882 (t0) cc_final: 0.8578 (t0) REVERT: M 46 VAL cc_start: 0.9354 (t) cc_final: 0.9131 (m) REVERT: M 56 ARG cc_start: 0.9304 (tpp80) cc_final: 0.8917 (ttm-80) REVERT: M 60 GLU cc_start: 0.9254 (tp30) cc_final: 0.9020 (tp30) REVERT: N 34 TYR cc_start: 0.9553 (m-10) cc_final: 0.9261 (m-10) REVERT: N 42 ASP cc_start: 0.9016 (t70) cc_final: 0.8278 (t70) REVERT: N 44 ASP cc_start: 0.8164 (p0) cc_final: 0.7945 (p0) REVERT: N 63 ARG cc_start: 0.9285 (mtp-110) cc_final: 0.9012 (mtp85) REVERT: N 64 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: N 74 ASN cc_start: 0.9019 (m-40) cc_final: 0.8632 (m-40) REVERT: N 112 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8241 (tp40) REVERT: N 126 ASP cc_start: 0.8919 (t0) cc_final: 0.8518 (t0) REVERT: N 140 GLU cc_start: 0.8812 (mp0) cc_final: 0.8383 (mp0) REVERT: N 169 LEU cc_start: 0.9694 (mt) cc_final: 0.9494 (mt) REVERT: O 15 ASP cc_start: 0.9300 (p0) cc_final: 0.8816 (p0) REVERT: O 39 PHE cc_start: 0.9154 (m-10) cc_final: 0.8862 (m-10) REVERT: O 42 ASP cc_start: 0.9444 (t0) cc_final: 0.8803 (t70) REVERT: O 44 ASP cc_start: 0.8649 (p0) cc_final: 0.8299 (p0) REVERT: O 53 HIS cc_start: 0.8840 (t70) cc_final: 0.7643 (t-90) REVERT: O 57 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8612 (mm-30) REVERT: O 60 GLU cc_start: 0.9206 (tp30) cc_final: 0.8758 (tp30) REVERT: O 64 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8952 (mm-30) REVERT: O 68 ARG cc_start: 0.9275 (ttm-80) cc_final: 0.8765 (ttm110) REVERT: O 71 LYS cc_start: 0.9500 (ttmm) cc_final: 0.9268 (tppt) REVERT: O 84 ASP cc_start: 0.8998 (m-30) cc_final: 0.8796 (t0) REVERT: O 124 ARG cc_start: 0.9309 (mmt-90) cc_final: 0.9068 (mmt-90) REVERT: O 126 ASP cc_start: 0.8951 (t0) cc_final: 0.8602 (t0) REVERT: O 132 PHE cc_start: 0.9241 (t80) cc_final: 0.8952 (t80) REVERT: O 136 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.8695 (p-80) REVERT: O 172 ARG cc_start: 0.9339 (mmp-170) cc_final: 0.8961 (mmp-170) REVERT: P 53 HIS cc_start: 0.9116 (t-170) cc_final: 0.8379 (t70) REVERT: P 57 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8422 (mm-30) REVERT: P 64 GLU cc_start: 0.9468 (tp30) cc_final: 0.8982 (tm-30) REVERT: P 68 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8415 (mtm-85) REVERT: P 107 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8958 (mm-30) REVERT: Q 29 GLN cc_start: 0.8879 (tp40) cc_final: 0.8649 (tp40) REVERT: Q 53 HIS cc_start: 0.9135 (t-170) cc_final: 0.8321 (t-90) REVERT: Q 57 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8995 (mm-30) REVERT: Q 64 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9013 (mm-30) REVERT: Q 67 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8805 (mt-10) REVERT: Q 68 ARG cc_start: 0.8954 (ttm170) cc_final: 0.8556 (ttm110) REVERT: Q 107 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8603 (mm-30) REVERT: Q 171 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8781 (tm-30) REVERT: Q 172 ARG cc_start: 0.9279 (mmp80) cc_final: 0.9027 (mmp80) REVERT: R 49 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8553 (tm-30) REVERT: R 53 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8638 (m90) REVERT: R 68 ARG cc_start: 0.9129 (mtm-85) cc_final: 0.8884 (mtt-85) REVERT: R 73 GLN cc_start: 0.9144 (tp40) cc_final: 0.8743 (tp40) REVERT: R 126 ASP cc_start: 0.9095 (t0) cc_final: 0.8628 (t0) REVERT: R 147 LYS cc_start: 0.9294 (ttmm) cc_final: 0.9093 (ttpt) REVERT: S 42 ASP cc_start: 0.9477 (t0) cc_final: 0.8559 (t0) REVERT: S 49 GLU cc_start: 0.9046 (tp30) cc_final: 0.8635 (tm-30) REVERT: S 68 ARG cc_start: 0.9146 (ptp-110) cc_final: 0.8846 (ptp-170) REVERT: S 72 MET cc_start: 0.9626 (tmm) cc_final: 0.9400 (tmm) REVERT: S 126 ASP cc_start: 0.8888 (t0) cc_final: 0.8301 (t0) REVERT: S 132 PHE cc_start: 0.9000 (t80) cc_final: 0.8750 (t80) REVERT: S 135 THR cc_start: 0.9350 (m) cc_final: 0.9078 (p) REVERT: S 136 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.8892 (p-80) REVERT: S 140 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9068 (mm-30) REVERT: S 143 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8601 (ptpp) REVERT: S 148 MET cc_start: 0.9278 (ttm) cc_final: 0.8986 (ttm) REVERT: T 7 GLN cc_start: 0.7996 (pm20) cc_final: 0.7413 (pm20) REVERT: T 29 GLN cc_start: 0.9056 (tt0) cc_final: 0.8701 (tt0) REVERT: T 53 HIS cc_start: 0.9091 (t-90) cc_final: 0.8275 (t-90) REVERT: T 57 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8460 (mm-30) REVERT: T 61 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8680 (mm-30) REVERT: T 63 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.7904 (ttm110) REVERT: T 74 ASN cc_start: 0.8962 (m-40) cc_final: 0.8538 (m-40) REVERT: T 86 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.9018 (ptmm) REVERT: T 104 MET cc_start: 0.8955 (tpp) cc_final: 0.8662 (tpp) REVERT: T 116 ASP cc_start: 0.9382 (p0) cc_final: 0.9167 (p0) REVERT: T 136 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8381 (p90) REVERT: T 137 PHE cc_start: 0.9275 (m-80) cc_final: 0.9054 (m-80) REVERT: T 148 MET cc_start: 0.9532 (mtt) cc_final: 0.8253 (mtp) REVERT: T 170 PHE cc_start: 0.9142 (t80) cc_final: 0.8864 (t80) REVERT: T 172 ARG cc_start: 0.9449 (mmp80) cc_final: 0.9127 (tpp80) REVERT: U 29 GLN cc_start: 0.9130 (tp40) cc_final: 0.8841 (tp40) REVERT: U 42 ASP cc_start: 0.9172 (t0) cc_final: 0.8633 (t0) REVERT: U 72 MET cc_start: 0.9391 (tmm) cc_final: 0.9176 (tmm) REVERT: U 100 MET cc_start: 0.9121 (mmm) cc_final: 0.8847 (mmt) REVERT: U 112 GLN cc_start: 0.9463 (tp40) cc_final: 0.8905 (tp40) REVERT: U 116 ASP cc_start: 0.9159 (m-30) cc_final: 0.8913 (m-30) REVERT: U 146 LYS cc_start: 0.8703 (tppt) cc_final: 0.8474 (tppt) REVERT: U 147 LYS cc_start: 0.9303 (ttpp) cc_final: 0.9064 (ptmm) REVERT: U 156 HIS cc_start: 0.8865 (m90) cc_final: 0.8449 (m90) REVERT: U 171 GLU cc_start: 0.9331 (tm-30) cc_final: 0.9001 (tm-30) REVERT: V 34 TYR cc_start: 0.9436 (m-10) cc_final: 0.9177 (m-10) REVERT: V 39 PHE cc_start: 0.9275 (m-80) cc_final: 0.9000 (m-80) REVERT: V 49 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8749 (tm-30) REVERT: V 53 HIS cc_start: 0.8659 (t70) cc_final: 0.8094 (t-90) REVERT: V 56 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8678 (tpp80) REVERT: V 57 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8352 (mm-30) REVERT: V 64 GLU cc_start: 0.9239 (tt0) cc_final: 0.9008 (pp20) REVERT: V 112 GLN cc_start: 0.9358 (tp40) cc_final: 0.9059 (tm-30) REVERT: V 124 ARG cc_start: 0.9528 (mmp80) cc_final: 0.9274 (mmp80) REVERT: V 126 ASP cc_start: 0.9097 (t0) cc_final: 0.8693 (t0) REVERT: V 136 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8358 (p-80) REVERT: V 139 ASP cc_start: 0.9009 (t70) cc_final: 0.8743 (t70) REVERT: V 140 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8816 (mp0) REVERT: V 171 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8862 (tm-30) REVERT: W 15 ASP cc_start: 0.9111 (t0) cc_final: 0.8759 (t0) REVERT: W 29 GLN cc_start: 0.9133 (tp40) cc_final: 0.8804 (mm110) REVERT: W 42 ASP cc_start: 0.9270 (t0) cc_final: 0.8922 (t70) REVERT: W 44 ASP cc_start: 0.9285 (p0) cc_final: 0.8758 (p0) REVERT: W 61 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8690 (tm-30) REVERT: W 67 GLU cc_start: 0.9541 (mt-10) cc_final: 0.9110 (mt-10) REVERT: W 68 ARG cc_start: 0.8882 (mtp180) cc_final: 0.8290 (mtp180) REVERT: W 124 ARG cc_start: 0.9264 (mmm-85) cc_final: 0.8993 (mmt90) REVERT: W 136 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.7919 (p-80) REVERT: X 12 TYR cc_start: 0.9249 (t80) cc_final: 0.8447 (t80) REVERT: X 53 HIS cc_start: 0.9074 (t-90) cc_final: 0.8826 (t70) REVERT: X 126 ASP cc_start: 0.8870 (t0) cc_final: 0.8548 (t0) outliers start: 178 outliers final: 92 residues processed: 1266 average time/residue: 0.5289 time to fit residues: 1038.6687 Evaluate side-chains 1183 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1064 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 79 ARG Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 136 HIS Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 136 HIS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 136 HIS Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain V residue 15 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 4 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 368 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 21 ASN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 136 HIS V 53 HIS ** V 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054256 restraints weight = 118874.996| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.20 r_work: 0.2850 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33816 Z= 0.194 Angle : 0.712 12.214 45480 Z= 0.369 Chirality : 0.043 0.282 4872 Planarity : 0.004 0.078 5952 Dihedral : 5.627 56.673 4578 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.75 % Favored : 97.06 % Rotamer: Outliers : 4.74 % Allowed : 24.71 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.13), residues: 4080 helix: 1.90 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -2.39 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 93 HIS 0.025 0.001 HIS F 53 PHE 0.030 0.003 PHE U 132 TYR 0.039 0.003 TYR G 66 ARG 0.008 0.001 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 2679) hydrogen bonds : angle 4.23260 ( 8037) covalent geometry : bond 0.00429 (33816) covalent geometry : angle 0.71170 (45480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 1117 time to evaluate : 4.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.9175 (p0) REVERT: A 12 TYR cc_start: 0.8630 (t80) cc_final: 0.8311 (t80) REVERT: A 29 GLN cc_start: 0.9153 (tp40) cc_final: 0.8946 (tp40) REVERT: A 42 ASP cc_start: 0.9290 (t0) cc_final: 0.8780 (t0) REVERT: A 52 SER cc_start: 0.9444 (t) cc_final: 0.9212 (m) REVERT: A 68 ARG cc_start: 0.8407 (ptp-170) cc_final: 0.7772 (ptm160) REVERT: A 72 MET cc_start: 0.9408 (tmm) cc_final: 0.9167 (tmm) REVERT: A 74 ASN cc_start: 0.9292 (m-40) cc_final: 0.8781 (m-40) REVERT: A 107 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8443 (mm-30) REVERT: A 112 GLN cc_start: 0.9337 (tp40) cc_final: 0.8869 (tp-100) REVERT: A 141 GLU cc_start: 0.8869 (tp30) cc_final: 0.8429 (tp30) REVERT: A 167 GLU cc_start: 0.9083 (tt0) cc_final: 0.8715 (tt0) REVERT: A 171 GLU cc_start: 0.9382 (tm-30) cc_final: 0.9068 (tm-30) REVERT: B 12 TYR cc_start: 0.8959 (t80) cc_final: 0.8472 (t80) REVERT: B 56 ARG cc_start: 0.9127 (tpp80) cc_final: 0.8684 (tpp80) REVERT: B 66 TYR cc_start: 0.9347 (p90) cc_final: 0.9122 (p90) REVERT: B 72 MET cc_start: 0.9712 (tmm) cc_final: 0.9328 (tmm) REVERT: B 98 ASP cc_start: 0.9495 (t0) cc_final: 0.9130 (m-30) REVERT: B 104 MET cc_start: 0.9282 (ttp) cc_final: 0.8952 (ttm) REVERT: B 112 GLN cc_start: 0.9315 (tp40) cc_final: 0.9006 (tp40) REVERT: B 126 ASP cc_start: 0.8774 (t0) cc_final: 0.8505 (t0) REVERT: C 12 TYR cc_start: 0.8540 (t80) cc_final: 0.8146 (t80) REVERT: C 42 ASP cc_start: 0.9315 (t70) cc_final: 0.8992 (t70) REVERT: C 58 LEU cc_start: 0.9576 (mp) cc_final: 0.9368 (tp) REVERT: C 66 TYR cc_start: 0.9391 (p90) cc_final: 0.9172 (p90) REVERT: C 68 ARG cc_start: 0.8984 (mtt180) cc_final: 0.8750 (mtt180) REVERT: C 104 MET cc_start: 0.9072 (tpp) cc_final: 0.8770 (tpp) REVERT: C 126 ASP cc_start: 0.9179 (t0) cc_final: 0.8505 (t0) REVERT: C 129 LEU cc_start: 0.9770 (tp) cc_final: 0.9552 (tp) REVERT: C 131 ASP cc_start: 0.9381 (t0) cc_final: 0.8756 (t0) REVERT: C 136 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.8053 (p-80) REVERT: C 144 LEU cc_start: 0.9747 (tp) cc_final: 0.9544 (tt) REVERT: C 176 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: D 7 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: D 52 SER cc_start: 0.9325 (t) cc_final: 0.8863 (m) REVERT: D 61 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9078 (tm-30) REVERT: D 66 TYR cc_start: 0.9488 (p90) cc_final: 0.9187 (p90) REVERT: D 72 MET cc_start: 0.9636 (tmm) cc_final: 0.9188 (tmm) REVERT: D 74 ASN cc_start: 0.9130 (m110) cc_final: 0.8664 (m-40) REVERT: D 112 GLN cc_start: 0.9271 (tp40) cc_final: 0.8593 (tp40) REVERT: D 116 ASP cc_start: 0.9285 (m-30) cc_final: 0.8706 (m-30) REVERT: D 126 ASP cc_start: 0.9155 (t0) cc_final: 0.8659 (t70) REVERT: D 143 LYS cc_start: 0.9479 (mtmm) cc_final: 0.9005 (mtmm) REVERT: D 167 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8399 (mp0) REVERT: E 12 TYR cc_start: 0.9290 (t80) cc_final: 0.9032 (t80) REVERT: E 26 LEU cc_start: 0.9493 (tp) cc_final: 0.9226 (tp) REVERT: E 40 TYR cc_start: 0.9202 (t80) cc_final: 0.8852 (t80) REVERT: E 44 ASP cc_start: 0.9312 (p0) cc_final: 0.8959 (p0) REVERT: E 48 LEU cc_start: 0.9380 (mt) cc_final: 0.8954 (mt) REVERT: E 52 SER cc_start: 0.9404 (t) cc_final: 0.8999 (m) REVERT: E 57 GLU cc_start: 0.9121 (tp30) cc_final: 0.8787 (tp30) REVERT: E 68 ARG cc_start: 0.9165 (ptp-110) cc_final: 0.8793 (ptp-170) REVERT: E 112 GLN cc_start: 0.9232 (tp40) cc_final: 0.8671 (tp40) REVERT: E 116 ASP cc_start: 0.8993 (m-30) cc_final: 0.8548 (m-30) REVERT: E 125 THR cc_start: 0.9435 (m) cc_final: 0.9143 (p) REVERT: E 168 TYR cc_start: 0.9146 (t80) cc_final: 0.8887 (t80) REVERT: E 171 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: F 42 ASP cc_start: 0.9223 (t70) cc_final: 0.8910 (t0) REVERT: F 44 ASP cc_start: 0.8334 (p0) cc_final: 0.7554 (p0) REVERT: F 52 SER cc_start: 0.9461 (t) cc_final: 0.9040 (m) REVERT: F 56 ARG cc_start: 0.8977 (tpp80) cc_final: 0.8597 (tpp80) REVERT: F 67 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8262 (mt-10) REVERT: F 79 ARG cc_start: 0.8898 (mmp80) cc_final: 0.8478 (mmp80) REVERT: F 107 GLU cc_start: 0.8815 (tp30) cc_final: 0.8458 (tp30) REVERT: F 112 GLN cc_start: 0.9258 (tp40) cc_final: 0.8473 (tp-100) REVERT: F 153 THR cc_start: 0.8986 (m) cc_final: 0.8712 (p) REVERT: G 53 HIS cc_start: 0.8804 (t-90) cc_final: 0.8200 (t-90) REVERT: G 60 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8321 (tm-30) REVERT: G 64 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8190 (mt-10) REVERT: G 73 GLN cc_start: 0.9110 (tp40) cc_final: 0.8808 (tm-30) REVERT: G 75 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9244 (mp10) REVERT: G 104 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8582 (ttm) REVERT: G 107 GLU cc_start: 0.8935 (tp30) cc_final: 0.8381 (tp30) REVERT: G 124 ARG cc_start: 0.9247 (mmp80) cc_final: 0.8907 (mmp80) REVERT: G 140 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8997 (mt-10) REVERT: H 17 GLU cc_start: 0.9051 (tt0) cc_final: 0.8781 (tt0) REVERT: H 35 LEU cc_start: 0.9661 (tp) cc_final: 0.9357 (tp) REVERT: H 42 ASP cc_start: 0.9212 (t70) cc_final: 0.8791 (t0) REVERT: H 63 ARG cc_start: 0.9269 (ttp80) cc_final: 0.9062 (ttp80) REVERT: H 67 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8832 (mm-30) REVERT: H 73 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: H 171 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8861 (tm-30) REVERT: I 42 ASP cc_start: 0.9356 (t70) cc_final: 0.9024 (t0) REVERT: I 61 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8927 (mm-30) REVERT: I 98 ASP cc_start: 0.9315 (OUTLIER) cc_final: 0.9002 (t0) REVERT: I 141 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8495 (tp30) REVERT: I 148 MET cc_start: 0.9402 (ttm) cc_final: 0.8999 (ttm) REVERT: J 15 ASP cc_start: 0.9063 (p0) cc_final: 0.8832 (p0) REVERT: J 60 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8910 (tm-30) REVERT: J 68 ARG cc_start: 0.9451 (mtt90) cc_final: 0.9116 (ttm-80) REVERT: J 73 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: J 109 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9183 (ptpp) REVERT: J 124 ARG cc_start: 0.9235 (mmt-90) cc_final: 0.9013 (mmt-90) REVERT: J 153 THR cc_start: 0.9106 (m) cc_final: 0.8898 (p) REVERT: K 7 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: K 42 ASP cc_start: 0.9438 (t70) cc_final: 0.8842 (t70) REVERT: K 56 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8474 (ttm-80) REVERT: K 66 TYR cc_start: 0.9296 (p90) cc_final: 0.9086 (p90) REVERT: K 71 LYS cc_start: 0.9396 (ttpt) cc_final: 0.9111 (ttpt) REVERT: K 72 MET cc_start: 0.9602 (ppp) cc_final: 0.9261 (ppp) REVERT: K 74 ASN cc_start: 0.9302 (m-40) cc_final: 0.8764 (m-40) REVERT: K 75 GLN cc_start: 0.9015 (mm110) cc_final: 0.8744 (mm110) REVERT: K 87 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8683 (ptpp) REVERT: K 104 MET cc_start: 0.9095 (mmm) cc_final: 0.8667 (tpp) REVERT: K 132 PHE cc_start: 0.9094 (t80) cc_final: 0.8669 (t80) REVERT: K 136 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8167 (p-80) REVERT: K 143 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9062 (mtmm) REVERT: L 29 GLN cc_start: 0.9462 (tt0) cc_final: 0.8978 (tm-30) REVERT: L 49 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8550 (tm-30) REVERT: L 52 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.9125 (p) REVERT: L 53 HIS cc_start: 0.9128 (t-90) cc_final: 0.8656 (t-90) REVERT: L 60 GLU cc_start: 0.9314 (tt0) cc_final: 0.9026 (tt0) REVERT: L 64 GLU cc_start: 0.9453 (mt-10) cc_final: 0.8860 (tm-30) REVERT: L 67 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8935 (tm-30) REVERT: L 68 ARG cc_start: 0.9060 (ttp-170) cc_final: 0.8802 (ttp-170) REVERT: L 74 ASN cc_start: 0.9334 (m-40) cc_final: 0.8794 (m-40) REVERT: L 112 GLN cc_start: 0.9145 (tp40) cc_final: 0.8689 (tp40) REVERT: L 126 ASP cc_start: 0.8996 (t0) cc_final: 0.8627 (t0) REVERT: L 143 LYS cc_start: 0.9539 (mtpt) cc_final: 0.9303 (mttm) REVERT: M 11 ASN cc_start: 0.8900 (t0) cc_final: 0.8620 (t0) REVERT: M 34 TYR cc_start: 0.9104 (m-10) cc_final: 0.8898 (m-10) REVERT: M 46 VAL cc_start: 0.9366 (t) cc_final: 0.9133 (p) REVERT: M 52 SER cc_start: 0.9352 (t) cc_final: 0.9051 (m) REVERT: M 56 ARG cc_start: 0.9306 (tpp80) cc_final: 0.8936 (ttm-80) REVERT: M 60 GLU cc_start: 0.9189 (tp30) cc_final: 0.8962 (tp30) REVERT: N 42 ASP cc_start: 0.9012 (t70) cc_final: 0.8223 (t70) REVERT: N 53 HIS cc_start: 0.9208 (t-170) cc_final: 0.8557 (t70) REVERT: N 57 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8822 (mm-30) REVERT: N 64 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8846 (mt-10) REVERT: N 74 ASN cc_start: 0.9030 (m-40) cc_final: 0.8570 (m-40) REVERT: N 112 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8193 (tp40) REVERT: N 140 GLU cc_start: 0.8799 (mp0) cc_final: 0.8416 (mp0) REVERT: O 15 ASP cc_start: 0.9207 (p0) cc_final: 0.8840 (p0) REVERT: O 42 ASP cc_start: 0.9473 (t0) cc_final: 0.8743 (t0) REVERT: O 44 ASP cc_start: 0.8584 (p0) cc_final: 0.8243 (p0) REVERT: O 60 GLU cc_start: 0.9223 (tp30) cc_final: 0.8724 (tp30) REVERT: O 64 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8931 (mm-30) REVERT: O 68 ARG cc_start: 0.9284 (ttm-80) cc_final: 0.8860 (ttm110) REVERT: O 71 LYS cc_start: 0.9529 (ttmm) cc_final: 0.9251 (tppt) REVERT: O 74 ASN cc_start: 0.9312 (m-40) cc_final: 0.8978 (t0) REVERT: O 84 ASP cc_start: 0.9039 (m-30) cc_final: 0.8824 (t0) REVERT: O 104 MET cc_start: 0.9249 (ttt) cc_final: 0.8965 (tpp) REVERT: O 124 ARG cc_start: 0.9345 (mmt-90) cc_final: 0.9112 (mmt-90) REVERT: O 126 ASP cc_start: 0.8955 (t0) cc_final: 0.8606 (t0) REVERT: O 172 ARG cc_start: 0.9381 (mmp-170) cc_final: 0.8983 (mmp-170) REVERT: P 53 HIS cc_start: 0.9133 (t-170) cc_final: 0.8412 (t70) REVERT: P 57 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8439 (mm-30) REVERT: P 64 GLU cc_start: 0.9478 (tp30) cc_final: 0.8889 (tm-30) REVERT: P 104 MET cc_start: 0.9430 (ttp) cc_final: 0.8908 (ttm) REVERT: P 126 ASP cc_start: 0.9038 (t0) cc_final: 0.8741 (t0) REVERT: P 148 MET cc_start: 0.9314 (mtt) cc_final: 0.9107 (mtp) REVERT: Q 53 HIS cc_start: 0.9093 (t-170) cc_final: 0.8340 (t-90) REVERT: Q 57 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8993 (mm-30) REVERT: Q 64 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8958 (mm-30) REVERT: Q 67 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8790 (mt-10) REVERT: Q 68 ARG cc_start: 0.8921 (ttm170) cc_final: 0.8475 (ttm110) REVERT: Q 107 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8689 (mm-30) REVERT: Q 112 GLN cc_start: 0.9121 (tp40) cc_final: 0.8913 (tp40) REVERT: Q 148 MET cc_start: 0.9371 (ttp) cc_final: 0.9162 (ttt) REVERT: Q 171 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8752 (tm-30) REVERT: Q 172 ARG cc_start: 0.9283 (mmp80) cc_final: 0.8953 (mmp80) REVERT: R 49 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8637 (tm-30) REVERT: R 53 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.8731 (m90) REVERT: R 68 ARG cc_start: 0.9146 (mtm-85) cc_final: 0.8901 (mtt-85) REVERT: R 73 GLN cc_start: 0.9218 (tp40) cc_final: 0.8986 (tp40) REVERT: R 126 ASP cc_start: 0.9122 (t0) cc_final: 0.8584 (t0) REVERT: S 42 ASP cc_start: 0.9493 (t0) cc_final: 0.8615 (t0) REVERT: S 49 GLU cc_start: 0.9018 (tp30) cc_final: 0.8677 (tm-30) REVERT: S 68 ARG cc_start: 0.9175 (ptp-110) cc_final: 0.8780 (ptp-170) REVERT: S 72 MET cc_start: 0.9614 (tmm) cc_final: 0.9392 (tmm) REVERT: S 74 ASN cc_start: 0.9223 (m110) cc_final: 0.8791 (m-40) REVERT: S 126 ASP cc_start: 0.8905 (t0) cc_final: 0.8299 (t0) REVERT: S 136 HIS cc_start: 0.9135 (OUTLIER) cc_final: 0.8802 (p-80) REVERT: S 143 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8843 (mtmm) REVERT: T 7 GLN cc_start: 0.8056 (pm20) cc_final: 0.7614 (pm20) REVERT: T 29 GLN cc_start: 0.9005 (tt0) cc_final: 0.8734 (tt0) REVERT: T 45 ASP cc_start: 0.8855 (p0) cc_final: 0.8448 (p0) REVERT: T 53 HIS cc_start: 0.8965 (t-90) cc_final: 0.8139 (t-90) REVERT: T 57 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8352 (mm-30) REVERT: T 61 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8616 (mm-30) REVERT: T 68 ARG cc_start: 0.9165 (ttp-170) cc_final: 0.8464 (ttm170) REVERT: T 74 ASN cc_start: 0.9024 (m-40) cc_final: 0.8623 (m-40) REVERT: T 86 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8909 (ptmm) REVERT: T 104 MET cc_start: 0.9021 (tpp) cc_final: 0.8690 (tpp) REVERT: T 107 GLU cc_start: 0.8803 (tp30) cc_final: 0.8377 (tp30) REVERT: T 132 PHE cc_start: 0.9110 (t80) cc_final: 0.8840 (t80) REVERT: T 135 THR cc_start: 0.9367 (t) cc_final: 0.8928 (p) REVERT: T 136 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8064 (p-80) REVERT: T 148 MET cc_start: 0.9587 (mtt) cc_final: 0.8295 (mtp) REVERT: U 29 GLN cc_start: 0.9156 (tp40) cc_final: 0.8845 (tp40) REVERT: U 42 ASP cc_start: 0.9095 (t0) cc_final: 0.8520 (t0) REVERT: U 44 ASP cc_start: 0.8414 (p0) cc_final: 0.8095 (p0) REVERT: U 100 MET cc_start: 0.9135 (mmm) cc_final: 0.8670 (mmt) REVERT: U 104 MET cc_start: 0.8560 (tpp) cc_final: 0.8227 (tpp) REVERT: U 112 GLN cc_start: 0.9455 (tp40) cc_final: 0.8904 (tp40) REVERT: U 116 ASP cc_start: 0.9151 (m-30) cc_final: 0.8885 (m-30) REVERT: U 146 LYS cc_start: 0.8665 (tppt) cc_final: 0.8452 (tppt) REVERT: U 148 MET cc_start: 0.9268 (mtp) cc_final: 0.8983 (ttp) REVERT: U 156 HIS cc_start: 0.8878 (m90) cc_final: 0.8430 (m90) REVERT: U 171 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9071 (tm-30) REVERT: U 172 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8760 (ttm-80) REVERT: V 34 TYR cc_start: 0.9543 (m-10) cc_final: 0.9269 (m-10) REVERT: V 49 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8840 (tm-30) REVERT: V 57 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8465 (mm-30) REVERT: V 60 GLU cc_start: 0.9181 (tp30) cc_final: 0.8773 (tp30) REVERT: V 63 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8133 (ttp80) REVERT: V 64 GLU cc_start: 0.9216 (tt0) cc_final: 0.8922 (pp20) REVERT: V 68 ARG cc_start: 0.9028 (ptm160) cc_final: 0.8288 (ptm160) REVERT: V 74 ASN cc_start: 0.9331 (m-40) cc_final: 0.8795 (t0) REVERT: V 112 GLN cc_start: 0.9365 (tp40) cc_final: 0.8906 (tm-30) REVERT: V 124 ARG cc_start: 0.9537 (mmp80) cc_final: 0.9296 (mmp80) REVERT: V 126 ASP cc_start: 0.9094 (t0) cc_final: 0.8691 (t0) REVERT: V 136 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8506 (p-80) REVERT: V 139 ASP cc_start: 0.8986 (t70) cc_final: 0.8593 (t70) REVERT: V 171 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8744 (tm-30) REVERT: V 172 ARG cc_start: 0.8999 (mmp80) cc_final: 0.8789 (mmp80) REVERT: W 29 GLN cc_start: 0.8989 (tp40) cc_final: 0.8531 (mm110) REVERT: W 42 ASP cc_start: 0.9333 (t0) cc_final: 0.8871 (t0) REVERT: W 61 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8681 (tm-30) REVERT: W 67 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9021 (mt-10) REVERT: W 68 ARG cc_start: 0.8886 (mtp180) cc_final: 0.8503 (mtp85) REVERT: W 126 ASP cc_start: 0.9334 (t0) cc_final: 0.8574 (t70) REVERT: W 136 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.8093 (p-80) REVERT: X 12 TYR cc_start: 0.9298 (t80) cc_final: 0.8511 (t80) REVERT: X 53 HIS cc_start: 0.9107 (t-90) cc_final: 0.8824 (t70) REVERT: X 57 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8874 (mm-30) REVERT: X 60 GLU cc_start: 0.9462 (tp30) cc_final: 0.9225 (tp30) REVERT: X 63 ARG cc_start: 0.9359 (ttp80) cc_final: 0.8941 (ttp80) REVERT: X 74 ASN cc_start: 0.9244 (m-40) cc_final: 0.8872 (m-40) REVERT: X 126 ASP cc_start: 0.8854 (t0) cc_final: 0.8501 (t0) outliers start: 165 outliers final: 102 residues processed: 1214 average time/residue: 0.5346 time to fit residues: 1007.0524 Evaluate side-chains 1129 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1001 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 136 HIS Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 58 LEU Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain V residue 15 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain V residue 145 ILE Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 11 ASN Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 283 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 398 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 381 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN H 7 GLN H 21 ASN H 29 GLN ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN O 154 ASN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Q 73 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 HIS R 83 GLN ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 ASN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 GLN V 53 HIS ** V 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053570 restraints weight = 119426.564| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.11 r_work: 0.2840 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33816 Z= 0.221 Angle : 0.734 11.776 45480 Z= 0.380 Chirality : 0.044 0.247 4872 Planarity : 0.004 0.049 5952 Dihedral : 5.516 54.175 4574 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.94 % Rotamer: Outliers : 4.77 % Allowed : 26.06 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.13), residues: 4080 helix: 1.78 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -2.33 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 93 HIS 0.008 0.001 HIS W 128 PHE 0.031 0.003 PHE O 170 TYR 0.044 0.003 TYR G 66 ARG 0.012 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 2679) hydrogen bonds : angle 4.29369 ( 8037) covalent geometry : bond 0.00488 (33816) covalent geometry : angle 0.73404 (45480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1064 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8720 (t80) cc_final: 0.8446 (t80) REVERT: A 29 GLN cc_start: 0.9141 (tp40) cc_final: 0.8929 (tp40) REVERT: A 42 ASP cc_start: 0.9292 (t0) cc_final: 0.8772 (t0) REVERT: A 52 SER cc_start: 0.9450 (t) cc_final: 0.9214 (m) REVERT: A 72 MET cc_start: 0.9453 (tmm) cc_final: 0.9215 (tmm) REVERT: A 74 ASN cc_start: 0.9306 (m-40) cc_final: 0.8823 (m-40) REVERT: A 107 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8582 (mm-30) REVERT: A 112 GLN cc_start: 0.9311 (tp40) cc_final: 0.9007 (tp40) REVERT: A 124 ARG cc_start: 0.9286 (mmt-90) cc_final: 0.9047 (mmt-90) REVERT: A 141 GLU cc_start: 0.8840 (tp30) cc_final: 0.8541 (tp30) REVERT: A 167 GLU cc_start: 0.9110 (tt0) cc_final: 0.8622 (tt0) REVERT: A 171 GLU cc_start: 0.9398 (tm-30) cc_final: 0.9092 (tm-30) REVERT: B 12 TYR cc_start: 0.9028 (t80) cc_final: 0.8769 (t80) REVERT: B 56 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8696 (tpp80) REVERT: B 63 ARG cc_start: 0.9351 (ttp80) cc_final: 0.8973 (ttp80) REVERT: B 72 MET cc_start: 0.9702 (tmm) cc_final: 0.9323 (tmm) REVERT: B 98 ASP cc_start: 0.9515 (t0) cc_final: 0.9219 (m-30) REVERT: B 104 MET cc_start: 0.9160 (ttp) cc_final: 0.8899 (ttm) REVERT: B 126 ASP cc_start: 0.8828 (t0) cc_final: 0.8534 (t0) REVERT: B 148 MET cc_start: 0.9550 (mtp) cc_final: 0.9193 (mtp) REVERT: C 12 TYR cc_start: 0.8697 (t80) cc_final: 0.8493 (t80) REVERT: C 42 ASP cc_start: 0.9328 (t70) cc_final: 0.8998 (t70) REVERT: C 58 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9363 (tp) REVERT: C 104 MET cc_start: 0.8973 (tpp) cc_final: 0.8573 (tpp) REVERT: C 126 ASP cc_start: 0.9201 (t0) cc_final: 0.8568 (t0) REVERT: C 129 LEU cc_start: 0.9785 (tp) cc_final: 0.9537 (tp) REVERT: C 131 ASP cc_start: 0.9393 (t0) cc_final: 0.8782 (t0) REVERT: C 136 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8179 (p-80) REVERT: C 147 LYS cc_start: 0.9383 (ttmm) cc_final: 0.9113 (ptmm) REVERT: C 148 MET cc_start: 0.9007 (ttp) cc_final: 0.8784 (ttp) REVERT: C 171 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8959 (tm-30) REVERT: C 176 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7846 (ttmm) REVERT: D 7 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: D 52 SER cc_start: 0.9359 (t) cc_final: 0.8938 (m) REVERT: D 61 GLU cc_start: 0.9529 (OUTLIER) cc_final: 0.9069 (tm-30) REVERT: D 74 ASN cc_start: 0.9141 (m110) cc_final: 0.8668 (m-40) REVERT: D 112 GLN cc_start: 0.9275 (tp40) cc_final: 0.8477 (tp-100) REVERT: D 116 ASP cc_start: 0.9262 (m-30) cc_final: 0.8604 (m-30) REVERT: D 126 ASP cc_start: 0.9193 (t0) cc_final: 0.8764 (t70) REVERT: D 143 LYS cc_start: 0.9474 (mtmm) cc_final: 0.9167 (mtmm) REVERT: D 167 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8442 (mp0) REVERT: E 26 LEU cc_start: 0.9495 (tp) cc_final: 0.9229 (tp) REVERT: E 44 ASP cc_start: 0.9293 (p0) cc_final: 0.9043 (p0) REVERT: E 48 LEU cc_start: 0.9382 (mt) cc_final: 0.9067 (mt) REVERT: E 49 GLU cc_start: 0.9000 (pp20) cc_final: 0.8756 (pp20) REVERT: E 57 GLU cc_start: 0.9146 (tp30) cc_final: 0.8813 (tp30) REVERT: E 112 GLN cc_start: 0.9223 (tp40) cc_final: 0.8595 (tp40) REVERT: E 116 ASP cc_start: 0.8945 (m-30) cc_final: 0.8462 (m-30) REVERT: E 126 ASP cc_start: 0.9075 (t0) cc_final: 0.8834 (t0) REVERT: E 168 TYR cc_start: 0.9158 (t80) cc_final: 0.8825 (t80) REVERT: E 171 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: F 12 TYR cc_start: 0.8638 (t80) cc_final: 0.8129 (t80) REVERT: F 44 ASP cc_start: 0.8460 (p0) cc_final: 0.7992 (p0) REVERT: F 52 SER cc_start: 0.9438 (t) cc_final: 0.9110 (m) REVERT: F 67 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8446 (mt-10) REVERT: F 79 ARG cc_start: 0.9170 (mmp80) cc_final: 0.8657 (mmp80) REVERT: F 112 GLN cc_start: 0.9233 (tp40) cc_final: 0.8354 (tp-100) REVERT: F 153 THR cc_start: 0.9000 (m) cc_final: 0.8719 (p) REVERT: G 53 HIS cc_start: 0.8834 (t-90) cc_final: 0.8188 (t-90) REVERT: G 60 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8538 (tm-30) REVERT: G 63 ARG cc_start: 0.9217 (ttm110) cc_final: 0.8990 (ttm110) REVERT: G 64 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8213 (mt-10) REVERT: G 73 GLN cc_start: 0.9140 (tp40) cc_final: 0.8759 (tm-30) REVERT: G 104 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8656 (ttm) REVERT: G 107 GLU cc_start: 0.8945 (tp30) cc_final: 0.8385 (tp30) REVERT: G 124 ARG cc_start: 0.9248 (mmp80) cc_final: 0.8916 (mmp80) REVERT: G 140 GLU cc_start: 0.9237 (mm-30) cc_final: 0.9001 (mt-10) REVERT: H 42 ASP cc_start: 0.9268 (t70) cc_final: 0.8853 (t0) REVERT: H 73 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: H 112 GLN cc_start: 0.9231 (tp40) cc_final: 0.8766 (tp-100) REVERT: I 42 ASP cc_start: 0.9399 (t70) cc_final: 0.9125 (t0) REVERT: I 60 GLU cc_start: 0.9403 (tp30) cc_final: 0.9186 (tp30) REVERT: I 61 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8967 (mm-30) REVERT: I 64 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9116 (mp0) REVERT: I 98 ASP cc_start: 0.9309 (OUTLIER) cc_final: 0.8994 (t0) REVERT: I 104 MET cc_start: 0.9424 (ttm) cc_final: 0.9134 (ttm) REVERT: I 124 ARG cc_start: 0.9221 (mmp80) cc_final: 0.8955 (mmp80) REVERT: I 148 MET cc_start: 0.9398 (ttm) cc_final: 0.9039 (ttm) REVERT: J 63 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8571 (ttp80) REVERT: J 68 ARG cc_start: 0.9415 (mtt90) cc_final: 0.9062 (ttp-170) REVERT: J 73 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: J 109 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9188 (ptpp) REVERT: J 124 ARG cc_start: 0.9235 (mmt-90) cc_final: 0.9031 (mmt-90) REVERT: J 153 THR cc_start: 0.9143 (m) cc_final: 0.8905 (p) REVERT: K 7 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: K 42 ASP cc_start: 0.9419 (t70) cc_final: 0.8763 (t70) REVERT: K 45 ASP cc_start: 0.8783 (m-30) cc_final: 0.8217 (m-30) REVERT: K 56 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8462 (ttm-80) REVERT: K 66 TYR cc_start: 0.9326 (p90) cc_final: 0.9104 (p90) REVERT: K 71 LYS cc_start: 0.9409 (ttpt) cc_final: 0.9132 (ttpt) REVERT: K 72 MET cc_start: 0.9611 (ppp) cc_final: 0.9314 (ppp) REVERT: K 74 ASN cc_start: 0.9379 (m-40) cc_final: 0.8980 (m-40) REVERT: K 83 GLN cc_start: 0.8939 (mm110) cc_final: 0.8652 (mm110) REVERT: K 87 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8754 (ptpp) REVERT: K 104 MET cc_start: 0.9079 (mmm) cc_final: 0.8665 (tpp) REVERT: K 136 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8213 (p-80) REVERT: K 143 LYS cc_start: 0.9365 (mtmm) cc_final: 0.9078 (mtmm) REVERT: L 29 GLN cc_start: 0.9462 (tt0) cc_final: 0.8992 (tm-30) REVERT: L 49 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8534 (tm-30) REVERT: L 52 SER cc_start: 0.9536 (OUTLIER) cc_final: 0.9105 (p) REVERT: L 53 HIS cc_start: 0.9152 (t-90) cc_final: 0.8639 (t-90) REVERT: L 60 GLU cc_start: 0.9383 (tt0) cc_final: 0.9116 (tm-30) REVERT: L 61 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9071 (mm-30) REVERT: L 64 GLU cc_start: 0.9469 (mt-10) cc_final: 0.8872 (tm-30) REVERT: L 67 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8954 (tm-30) REVERT: L 68 ARG cc_start: 0.9084 (ttp-170) cc_final: 0.8832 (ttm-80) REVERT: L 74 ASN cc_start: 0.9396 (m-40) cc_final: 0.9059 (m-40) REVERT: L 112 GLN cc_start: 0.9149 (tp40) cc_final: 0.8654 (tp40) REVERT: L 124 ARG cc_start: 0.9357 (mmt-90) cc_final: 0.9051 (mmp80) REVERT: L 126 ASP cc_start: 0.8992 (t0) cc_final: 0.8695 (t70) REVERT: L 132 PHE cc_start: 0.9364 (t80) cc_final: 0.9080 (t80) REVERT: L 143 LYS cc_start: 0.9580 (mtpt) cc_final: 0.9337 (mttm) REVERT: M 11 ASN cc_start: 0.8830 (t0) cc_final: 0.8571 (t0) REVERT: M 46 VAL cc_start: 0.9392 (t) cc_final: 0.9170 (p) REVERT: M 56 ARG cc_start: 0.9302 (tpp80) cc_final: 0.8909 (ttm-80) REVERT: N 42 ASP cc_start: 0.9074 (t70) cc_final: 0.8200 (t70) REVERT: N 53 HIS cc_start: 0.9131 (t-170) cc_final: 0.8464 (t70) REVERT: N 57 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8745 (mm-30) REVERT: N 64 GLU cc_start: 0.9162 (mp0) cc_final: 0.8665 (mp0) REVERT: N 74 ASN cc_start: 0.9016 (m-40) cc_final: 0.8474 (m-40) REVERT: N 112 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8116 (tp40) REVERT: N 140 GLU cc_start: 0.8855 (mp0) cc_final: 0.8515 (mp0) REVERT: O 15 ASP cc_start: 0.9186 (p0) cc_final: 0.8818 (p0) REVERT: O 42 ASP cc_start: 0.9443 (t0) cc_final: 0.8961 (t70) REVERT: O 44 ASP cc_start: 0.8629 (p0) cc_final: 0.8289 (p0) REVERT: O 60 GLU cc_start: 0.9248 (tp30) cc_final: 0.8920 (tp30) REVERT: O 64 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8962 (mm-30) REVERT: O 68 ARG cc_start: 0.9283 (ttm-80) cc_final: 0.8988 (ttm110) REVERT: O 71 LYS cc_start: 0.9488 (ttmm) cc_final: 0.9255 (tppt) REVERT: O 74 ASN cc_start: 0.9301 (m-40) cc_final: 0.9005 (t0) REVERT: O 126 ASP cc_start: 0.8943 (t0) cc_final: 0.8649 (t0) REVERT: O 148 MET cc_start: 0.9182 (ttm) cc_final: 0.8833 (ttm) REVERT: O 172 ARG cc_start: 0.9424 (mmp-170) cc_final: 0.9049 (mmp-170) REVERT: P 53 HIS cc_start: 0.9147 (t-170) cc_final: 0.8403 (t70) REVERT: P 57 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8465 (mm-30) REVERT: P 64 GLU cc_start: 0.9511 (tp30) cc_final: 0.8941 (tm-30) REVERT: P 104 MET cc_start: 0.9482 (ttp) cc_final: 0.8922 (ttm) REVERT: P 148 MET cc_start: 0.9322 (mtt) cc_final: 0.9072 (mtp) REVERT: P 162 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7356 (pp20) REVERT: Q 29 GLN cc_start: 0.8931 (tp40) cc_final: 0.8703 (tp40) REVERT: Q 53 HIS cc_start: 0.9096 (t-170) cc_final: 0.8288 (t-90) REVERT: Q 57 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8972 (mm-30) REVERT: Q 61 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9009 (tm-30) REVERT: Q 64 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8912 (mm-30) REVERT: Q 67 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8707 (mt-10) REVERT: Q 68 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8596 (ttm110) REVERT: Q 107 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8688 (mm-30) REVERT: Q 112 GLN cc_start: 0.9154 (tp40) cc_final: 0.8848 (tp40) REVERT: Q 148 MET cc_start: 0.9401 (ttp) cc_final: 0.9127 (ttt) REVERT: Q 171 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8735 (tm-30) REVERT: Q 172 ARG cc_start: 0.9255 (mmp80) cc_final: 0.8853 (mmp80) REVERT: R 42 ASP cc_start: 0.9442 (t0) cc_final: 0.9223 (t0) REVERT: R 49 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8667 (tm-30) REVERT: R 53 HIS cc_start: 0.9059 (m-70) cc_final: 0.8778 (m90) REVERT: R 67 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8734 (pp20) REVERT: R 68 ARG cc_start: 0.9175 (mtm-85) cc_final: 0.8745 (mtm-85) REVERT: R 73 GLN cc_start: 0.9181 (tp40) cc_final: 0.8896 (tp40) REVERT: R 126 ASP cc_start: 0.9142 (t0) cc_final: 0.8581 (t70) REVERT: S 42 ASP cc_start: 0.9479 (t0) cc_final: 0.8601 (t0) REVERT: S 49 GLU cc_start: 0.9008 (tp30) cc_final: 0.8692 (tm-30) REVERT: S 68 ARG cc_start: 0.9192 (ptp-110) cc_final: 0.8762 (ptp-170) REVERT: S 72 MET cc_start: 0.9609 (tmm) cc_final: 0.9378 (tmm) REVERT: S 74 ASN cc_start: 0.9254 (m110) cc_final: 0.8823 (m-40) REVERT: S 126 ASP cc_start: 0.8887 (t0) cc_final: 0.8318 (t0) REVERT: S 136 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8824 (p-80) REVERT: S 143 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8784 (mtmm) REVERT: T 12 TYR cc_start: 0.8745 (t80) cc_final: 0.8491 (t80) REVERT: T 29 GLN cc_start: 0.8965 (tt0) cc_final: 0.8666 (tt0) REVERT: T 45 ASP cc_start: 0.8832 (p0) cc_final: 0.8531 (p0) REVERT: T 53 HIS cc_start: 0.9051 (t-90) cc_final: 0.8011 (t-90) REVERT: T 57 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8625 (mm-30) REVERT: T 63 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8054 (ttm110) REVERT: T 68 ARG cc_start: 0.9245 (ttp-170) cc_final: 0.8491 (ttm170) REVERT: T 86 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8904 (ptmm) REVERT: T 104 MET cc_start: 0.9067 (tpp) cc_final: 0.8710 (tpp) REVERT: T 107 GLU cc_start: 0.8777 (tp30) cc_final: 0.8550 (tp30) REVERT: T 126 ASP cc_start: 0.9071 (t0) cc_final: 0.8801 (t70) REVERT: T 132 PHE cc_start: 0.9065 (t80) cc_final: 0.8687 (t80) REVERT: T 135 THR cc_start: 0.9332 (t) cc_final: 0.8998 (p) REVERT: T 136 HIS cc_start: 0.8822 (OUTLIER) cc_final: 0.8191 (p-80) REVERT: T 148 MET cc_start: 0.9420 (mtt) cc_final: 0.8116 (mtp) REVERT: T 170 PHE cc_start: 0.9129 (t80) cc_final: 0.8894 (t80) REVERT: U 29 GLN cc_start: 0.9161 (tp40) cc_final: 0.8883 (tp40) REVERT: U 42 ASP cc_start: 0.9126 (t0) cc_final: 0.8558 (t0) REVERT: U 44 ASP cc_start: 0.8417 (p0) cc_final: 0.8057 (p0) REVERT: U 63 ARG cc_start: 0.9440 (mtp-110) cc_final: 0.9150 (ttm-80) REVERT: U 100 MET cc_start: 0.9090 (mmm) cc_final: 0.8872 (mmt) REVERT: U 112 GLN cc_start: 0.9477 (tp40) cc_final: 0.9070 (tp40) REVERT: U 156 HIS cc_start: 0.8884 (m90) cc_final: 0.8431 (m90) REVERT: U 171 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9049 (tm-30) REVERT: U 172 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8727 (ttm-80) REVERT: V 34 TYR cc_start: 0.9520 (m-10) cc_final: 0.9295 (m-10) REVERT: V 49 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8869 (tm-30) REVERT: V 52 SER cc_start: 0.9624 (t) cc_final: 0.9243 (m) REVERT: V 53 HIS cc_start: 0.8689 (t70) cc_final: 0.8170 (t-90) REVERT: V 57 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8405 (mm-30) REVERT: V 63 ARG cc_start: 0.9017 (ttp80) cc_final: 0.8682 (ttm110) REVERT: V 64 GLU cc_start: 0.9228 (tt0) cc_final: 0.8929 (pp20) REVERT: V 68 ARG cc_start: 0.9066 (ptm160) cc_final: 0.8372 (ptm160) REVERT: V 74 ASN cc_start: 0.9328 (m-40) cc_final: 0.8799 (t0) REVERT: V 112 GLN cc_start: 0.9383 (tp40) cc_final: 0.9045 (mm-40) REVERT: V 124 ARG cc_start: 0.9549 (mmp80) cc_final: 0.9310 (mmp80) REVERT: V 126 ASP cc_start: 0.9047 (t0) cc_final: 0.8667 (t0) REVERT: V 136 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.7807 (p-80) REVERT: V 137 PHE cc_start: 0.9054 (m-10) cc_final: 0.8824 (m-10) REVERT: V 171 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8732 (tm-30) REVERT: V 172 ARG cc_start: 0.9031 (mmp80) cc_final: 0.8753 (mmp80) REVERT: W 29 GLN cc_start: 0.9005 (tp40) cc_final: 0.8486 (mm110) REVERT: W 42 ASP cc_start: 0.9278 (t0) cc_final: 0.8793 (t0) REVERT: W 61 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8778 (tm-30) REVERT: W 67 GLU cc_start: 0.9554 (mt-10) cc_final: 0.9102 (mt-10) REVERT: W 68 ARG cc_start: 0.8896 (mtp180) cc_final: 0.8357 (mtp180) REVERT: W 126 ASP cc_start: 0.9362 (t0) cc_final: 0.8666 (t70) REVERT: W 136 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.7844 (p-80) REVERT: X 12 TYR cc_start: 0.9330 (t80) cc_final: 0.9019 (t80) REVERT: X 53 HIS cc_start: 0.9121 (t-90) cc_final: 0.8847 (t70) REVERT: X 57 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8770 (mm-30) REVERT: X 74 ASN cc_start: 0.9258 (m-40) cc_final: 0.8878 (m-40) REVERT: X 126 ASP cc_start: 0.8870 (t0) cc_final: 0.8556 (t0) outliers start: 166 outliers final: 104 residues processed: 1161 average time/residue: 0.5195 time to fit residues: 938.3487 Evaluate side-chains 1113 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 986 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 74 ASN Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain V residue 145 ILE Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 11 ASN Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 131 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 19 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 364 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 296 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN F 53 HIS ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN I 29 GLN J 111 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 HIS W 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052916 restraints weight = 120344.323| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.12 r_work: 0.2822 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 33816 Z= 0.252 Angle : 0.766 14.038 45480 Z= 0.394 Chirality : 0.045 0.243 4872 Planarity : 0.005 0.059 5952 Dihedral : 5.530 53.949 4570 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Rotamer: Outliers : 4.51 % Allowed : 26.41 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.13), residues: 4080 helix: 1.72 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -2.44 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 93 HIS 0.010 0.001 HIS F 53 PHE 0.035 0.003 PHE X 39 TYR 0.040 0.003 TYR G 34 ARG 0.012 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 2679) hydrogen bonds : angle 4.36366 ( 8037) covalent geometry : bond 0.00552 (33816) covalent geometry : angle 0.76561 (45480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1042 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8682 (t80) cc_final: 0.8338 (t80) REVERT: A 15 ASP cc_start: 0.9339 (p0) cc_final: 0.9034 (p0) REVERT: A 29 GLN cc_start: 0.9126 (tp40) cc_final: 0.8808 (tp40) REVERT: A 42 ASP cc_start: 0.9302 (t0) cc_final: 0.8802 (t0) REVERT: A 52 SER cc_start: 0.9469 (t) cc_final: 0.9241 (m) REVERT: A 68 ARG cc_start: 0.8420 (ptp-170) cc_final: 0.7837 (ptm160) REVERT: A 72 MET cc_start: 0.9448 (tmm) cc_final: 0.9236 (tmm) REVERT: A 74 ASN cc_start: 0.9307 (m-40) cc_final: 0.8928 (m-40) REVERT: A 107 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8501 (mm-30) REVERT: A 124 ARG cc_start: 0.9312 (mmt-90) cc_final: 0.8947 (mmp80) REVERT: A 141 GLU cc_start: 0.8864 (tp30) cc_final: 0.8602 (tp30) REVERT: A 167 GLU cc_start: 0.9096 (tt0) cc_final: 0.8584 (tt0) REVERT: A 171 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9091 (tm-30) REVERT: B 12 TYR cc_start: 0.9083 (t80) cc_final: 0.8699 (t80) REVERT: B 27 TYR cc_start: 0.9403 (m-80) cc_final: 0.9154 (m-80) REVERT: B 56 ARG cc_start: 0.9167 (tpp80) cc_final: 0.8795 (tpp80) REVERT: B 72 MET cc_start: 0.9717 (tmm) cc_final: 0.9142 (tmm) REVERT: B 98 ASP cc_start: 0.9524 (t0) cc_final: 0.9226 (m-30) REVERT: B 126 ASP cc_start: 0.8802 (t0) cc_final: 0.8501 (t0) REVERT: B 148 MET cc_start: 0.9590 (mtp) cc_final: 0.9283 (mtp) REVERT: C 12 TYR cc_start: 0.8695 (t80) cc_final: 0.8447 (t80) REVERT: C 42 ASP cc_start: 0.9318 (t70) cc_final: 0.9016 (t70) REVERT: C 58 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9374 (tp) REVERT: C 104 MET cc_start: 0.9034 (tpp) cc_final: 0.8717 (tpp) REVERT: C 126 ASP cc_start: 0.9207 (t0) cc_final: 0.8596 (t0) REVERT: C 129 LEU cc_start: 0.9809 (tp) cc_final: 0.9588 (tp) REVERT: C 131 ASP cc_start: 0.9388 (t0) cc_final: 0.8846 (t0) REVERT: C 136 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8254 (p-80) REVERT: C 137 PHE cc_start: 0.9132 (m-80) cc_final: 0.8928 (m-80) REVERT: C 147 LYS cc_start: 0.9411 (ttmm) cc_final: 0.9142 (ptmm) REVERT: C 176 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7872 (ttmm) REVERT: D 7 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: D 14 THR cc_start: 0.9458 (p) cc_final: 0.9236 (t) REVERT: D 52 SER cc_start: 0.9350 (t) cc_final: 0.8951 (m) REVERT: D 61 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9109 (tm-30) REVERT: D 63 ARG cc_start: 0.9036 (mmm-85) cc_final: 0.8438 (ttp80) REVERT: D 66 TYR cc_start: 0.9577 (p90) cc_final: 0.9375 (p90) REVERT: D 68 ARG cc_start: 0.9182 (ttm-80) cc_final: 0.8972 (ttm-80) REVERT: D 74 ASN cc_start: 0.9162 (m110) cc_final: 0.8720 (m-40) REVERT: D 112 GLN cc_start: 0.9273 (tp40) cc_final: 0.8495 (tp-100) REVERT: D 116 ASP cc_start: 0.9265 (m-30) cc_final: 0.8601 (m-30) REVERT: D 126 ASP cc_start: 0.9158 (t0) cc_final: 0.8711 (t70) REVERT: D 140 GLU cc_start: 0.9234 (tm-30) cc_final: 0.9033 (tm-30) REVERT: D 143 LYS cc_start: 0.9467 (mtmm) cc_final: 0.9189 (mtmm) REVERT: D 167 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8421 (mp0) REVERT: D 171 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8918 (tm-30) REVERT: E 26 LEU cc_start: 0.9502 (tp) cc_final: 0.9219 (tp) REVERT: E 44 ASP cc_start: 0.9336 (p0) cc_final: 0.9084 (p0) REVERT: E 48 LEU cc_start: 0.9381 (mt) cc_final: 0.8993 (mt) REVERT: E 49 GLU cc_start: 0.8953 (pp20) cc_final: 0.8692 (pp20) REVERT: E 52 SER cc_start: 0.9298 (t) cc_final: 0.9043 (m) REVERT: E 57 GLU cc_start: 0.9120 (tp30) cc_final: 0.8777 (tp30) REVERT: E 63 ARG cc_start: 0.8804 (ttp80) cc_final: 0.7886 (ttp80) REVERT: E 112 GLN cc_start: 0.9233 (tp40) cc_final: 0.8695 (tp40) REVERT: E 116 ASP cc_start: 0.8934 (m-30) cc_final: 0.8536 (m-30) REVERT: E 153 THR cc_start: 0.9543 (m) cc_final: 0.9164 (p) REVERT: E 168 TYR cc_start: 0.9177 (t80) cc_final: 0.8847 (t80) REVERT: E 171 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: F 12 TYR cc_start: 0.8747 (t80) cc_final: 0.8215 (t80) REVERT: F 31 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9218 (m) REVERT: F 44 ASP cc_start: 0.8305 (p0) cc_final: 0.8082 (p0) REVERT: F 52 SER cc_start: 0.9472 (t) cc_final: 0.9176 (m) REVERT: F 67 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8216 (mt-10) REVERT: F 79 ARG cc_start: 0.9095 (mmp80) cc_final: 0.8494 (mmp80) REVERT: F 112 GLN cc_start: 0.9228 (tp40) cc_final: 0.8357 (tp-100) REVERT: F 153 THR cc_start: 0.9019 (m) cc_final: 0.8725 (p) REVERT: G 53 HIS cc_start: 0.8775 (t-90) cc_final: 0.8155 (t-90) REVERT: G 56 ARG cc_start: 0.9194 (tpp80) cc_final: 0.8957 (tpp80) REVERT: G 60 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8482 (tm-30) REVERT: G 63 ARG cc_start: 0.9253 (ttm110) cc_final: 0.9004 (ttm110) REVERT: G 64 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8297 (mt-10) REVERT: G 73 GLN cc_start: 0.9194 (tp40) cc_final: 0.8801 (tm-30) REVERT: G 75 GLN cc_start: 0.9389 (mp-120) cc_final: 0.9158 (mp10) REVERT: G 104 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8716 (ttm) REVERT: G 107 GLU cc_start: 0.9014 (tp30) cc_final: 0.8422 (tp30) REVERT: G 124 ARG cc_start: 0.9251 (mmp80) cc_final: 0.8954 (mmp80) REVERT: G 140 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8999 (mt-10) REVERT: H 42 ASP cc_start: 0.9289 (t70) cc_final: 0.8890 (t0) REVERT: H 57 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8655 (mt-10) REVERT: H 112 GLN cc_start: 0.9194 (tp40) cc_final: 0.8761 (tp-100) REVERT: H 124 ARG cc_start: 0.9426 (tpp-160) cc_final: 0.8901 (mmt-90) REVERT: H 172 ARG cc_start: 0.9053 (mmm160) cc_final: 0.8795 (mmm160) REVERT: I 29 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8931 (tp40) REVERT: I 42 ASP cc_start: 0.9388 (t70) cc_final: 0.9107 (t0) REVERT: I 61 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8959 (mm-30) REVERT: I 64 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9112 (mp0) REVERT: I 98 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.9010 (t0) REVERT: I 104 MET cc_start: 0.9445 (ttm) cc_final: 0.9176 (ttm) REVERT: I 107 GLU cc_start: 0.9014 (tp30) cc_final: 0.8515 (tp30) REVERT: I 112 GLN cc_start: 0.9416 (tp40) cc_final: 0.8937 (tp-100) REVERT: J 68 ARG cc_start: 0.9392 (mtt90) cc_final: 0.8910 (ttm170) REVERT: J 73 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: J 124 ARG cc_start: 0.9252 (mmt-90) cc_final: 0.8983 (mmt-90) REVERT: J 153 THR cc_start: 0.9150 (m) cc_final: 0.8928 (p) REVERT: K 7 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: K 42 ASP cc_start: 0.9445 (t70) cc_final: 0.8796 (t70) REVERT: K 45 ASP cc_start: 0.8854 (m-30) cc_final: 0.8369 (m-30) REVERT: K 56 ARG cc_start: 0.9032 (ttm-80) cc_final: 0.8452 (ttm-80) REVERT: K 66 TYR cc_start: 0.9358 (p90) cc_final: 0.9114 (p90) REVERT: K 72 MET cc_start: 0.9625 (ppp) cc_final: 0.9382 (ppp) REVERT: K 74 ASN cc_start: 0.9400 (m-40) cc_final: 0.8999 (m-40) REVERT: K 83 GLN cc_start: 0.8989 (mm110) cc_final: 0.8700 (mm110) REVERT: K 87 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8856 (ptpp) REVERT: K 104 MET cc_start: 0.9091 (mmm) cc_final: 0.8658 (tpp) REVERT: K 143 LYS cc_start: 0.9382 (mtmm) cc_final: 0.9107 (mtmm) REVERT: K 170 PHE cc_start: 0.9427 (t80) cc_final: 0.9101 (t80) REVERT: L 29 GLN cc_start: 0.9468 (tt0) cc_final: 0.8999 (tm-30) REVERT: L 49 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8564 (tm-30) REVERT: L 52 SER cc_start: 0.9534 (OUTLIER) cc_final: 0.9143 (p) REVERT: L 53 HIS cc_start: 0.9193 (t-90) cc_final: 0.8677 (t-90) REVERT: L 60 GLU cc_start: 0.9408 (tt0) cc_final: 0.9149 (tm-30) REVERT: L 61 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9091 (mm-30) REVERT: L 64 GLU cc_start: 0.9472 (mt-10) cc_final: 0.8884 (tm-30) REVERT: L 67 GLU cc_start: 0.9300 (tm-30) cc_final: 0.8962 (tm-30) REVERT: L 68 ARG cc_start: 0.9113 (ttp-170) cc_final: 0.8878 (ttm-80) REVERT: L 74 ASN cc_start: 0.9463 (m-40) cc_final: 0.9114 (m-40) REVERT: L 126 ASP cc_start: 0.8972 (t0) cc_final: 0.8686 (t70) REVERT: L 132 PHE cc_start: 0.9348 (t80) cc_final: 0.9102 (t80) REVERT: L 143 LYS cc_start: 0.9567 (mtpt) cc_final: 0.9149 (mtmm) REVERT: M 11 ASN cc_start: 0.8723 (t0) cc_final: 0.8415 (t0) REVERT: M 56 ARG cc_start: 0.9285 (tpp80) cc_final: 0.8893 (ttm-80) REVERT: M 60 GLU cc_start: 0.9309 (tp30) cc_final: 0.9023 (tp30) REVERT: M 63 ARG cc_start: 0.9277 (mtp-110) cc_final: 0.8907 (ttp80) REVERT: N 42 ASP cc_start: 0.9072 (t70) cc_final: 0.8212 (t70) REVERT: N 53 HIS cc_start: 0.9136 (t-170) cc_final: 0.8568 (t70) REVERT: N 57 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8840 (mm-30) REVERT: N 64 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: N 74 ASN cc_start: 0.9032 (m-40) cc_final: 0.8469 (m-40) REVERT: N 75 GLN cc_start: 0.9249 (mm-40) cc_final: 0.9040 (mm-40) REVERT: N 112 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8261 (tp40) REVERT: N 126 ASP cc_start: 0.8991 (t0) cc_final: 0.8658 (t70) REVERT: N 140 GLU cc_start: 0.8860 (mp0) cc_final: 0.8556 (mp0) REVERT: O 15 ASP cc_start: 0.9194 (p0) cc_final: 0.8831 (p0) REVERT: O 42 ASP cc_start: 0.9431 (t0) cc_final: 0.8921 (t70) REVERT: O 44 ASP cc_start: 0.8692 (p0) cc_final: 0.8343 (p0) REVERT: O 60 GLU cc_start: 0.9262 (tp30) cc_final: 0.8997 (tp30) REVERT: O 63 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8675 (ttp80) REVERT: O 64 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9068 (mm-30) REVERT: O 68 ARG cc_start: 0.9300 (ttm-80) cc_final: 0.9022 (ttm-80) REVERT: O 71 LYS cc_start: 0.9517 (ttmm) cc_final: 0.9224 (tppt) REVERT: O 74 ASN cc_start: 0.9310 (m-40) cc_final: 0.8982 (t0) REVERT: O 126 ASP cc_start: 0.8924 (t0) cc_final: 0.8640 (t0) REVERT: O 172 ARG cc_start: 0.9457 (mmp-170) cc_final: 0.9060 (mmp-170) REVERT: P 53 HIS cc_start: 0.9158 (t-170) cc_final: 0.8394 (t70) REVERT: P 57 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8517 (mm-30) REVERT: P 64 GLU cc_start: 0.9530 (tp30) cc_final: 0.9057 (tm-30) REVERT: P 68 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8814 (mtm-85) REVERT: P 104 MET cc_start: 0.9475 (ttp) cc_final: 0.8937 (ttm) REVERT: P 143 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9260 (mtmm) REVERT: P 148 MET cc_start: 0.9320 (mtt) cc_final: 0.9070 (mtp) REVERT: P 162 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: Q 53 HIS cc_start: 0.9105 (t-170) cc_final: 0.8268 (t-90) REVERT: Q 57 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8960 (mm-30) REVERT: Q 61 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8978 (tm-30) REVERT: Q 63 ARG cc_start: 0.9135 (ttm-80) cc_final: 0.8370 (ttm-80) REVERT: Q 64 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8924 (mm-30) REVERT: Q 67 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8834 (mt-10) REVERT: Q 68 ARG cc_start: 0.9053 (ttm170) cc_final: 0.8660 (ttm110) REVERT: Q 104 MET cc_start: 0.9263 (mmm) cc_final: 0.9031 (tpp) REVERT: Q 107 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8697 (mm-30) REVERT: Q 112 GLN cc_start: 0.9175 (tp40) cc_final: 0.8845 (tp40) REVERT: Q 148 MET cc_start: 0.9500 (ttp) cc_final: 0.9262 (ttt) REVERT: Q 171 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8839 (tm-30) REVERT: R 49 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8715 (tm-30) REVERT: R 53 HIS cc_start: 0.9088 (m-70) cc_final: 0.8765 (m90) REVERT: R 67 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8704 (pp20) REVERT: R 68 ARG cc_start: 0.9227 (mtm-85) cc_final: 0.8845 (mtm-85) REVERT: R 126 ASP cc_start: 0.9111 (t0) cc_final: 0.8643 (t0) REVERT: S 42 ASP cc_start: 0.9509 (t0) cc_final: 0.8772 (t0) REVERT: S 49 GLU cc_start: 0.9001 (tp30) cc_final: 0.8697 (tm-30) REVERT: S 68 ARG cc_start: 0.9206 (ptp-110) cc_final: 0.8926 (ptp-170) REVERT: S 72 MET cc_start: 0.9618 (tmm) cc_final: 0.9396 (tmm) REVERT: S 126 ASP cc_start: 0.8894 (t0) cc_final: 0.8337 (t0) REVERT: S 143 LYS cc_start: 0.9268 (mtmm) cc_final: 0.8819 (mtmm) REVERT: T 12 TYR cc_start: 0.8814 (t80) cc_final: 0.8534 (t80) REVERT: T 29 GLN cc_start: 0.8983 (tt0) cc_final: 0.8683 (tt0) REVERT: T 45 ASP cc_start: 0.8817 (p0) cc_final: 0.8453 (p0) REVERT: T 53 HIS cc_start: 0.9039 (t-90) cc_final: 0.8148 (t-90) REVERT: T 63 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8005 (ttm110) REVERT: T 68 ARG cc_start: 0.9225 (ttp-170) cc_final: 0.8189 (ttp-170) REVERT: T 74 ASN cc_start: 0.9191 (m-40) cc_final: 0.8854 (m-40) REVERT: T 86 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8902 (ptmm) REVERT: T 104 MET cc_start: 0.9122 (tpp) cc_final: 0.8745 (tpp) REVERT: T 107 GLU cc_start: 0.8759 (tp30) cc_final: 0.8463 (tm-30) REVERT: T 126 ASP cc_start: 0.9059 (t0) cc_final: 0.8678 (t70) REVERT: T 132 PHE cc_start: 0.9114 (t80) cc_final: 0.8790 (t80) REVERT: T 135 THR cc_start: 0.9305 (t) cc_final: 0.8965 (p) REVERT: T 136 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.7880 (p-80) REVERT: T 148 MET cc_start: 0.9431 (mtt) cc_final: 0.8683 (mtt) REVERT: U 29 GLN cc_start: 0.9139 (tp40) cc_final: 0.8874 (tp40) REVERT: U 42 ASP cc_start: 0.9120 (t0) cc_final: 0.8563 (t0) REVERT: U 44 ASP cc_start: 0.8425 (p0) cc_final: 0.8080 (p0) REVERT: U 63 ARG cc_start: 0.9443 (mtp-110) cc_final: 0.9023 (mtp-110) REVERT: U 100 MET cc_start: 0.9116 (mmm) cc_final: 0.8762 (mmt) REVERT: U 112 GLN cc_start: 0.9416 (tp40) cc_final: 0.9148 (tp40) REVERT: U 148 MET cc_start: 0.9247 (mtp) cc_final: 0.8929 (ttm) REVERT: U 156 HIS cc_start: 0.8922 (m90) cc_final: 0.8423 (m90) REVERT: V 34 TYR cc_start: 0.9520 (m-10) cc_final: 0.9306 (m-10) REVERT: V 49 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8834 (tm-30) REVERT: V 57 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8476 (mm-30) REVERT: V 64 GLU cc_start: 0.9221 (tt0) cc_final: 0.8944 (pp20) REVERT: V 68 ARG cc_start: 0.9055 (ptm160) cc_final: 0.8587 (ptm160) REVERT: V 74 ASN cc_start: 0.9308 (m-40) cc_final: 0.8793 (t0) REVERT: V 84 ASP cc_start: 0.8985 (m-30) cc_final: 0.8752 (t0) REVERT: V 100 MET cc_start: 0.9384 (tpp) cc_final: 0.8660 (mmt) REVERT: V 126 ASP cc_start: 0.9006 (t0) cc_final: 0.8644 (t0) REVERT: V 136 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.8380 (p-80) REVERT: V 137 PHE cc_start: 0.9022 (m-10) cc_final: 0.8569 (m-10) REVERT: V 148 MET cc_start: 0.9265 (mmm) cc_final: 0.8940 (mmm) REVERT: V 171 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8732 (tm-30) REVERT: V 172 ARG cc_start: 0.9063 (mmp80) cc_final: 0.8750 (mmp80) REVERT: W 29 GLN cc_start: 0.8990 (tp40) cc_final: 0.8464 (mm110) REVERT: W 42 ASP cc_start: 0.9267 (t0) cc_final: 0.8775 (t0) REVERT: W 58 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9326 (tp) REVERT: W 61 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8785 (tm-30) REVERT: W 67 GLU cc_start: 0.9549 (mt-10) cc_final: 0.8966 (mt-10) REVERT: W 68 ARG cc_start: 0.8907 (mtp180) cc_final: 0.8361 (mtp180) REVERT: W 124 ARG cc_start: 0.9060 (mmt90) cc_final: 0.8834 (mmt90) REVERT: W 126 ASP cc_start: 0.9375 (t0) cc_final: 0.8722 (t70) REVERT: W 136 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.7805 (p-80) REVERT: W 153 THR cc_start: 0.9082 (m) cc_final: 0.8882 (p) REVERT: X 12 TYR cc_start: 0.9344 (t80) cc_final: 0.8698 (t80) REVERT: X 53 HIS cc_start: 0.9131 (t-90) cc_final: 0.8882 (t70) REVERT: X 63 ARG cc_start: 0.9356 (ttp80) cc_final: 0.9022 (ttp80) REVERT: X 126 ASP cc_start: 0.8871 (t0) cc_final: 0.8565 (t0) REVERT: X 172 ARG cc_start: 0.9252 (tpp-160) cc_final: 0.8941 (tpp80) outliers start: 157 outliers final: 108 residues processed: 1134 average time/residue: 0.5245 time to fit residues: 917.2481 Evaluate side-chains 1102 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 973 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain V residue 145 ILE Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 11 ASN Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 131 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 156 optimal weight: 7.9990 chunk 300 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN I 29 GLN J 111 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 GLN ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 ASN ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 HIS W 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053997 restraints weight = 120469.482| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.15 r_work: 0.2840 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33816 Z= 0.220 Angle : 0.763 12.587 45480 Z= 0.394 Chirality : 0.044 0.250 4872 Planarity : 0.004 0.060 5952 Dihedral : 5.455 53.880 4568 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 4.11 % Allowed : 27.33 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.13), residues: 4080 helix: 1.61 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -2.15 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 93 HIS 0.008 0.001 HIS L 136 PHE 0.034 0.003 PHE O 170 TYR 0.053 0.003 TYR X 40 ARG 0.013 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 2679) hydrogen bonds : angle 4.42659 ( 8037) covalent geometry : bond 0.00491 (33816) covalent geometry : angle 0.76261 (45480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1045 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8661 (t80) cc_final: 0.8273 (t80) REVERT: A 29 GLN cc_start: 0.9141 (tp40) cc_final: 0.8780 (tp40) REVERT: A 42 ASP cc_start: 0.9301 (t0) cc_final: 0.8810 (t0) REVERT: A 52 SER cc_start: 0.9417 (t) cc_final: 0.9179 (m) REVERT: A 68 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.7725 (ptm160) REVERT: A 74 ASN cc_start: 0.9308 (m-40) cc_final: 0.8837 (m-40) REVERT: A 107 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8536 (mm-30) REVERT: A 112 GLN cc_start: 0.9390 (tp40) cc_final: 0.8923 (tp40) REVERT: A 124 ARG cc_start: 0.9337 (mmt-90) cc_final: 0.9041 (mmp80) REVERT: A 141 GLU cc_start: 0.8895 (tp30) cc_final: 0.8672 (tp30) REVERT: A 167 GLU cc_start: 0.9127 (tt0) cc_final: 0.8604 (tt0) REVERT: A 171 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9119 (tm-30) REVERT: B 12 TYR cc_start: 0.9052 (t80) cc_final: 0.8765 (t80) REVERT: B 27 TYR cc_start: 0.9427 (m-80) cc_final: 0.9217 (m-80) REVERT: B 56 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8846 (tpp80) REVERT: B 72 MET cc_start: 0.9704 (tmm) cc_final: 0.9284 (tmm) REVERT: B 98 ASP cc_start: 0.9522 (t0) cc_final: 0.9222 (m-30) REVERT: B 126 ASP cc_start: 0.8686 (t0) cc_final: 0.8406 (t0) REVERT: B 148 MET cc_start: 0.9615 (mtp) cc_final: 0.9303 (mtp) REVERT: C 12 TYR cc_start: 0.8677 (t80) cc_final: 0.8456 (t80) REVERT: C 42 ASP cc_start: 0.9328 (t70) cc_final: 0.9017 (t70) REVERT: C 58 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9419 (tp) REVERT: C 126 ASP cc_start: 0.9207 (t0) cc_final: 0.8591 (t0) REVERT: C 129 LEU cc_start: 0.9803 (tp) cc_final: 0.9576 (tp) REVERT: C 131 ASP cc_start: 0.9330 (t0) cc_final: 0.8816 (t0) REVERT: C 136 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8055 (p-80) REVERT: C 147 LYS cc_start: 0.9277 (ttmm) cc_final: 0.9047 (ptmm) REVERT: C 176 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7832 (ttmm) REVERT: D 7 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: D 14 THR cc_start: 0.9459 (p) cc_final: 0.9250 (t) REVERT: D 63 ARG cc_start: 0.8984 (mmm-85) cc_final: 0.8523 (ttp80) REVERT: D 66 TYR cc_start: 0.9550 (p90) cc_final: 0.9205 (p90) REVERT: D 74 ASN cc_start: 0.9184 (m110) cc_final: 0.8731 (m-40) REVERT: D 112 GLN cc_start: 0.9254 (tp40) cc_final: 0.8454 (tp-100) REVERT: D 116 ASP cc_start: 0.9250 (m-30) cc_final: 0.8559 (m-30) REVERT: D 126 ASP cc_start: 0.9168 (t0) cc_final: 0.8722 (t70) REVERT: D 143 LYS cc_start: 0.9479 (mtmm) cc_final: 0.9115 (mtmm) REVERT: D 167 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8370 (mp0) REVERT: D 171 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8957 (tm-30) REVERT: E 12 TYR cc_start: 0.9093 (t80) cc_final: 0.8754 (t80) REVERT: E 26 LEU cc_start: 0.9501 (tp) cc_final: 0.9230 (tp) REVERT: E 44 ASP cc_start: 0.9320 (p0) cc_final: 0.9082 (p0) REVERT: E 48 LEU cc_start: 0.9382 (mt) cc_final: 0.8972 (mt) REVERT: E 52 SER cc_start: 0.9299 (t) cc_final: 0.9037 (m) REVERT: E 57 GLU cc_start: 0.9088 (tp30) cc_final: 0.8837 (tp30) REVERT: E 112 GLN cc_start: 0.9222 (tp40) cc_final: 0.8641 (tp40) REVERT: E 116 ASP cc_start: 0.8902 (m-30) cc_final: 0.8471 (m-30) REVERT: E 168 TYR cc_start: 0.9159 (t80) cc_final: 0.8830 (t80) REVERT: E 171 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: F 12 TYR cc_start: 0.8744 (t80) cc_final: 0.8187 (t80) REVERT: F 31 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9216 (m) REVERT: F 44 ASP cc_start: 0.8314 (p0) cc_final: 0.8048 (p0) REVERT: F 52 SER cc_start: 0.9489 (t) cc_final: 0.9148 (m) REVERT: F 67 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8424 (mt-10) REVERT: F 79 ARG cc_start: 0.9119 (mmp80) cc_final: 0.8578 (mmp80) REVERT: F 112 GLN cc_start: 0.9200 (tp40) cc_final: 0.8363 (tp-100) REVERT: F 124 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8704 (mtp85) REVERT: F 153 THR cc_start: 0.9021 (m) cc_final: 0.8755 (p) REVERT: G 53 HIS cc_start: 0.8765 (t-90) cc_final: 0.8124 (t-90) REVERT: G 60 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8410 (tm-30) REVERT: G 64 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8213 (mt-10) REVERT: G 73 GLN cc_start: 0.9180 (tp40) cc_final: 0.8792 (tm-30) REVERT: G 75 GLN cc_start: 0.9361 (mp-120) cc_final: 0.9140 (mm-40) REVERT: G 104 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8657 (ttm) REVERT: G 107 GLU cc_start: 0.9038 (tp30) cc_final: 0.8411 (tp30) REVERT: G 124 ARG cc_start: 0.9261 (mmp80) cc_final: 0.8960 (mmp80) REVERT: H 42 ASP cc_start: 0.9255 (t70) cc_final: 0.8886 (t0) REVERT: H 57 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8638 (mt-10) REVERT: H 112 GLN cc_start: 0.9171 (tp40) cc_final: 0.8802 (tp-100) REVERT: H 172 ARG cc_start: 0.9010 (mmm160) cc_final: 0.8756 (mmm160) REVERT: I 29 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.9123 (tp40) REVERT: I 42 ASP cc_start: 0.9401 (t70) cc_final: 0.9157 (t0) REVERT: I 52 SER cc_start: 0.9329 (t) cc_final: 0.9031 (m) REVERT: I 61 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8931 (mm-30) REVERT: I 98 ASP cc_start: 0.9297 (OUTLIER) cc_final: 0.9034 (t0) REVERT: I 104 MET cc_start: 0.9437 (ttm) cc_final: 0.9172 (ttm) REVERT: I 112 GLN cc_start: 0.9386 (tp40) cc_final: 0.8870 (tp-100) REVERT: J 73 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: J 124 ARG cc_start: 0.9228 (mmt-90) cc_final: 0.8952 (mmt-90) REVERT: J 153 THR cc_start: 0.9153 (m) cc_final: 0.8932 (p) REVERT: K 7 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: K 42 ASP cc_start: 0.9461 (t70) cc_final: 0.8838 (t70) REVERT: K 45 ASP cc_start: 0.8834 (m-30) cc_final: 0.8375 (m-30) REVERT: K 56 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8444 (ttm-80) REVERT: K 66 TYR cc_start: 0.9377 (p90) cc_final: 0.9130 (p90) REVERT: K 72 MET cc_start: 0.9622 (ppp) cc_final: 0.9393 (ppp) REVERT: K 74 ASN cc_start: 0.9376 (m-40) cc_final: 0.8850 (m-40) REVERT: K 75 GLN cc_start: 0.9012 (mm110) cc_final: 0.8755 (mm110) REVERT: K 83 GLN cc_start: 0.8983 (mm110) cc_final: 0.8703 (mm110) REVERT: K 104 MET cc_start: 0.9098 (mmm) cc_final: 0.8680 (tpp) REVERT: K 143 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9079 (mtmm) REVERT: K 170 PHE cc_start: 0.9431 (t80) cc_final: 0.9104 (t80) REVERT: L 29 GLN cc_start: 0.9459 (tt0) cc_final: 0.8978 (tm-30) REVERT: L 49 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8573 (tm-30) REVERT: L 52 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9070 (p) REVERT: L 53 HIS cc_start: 0.9183 (t-90) cc_final: 0.8640 (t-90) REVERT: L 60 GLU cc_start: 0.9419 (tt0) cc_final: 0.9133 (tm-30) REVERT: L 61 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9098 (mm-30) REVERT: L 64 GLU cc_start: 0.9466 (mt-10) cc_final: 0.8872 (tm-30) REVERT: L 67 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8955 (tm-30) REVERT: L 68 ARG cc_start: 0.9080 (ttp-170) cc_final: 0.8852 (ttm-80) REVERT: L 74 ASN cc_start: 0.9448 (m-40) cc_final: 0.9132 (m-40) REVERT: L 126 ASP cc_start: 0.8976 (t0) cc_final: 0.8684 (t70) REVERT: L 143 LYS cc_start: 0.9528 (mtpt) cc_final: 0.9092 (mtmm) REVERT: L 172 ARG cc_start: 0.9423 (mmp-170) cc_final: 0.8994 (mmp80) REVERT: M 11 ASN cc_start: 0.8696 (t0) cc_final: 0.8345 (t0) REVERT: M 52 SER cc_start: 0.9352 (t) cc_final: 0.9080 (m) REVERT: M 56 ARG cc_start: 0.9258 (tpp80) cc_final: 0.8863 (ttm-80) REVERT: M 60 GLU cc_start: 0.9285 (tp30) cc_final: 0.8845 (tp30) REVERT: M 63 ARG cc_start: 0.9323 (mtp-110) cc_final: 0.8775 (ttp80) REVERT: N 42 ASP cc_start: 0.9070 (t70) cc_final: 0.8245 (t70) REVERT: N 53 HIS cc_start: 0.9113 (t-170) cc_final: 0.8530 (t70) REVERT: N 57 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8772 (mm-30) REVERT: N 64 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8632 (mp0) REVERT: N 74 ASN cc_start: 0.8987 (m-40) cc_final: 0.8399 (m-40) REVERT: N 75 GLN cc_start: 0.9222 (mm-40) cc_final: 0.9013 (mm-40) REVERT: N 112 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8214 (tp40) REVERT: N 126 ASP cc_start: 0.8994 (t0) cc_final: 0.8649 (t70) REVERT: N 140 GLU cc_start: 0.8821 (mp0) cc_final: 0.8544 (mp0) REVERT: O 15 ASP cc_start: 0.9294 (p0) cc_final: 0.8930 (p0) REVERT: O 42 ASP cc_start: 0.9426 (t0) cc_final: 0.8906 (t70) REVERT: O 44 ASP cc_start: 0.8753 (p0) cc_final: 0.8469 (p0) REVERT: O 57 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8514 (mm-30) REVERT: O 60 GLU cc_start: 0.9258 (tp30) cc_final: 0.8948 (tp30) REVERT: O 63 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8678 (ttp80) REVERT: O 64 GLU cc_start: 0.9307 (mt-10) cc_final: 0.9022 (mm-30) REVERT: O 68 ARG cc_start: 0.9285 (ttm-80) cc_final: 0.9079 (ttm-80) REVERT: O 74 ASN cc_start: 0.9302 (m-40) cc_final: 0.9013 (t0) REVERT: O 104 MET cc_start: 0.9269 (ttt) cc_final: 0.8822 (tpp) REVERT: O 126 ASP cc_start: 0.8885 (t0) cc_final: 0.8635 (t0) REVERT: O 148 MET cc_start: 0.9171 (ttm) cc_final: 0.8651 (ttm) REVERT: O 172 ARG cc_start: 0.9454 (mmp-170) cc_final: 0.9136 (mmp80) REVERT: P 17 GLU cc_start: 0.9202 (tt0) cc_final: 0.8884 (tt0) REVERT: P 53 HIS cc_start: 0.9157 (t-170) cc_final: 0.8347 (t70) REVERT: P 57 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8436 (mm-30) REVERT: P 64 GLU cc_start: 0.9521 (tp30) cc_final: 0.8956 (tm-30) REVERT: P 104 MET cc_start: 0.9471 (ttp) cc_final: 0.8905 (ttm) REVERT: P 143 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9249 (mtmm) REVERT: P 148 MET cc_start: 0.9298 (mtt) cc_final: 0.9022 (mtp) REVERT: P 162 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: P 167 GLU cc_start: 0.9251 (tt0) cc_final: 0.8887 (mt-10) REVERT: Q 29 GLN cc_start: 0.8888 (tp40) cc_final: 0.8665 (tp40) REVERT: Q 44 ASP cc_start: 0.8541 (p0) cc_final: 0.8333 (p0) REVERT: Q 53 HIS cc_start: 0.9051 (t-170) cc_final: 0.8195 (t-90) REVERT: Q 57 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8942 (mm-30) REVERT: Q 61 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8953 (tm-30) REVERT: Q 64 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8871 (mm-30) REVERT: Q 67 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8707 (mt-10) REVERT: Q 68 ARG cc_start: 0.9024 (ttm170) cc_final: 0.8614 (ttm110) REVERT: Q 104 MET cc_start: 0.9256 (mmm) cc_final: 0.8950 (tpp) REVERT: Q 107 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8714 (mm-30) REVERT: Q 112 GLN cc_start: 0.9201 (tp40) cc_final: 0.8851 (tp40) REVERT: Q 144 LEU cc_start: 0.9401 (tt) cc_final: 0.9200 (tp) REVERT: Q 171 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8691 (tm-30) REVERT: Q 172 ARG cc_start: 0.9268 (mmp80) cc_final: 0.8963 (mmp80) REVERT: R 49 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8678 (tm-30) REVERT: R 53 HIS cc_start: 0.9063 (m-70) cc_final: 0.8737 (m90) REVERT: R 67 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8685 (pp20) REVERT: R 68 ARG cc_start: 0.9201 (mtm-85) cc_final: 0.8828 (mtm-85) REVERT: R 126 ASP cc_start: 0.9171 (t0) cc_final: 0.8692 (t0) REVERT: S 42 ASP cc_start: 0.9506 (t0) cc_final: 0.8666 (t0) REVERT: S 49 GLU cc_start: 0.9000 (tp30) cc_final: 0.8735 (tm-30) REVERT: S 52 SER cc_start: 0.9632 (t) cc_final: 0.9369 (t) REVERT: S 68 ARG cc_start: 0.9151 (ptp-110) cc_final: 0.8824 (ptp-170) REVERT: S 72 MET cc_start: 0.9635 (tmm) cc_final: 0.9411 (tmm) REVERT: S 126 ASP cc_start: 0.8920 (t0) cc_final: 0.8389 (t0) REVERT: S 143 LYS cc_start: 0.9240 (mtmm) cc_final: 0.8784 (mtmm) REVERT: T 12 TYR cc_start: 0.8813 (t80) cc_final: 0.8596 (t80) REVERT: T 29 GLN cc_start: 0.8944 (tt0) cc_final: 0.8669 (tt0) REVERT: T 53 HIS cc_start: 0.8975 (t-90) cc_final: 0.8661 (t-90) REVERT: T 63 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8114 (ttm110) REVERT: T 68 ARG cc_start: 0.9244 (ttp-170) cc_final: 0.8381 (ttp-170) REVERT: T 74 ASN cc_start: 0.9186 (m-40) cc_final: 0.8903 (m-40) REVERT: T 86 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8940 (ptmm) REVERT: T 104 MET cc_start: 0.9059 (tpp) cc_final: 0.8688 (tpp) REVERT: T 132 PHE cc_start: 0.9069 (t80) cc_final: 0.8807 (t80) REVERT: T 135 THR cc_start: 0.9265 (t) cc_final: 0.8945 (p) REVERT: T 136 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.7989 (p-80) REVERT: T 148 MET cc_start: 0.9466 (mtt) cc_final: 0.8511 (mtp) REVERT: U 29 GLN cc_start: 0.9141 (tp40) cc_final: 0.8872 (tp40) REVERT: U 42 ASP cc_start: 0.9121 (t0) cc_final: 0.8538 (t0) REVERT: U 44 ASP cc_start: 0.8329 (p0) cc_final: 0.8083 (p0) REVERT: U 64 GLU cc_start: 0.8446 (tp30) cc_final: 0.8081 (tm-30) REVERT: U 100 MET cc_start: 0.9073 (mmm) cc_final: 0.8499 (mmt) REVERT: U 156 HIS cc_start: 0.8939 (m90) cc_final: 0.8422 (m90) REVERT: V 9 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8149 (mmm160) REVERT: V 34 TYR cc_start: 0.9514 (m-10) cc_final: 0.9293 (m-10) REVERT: V 49 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8907 (tm-30) REVERT: V 53 HIS cc_start: 0.8709 (t70) cc_final: 0.8026 (t-90) REVERT: V 57 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8420 (mm-30) REVERT: V 61 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8854 (mm-30) REVERT: V 64 GLU cc_start: 0.9211 (tt0) cc_final: 0.8741 (pt0) REVERT: V 67 GLU cc_start: 0.9302 (tm-30) cc_final: 0.9009 (tm-30) REVERT: V 68 ARG cc_start: 0.9055 (ptm160) cc_final: 0.8794 (ptm160) REVERT: V 74 ASN cc_start: 0.9272 (m-40) cc_final: 0.8774 (t0) REVERT: V 84 ASP cc_start: 0.9002 (m-30) cc_final: 0.8678 (t0) REVERT: V 171 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8735 (tm-30) REVERT: V 172 ARG cc_start: 0.9046 (mmp80) cc_final: 0.8711 (mmp80) REVERT: W 15 ASP cc_start: 0.9078 (t0) cc_final: 0.8819 (t0) REVERT: W 29 GLN cc_start: 0.8969 (tp40) cc_final: 0.8407 (mm110) REVERT: W 42 ASP cc_start: 0.9245 (t0) cc_final: 0.8745 (t0) REVERT: W 58 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9328 (tp) REVERT: W 61 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8755 (tm-30) REVERT: W 68 ARG cc_start: 0.8821 (mtp180) cc_final: 0.8310 (mtp180) REVERT: W 124 ARG cc_start: 0.9060 (mmt90) cc_final: 0.8811 (mmt90) REVERT: W 126 ASP cc_start: 0.9398 (t0) cc_final: 0.8689 (t70) REVERT: W 136 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.7838 (p-80) REVERT: W 143 LYS cc_start: 0.9352 (mtmm) cc_final: 0.8978 (mtmm) REVERT: X 12 TYR cc_start: 0.9326 (t80) cc_final: 0.8694 (t80) REVERT: X 53 HIS cc_start: 0.9005 (t-90) cc_final: 0.8718 (t70) REVERT: X 57 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8487 (mm-30) REVERT: X 74 ASN cc_start: 0.9272 (m-40) cc_final: 0.8823 (m-40) REVERT: X 126 ASP cc_start: 0.8854 (t0) cc_final: 0.8547 (t70) outliers start: 143 outliers final: 102 residues processed: 1126 average time/residue: 0.5672 time to fit residues: 1000.9573 Evaluate side-chains 1127 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1006 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 162 GLU Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain V residue 136 HIS Chi-restraints excluded: chain V residue 145 ILE Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain W residue 171 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 11 ASN Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 378 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 399 optimal weight: 0.0970 chunk 295 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN I 29 GLN J 111 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 ASN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN V 53 HIS W 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053546 restraints weight = 119949.510| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.22 r_work: 0.2847 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33816 Z= 0.223 Angle : 0.791 14.080 45480 Z= 0.405 Chirality : 0.045 0.246 4872 Planarity : 0.005 0.068 5952 Dihedral : 5.452 51.962 4568 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 3.56 % Allowed : 27.59 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.13), residues: 4080 helix: 1.61 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -2.27 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 93 HIS 0.008 0.001 HIS C 128 PHE 0.041 0.003 PHE O 170 TYR 0.055 0.003 TYR X 40 ARG 0.014 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 2679) hydrogen bonds : angle 4.48429 ( 8037) covalent geometry : bond 0.00498 (33816) covalent geometry : angle 0.79054 (45480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1055 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8682 (t80) cc_final: 0.8394 (t80) REVERT: A 29 GLN cc_start: 0.9137 (tp40) cc_final: 0.8806 (tp40) REVERT: A 42 ASP cc_start: 0.9319 (t0) cc_final: 0.8841 (t0) REVERT: A 52 SER cc_start: 0.9407 (t) cc_final: 0.9166 (m) REVERT: A 67 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8760 (mt-10) REVERT: A 68 ARG cc_start: 0.8167 (ptp-170) cc_final: 0.7571 (ptm160) REVERT: A 74 ASN cc_start: 0.9327 (m-40) cc_final: 0.8877 (m-40) REVERT: A 107 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8511 (mm-30) REVERT: A 124 ARG cc_start: 0.9357 (mmt-90) cc_final: 0.9034 (mmp80) REVERT: A 141 GLU cc_start: 0.8914 (tp30) cc_final: 0.8675 (tp30) REVERT: A 167 GLU cc_start: 0.9164 (tt0) cc_final: 0.8642 (tt0) REVERT: A 171 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9126 (tm-30) REVERT: B 12 TYR cc_start: 0.9071 (t80) cc_final: 0.8801 (t80) REVERT: B 56 ARG cc_start: 0.9183 (tpp80) cc_final: 0.8866 (tpp80) REVERT: B 72 MET cc_start: 0.9722 (tmm) cc_final: 0.9308 (tmm) REVERT: B 98 ASP cc_start: 0.9525 (t0) cc_final: 0.9218 (m-30) REVERT: B 124 ARG cc_start: 0.9078 (mtp85) cc_final: 0.8752 (mtp85) REVERT: B 126 ASP cc_start: 0.8709 (t0) cc_final: 0.8429 (t0) REVERT: B 131 ASP cc_start: 0.9060 (t70) cc_final: 0.8854 (t0) REVERT: C 12 TYR cc_start: 0.8667 (t80) cc_final: 0.8420 (t80) REVERT: C 42 ASP cc_start: 0.9314 (t70) cc_final: 0.8992 (t70) REVERT: C 58 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9376 (tp) REVERT: C 108 LYS cc_start: 0.8886 (mttt) cc_final: 0.8679 (mmtp) REVERT: C 126 ASP cc_start: 0.9190 (t0) cc_final: 0.8595 (t0) REVERT: C 129 LEU cc_start: 0.9805 (tp) cc_final: 0.9579 (tp) REVERT: C 131 ASP cc_start: 0.9340 (t0) cc_final: 0.8829 (t0) REVERT: C 176 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7905 (ttmm) REVERT: D 7 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: D 14 THR cc_start: 0.9465 (p) cc_final: 0.9259 (t) REVERT: D 63 ARG cc_start: 0.8983 (mmm-85) cc_final: 0.8377 (ttp80) REVERT: D 66 TYR cc_start: 0.9539 (p90) cc_final: 0.9236 (p90) REVERT: D 74 ASN cc_start: 0.9193 (m110) cc_final: 0.8772 (m-40) REVERT: D 112 GLN cc_start: 0.9276 (tp40) cc_final: 0.8552 (tp40) REVERT: D 116 ASP cc_start: 0.9282 (m-30) cc_final: 0.8670 (m-30) REVERT: D 143 LYS cc_start: 0.9460 (mtmm) cc_final: 0.9178 (mtmm) REVERT: D 167 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8406 (mp0) REVERT: D 171 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8968 (tm-30) REVERT: E 12 TYR cc_start: 0.9103 (t80) cc_final: 0.8601 (t80) REVERT: E 26 LEU cc_start: 0.9507 (tp) cc_final: 0.9246 (tp) REVERT: E 44 ASP cc_start: 0.9305 (p0) cc_final: 0.9087 (p0) REVERT: E 48 LEU cc_start: 0.9382 (mt) cc_final: 0.8982 (mt) REVERT: E 49 GLU cc_start: 0.8888 (pp20) cc_final: 0.8659 (pp20) REVERT: E 52 SER cc_start: 0.9305 (t) cc_final: 0.9040 (m) REVERT: E 68 ARG cc_start: 0.9021 (ptp-110) cc_final: 0.8815 (ptp-170) REVERT: E 112 GLN cc_start: 0.9232 (tp40) cc_final: 0.8669 (tp40) REVERT: E 116 ASP cc_start: 0.8957 (m-30) cc_final: 0.8563 (m-30) REVERT: E 168 TYR cc_start: 0.9146 (t80) cc_final: 0.8809 (t80) REVERT: E 171 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: F 12 TYR cc_start: 0.8745 (t80) cc_final: 0.8174 (t80) REVERT: F 31 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9223 (m) REVERT: F 44 ASP cc_start: 0.8340 (p0) cc_final: 0.8102 (p0) REVERT: F 52 SER cc_start: 0.9472 (t) cc_final: 0.9058 (m) REVERT: F 67 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8434 (mt-10) REVERT: F 79 ARG cc_start: 0.9097 (mmp80) cc_final: 0.8507 (mmp80) REVERT: F 112 GLN cc_start: 0.9190 (tp40) cc_final: 0.8373 (tp-100) REVERT: F 153 THR cc_start: 0.9023 (m) cc_final: 0.8746 (p) REVERT: G 53 HIS cc_start: 0.8751 (t-90) cc_final: 0.8128 (t-90) REVERT: G 60 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8433 (tm-30) REVERT: G 64 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8429 (mt-10) REVERT: G 73 GLN cc_start: 0.9101 (tp40) cc_final: 0.8759 (tm-30) REVERT: G 75 GLN cc_start: 0.9373 (mp-120) cc_final: 0.9123 (mm-40) REVERT: G 84 ASP cc_start: 0.8725 (m-30) cc_final: 0.8495 (t0) REVERT: G 104 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8678 (ttm) REVERT: G 107 GLU cc_start: 0.9057 (tp30) cc_final: 0.8493 (tp30) REVERT: G 124 ARG cc_start: 0.9299 (mmp80) cc_final: 0.8994 (mmp80) REVERT: H 42 ASP cc_start: 0.9301 (t70) cc_final: 0.8892 (t0) REVERT: H 57 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8644 (mt-10) REVERT: H 63 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8710 (ttp80) REVERT: H 112 GLN cc_start: 0.9169 (tp40) cc_final: 0.8807 (tp-100) REVERT: H 172 ARG cc_start: 0.9005 (mmm160) cc_final: 0.8738 (mmm160) REVERT: I 29 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8941 (tp40) REVERT: I 42 ASP cc_start: 0.9386 (t70) cc_final: 0.9114 (t0) REVERT: I 52 SER cc_start: 0.9323 (t) cc_final: 0.9017 (m) REVERT: I 61 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8973 (mm-30) REVERT: I 98 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.9055 (t0) REVERT: I 100 MET cc_start: 0.9428 (tpp) cc_final: 0.8906 (tpp) REVERT: I 112 GLN cc_start: 0.9394 (tp40) cc_final: 0.8905 (tp-100) REVERT: J 73 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8538 (tm-30) REVERT: J 124 ARG cc_start: 0.9251 (mmt-90) cc_final: 0.9032 (mmt-90) REVERT: J 126 ASP cc_start: 0.9239 (t0) cc_final: 0.8696 (t0) REVERT: J 153 THR cc_start: 0.9153 (m) cc_final: 0.8918 (p) REVERT: K 7 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: K 42 ASP cc_start: 0.9487 (t70) cc_final: 0.8889 (t70) REVERT: K 45 ASP cc_start: 0.8894 (m-30) cc_final: 0.8483 (m-30) REVERT: K 56 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8443 (ttm-80) REVERT: K 66 TYR cc_start: 0.9385 (p90) cc_final: 0.9148 (p90) REVERT: K 72 MET cc_start: 0.9618 (ppp) cc_final: 0.9386 (ppp) REVERT: K 74 ASN cc_start: 0.9389 (m-40) cc_final: 0.8963 (m-40) REVERT: K 75 GLN cc_start: 0.9004 (mm110) cc_final: 0.8745 (mm110) REVERT: K 83 GLN cc_start: 0.9020 (mm110) cc_final: 0.8753 (mm110) REVERT: K 104 MET cc_start: 0.9086 (mmm) cc_final: 0.8664 (tpp) REVERT: K 143 LYS cc_start: 0.9380 (mtmm) cc_final: 0.9093 (mtmm) REVERT: L 29 GLN cc_start: 0.9464 (tt0) cc_final: 0.8984 (tm-30) REVERT: L 49 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8621 (tm-30) REVERT: L 52 SER cc_start: 0.9542 (t) cc_final: 0.9164 (p) REVERT: L 53 HIS cc_start: 0.9161 (t-90) cc_final: 0.8639 (t-90) REVERT: L 60 GLU cc_start: 0.9405 (tt0) cc_final: 0.9139 (tm-30) REVERT: L 61 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9117 (mm-30) REVERT: L 64 GLU cc_start: 0.9471 (mt-10) cc_final: 0.8856 (tm-30) REVERT: L 67 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8935 (tm-30) REVERT: L 68 ARG cc_start: 0.9073 (ttp-170) cc_final: 0.8784 (ttm-80) REVERT: L 72 MET cc_start: 0.9695 (ppp) cc_final: 0.9426 (ppp) REVERT: L 74 ASN cc_start: 0.9429 (m-40) cc_final: 0.9082 (m-40) REVERT: L 112 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8791 (tp40) REVERT: L 124 ARG cc_start: 0.9380 (mmt-90) cc_final: 0.9022 (mmp80) REVERT: L 126 ASP cc_start: 0.8980 (t0) cc_final: 0.8691 (t70) REVERT: L 143 LYS cc_start: 0.9483 (mtpt) cc_final: 0.9071 (mtmm) REVERT: L 172 ARG cc_start: 0.9367 (mmp-170) cc_final: 0.9084 (mmp80) REVERT: M 11 ASN cc_start: 0.8581 (t0) cc_final: 0.8189 (t0) REVERT: M 52 SER cc_start: 0.9354 (t) cc_final: 0.9061 (m) REVERT: M 53 HIS cc_start: 0.8621 (t-90) cc_final: 0.7436 (t-90) REVERT: M 56 ARG cc_start: 0.9248 (tpp80) cc_final: 0.8794 (ttm-80) REVERT: M 57 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8405 (mm-30) REVERT: M 60 GLU cc_start: 0.9360 (tp30) cc_final: 0.8805 (tp30) REVERT: M 63 ARG cc_start: 0.9283 (mtp-110) cc_final: 0.8811 (ttp80) REVERT: M 68 ARG cc_start: 0.9064 (ttm170) cc_final: 0.8646 (ttp80) REVERT: N 42 ASP cc_start: 0.9093 (t70) cc_final: 0.8187 (t70) REVERT: N 53 HIS cc_start: 0.9086 (t-170) cc_final: 0.8332 (t70) REVERT: N 57 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8671 (mm-30) REVERT: N 64 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: N 74 ASN cc_start: 0.9002 (m-40) cc_final: 0.8431 (m-40) REVERT: N 75 GLN cc_start: 0.9232 (mm-40) cc_final: 0.9005 (mm-40) REVERT: N 112 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8146 (tp40) REVERT: N 140 GLU cc_start: 0.8823 (mp0) cc_final: 0.8548 (mp0) REVERT: O 15 ASP cc_start: 0.9277 (p0) cc_final: 0.8866 (p0) REVERT: O 42 ASP cc_start: 0.9430 (t0) cc_final: 0.8930 (t70) REVERT: O 53 HIS cc_start: 0.8655 (t-90) cc_final: 0.7431 (t-90) REVERT: O 57 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8515 (mm-30) REVERT: O 60 GLU cc_start: 0.9245 (tp30) cc_final: 0.8861 (tp30) REVERT: O 64 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9029 (mm-30) REVERT: O 68 ARG cc_start: 0.9322 (ttm-80) cc_final: 0.9075 (ttm-80) REVERT: O 74 ASN cc_start: 0.9265 (m-40) cc_final: 0.8946 (t0) REVERT: O 104 MET cc_start: 0.9278 (ttt) cc_final: 0.8836 (tpp) REVERT: O 124 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8843 (mmm-85) REVERT: O 126 ASP cc_start: 0.8938 (t0) cc_final: 0.8665 (t0) REVERT: O 148 MET cc_start: 0.9186 (ttm) cc_final: 0.8630 (ttm) REVERT: O 172 ARG cc_start: 0.9465 (mmp-170) cc_final: 0.9146 (mmp80) REVERT: P 53 HIS cc_start: 0.9175 (t-170) cc_final: 0.8639 (t-90) REVERT: P 57 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8632 (mt-10) REVERT: P 64 GLU cc_start: 0.9533 (tp30) cc_final: 0.8958 (tm-30) REVERT: P 104 MET cc_start: 0.9464 (ttp) cc_final: 0.8914 (ttm) REVERT: P 143 LYS cc_start: 0.9612 (OUTLIER) cc_final: 0.9328 (mtmm) REVERT: P 148 MET cc_start: 0.9291 (mtt) cc_final: 0.9063 (mtp) REVERT: Q 29 GLN cc_start: 0.8906 (tp40) cc_final: 0.8679 (tp40) REVERT: Q 53 HIS cc_start: 0.9079 (t-170) cc_final: 0.8237 (t-90) REVERT: Q 57 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8960 (mm-30) REVERT: Q 61 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8660 (tm-30) REVERT: Q 67 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8818 (mt-10) REVERT: Q 68 ARG cc_start: 0.9042 (ttm170) cc_final: 0.8675 (ttm110) REVERT: Q 104 MET cc_start: 0.9225 (mmm) cc_final: 0.8839 (tpp) REVERT: Q 107 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8279 (mm-30) REVERT: Q 112 GLN cc_start: 0.9183 (tp40) cc_final: 0.8879 (tp40) REVERT: Q 141 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8748 (tp30) REVERT: Q 148 MET cc_start: 0.9292 (ttp) cc_final: 0.9057 (ttt) REVERT: Q 171 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8724 (tm-30) REVERT: Q 172 ARG cc_start: 0.9269 (mmp80) cc_final: 0.8936 (mmp80) REVERT: R 12 TYR cc_start: 0.9007 (t80) cc_final: 0.8778 (t80) REVERT: R 49 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8769 (tm-30) REVERT: R 53 HIS cc_start: 0.9112 (m-70) cc_final: 0.8782 (m90) REVERT: R 67 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8687 (pp20) REVERT: R 68 ARG cc_start: 0.9214 (mtm-85) cc_final: 0.8819 (mtm-85) REVERT: R 126 ASP cc_start: 0.9188 (t0) cc_final: 0.8685 (t0) REVERT: S 42 ASP cc_start: 0.9497 (t0) cc_final: 0.8687 (t0) REVERT: S 52 SER cc_start: 0.9626 (t) cc_final: 0.9337 (t) REVERT: S 68 ARG cc_start: 0.9174 (ptp-110) cc_final: 0.8839 (ptp-170) REVERT: S 72 MET cc_start: 0.9631 (tmm) cc_final: 0.9403 (tmm) REVERT: S 126 ASP cc_start: 0.8943 (t0) cc_final: 0.8409 (t0) REVERT: S 140 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8854 (mm-30) REVERT: S 142 VAL cc_start: 0.9301 (t) cc_final: 0.9015 (p) REVERT: S 143 LYS cc_start: 0.9311 (mtmm) cc_final: 0.8884 (mtmm) REVERT: T 12 TYR cc_start: 0.8849 (t80) cc_final: 0.8580 (t80) REVERT: T 29 GLN cc_start: 0.9030 (tt0) cc_final: 0.8729 (tt0) REVERT: T 53 HIS cc_start: 0.8899 (t-90) cc_final: 0.8472 (t-90) REVERT: T 63 ARG cc_start: 0.8763 (ttm110) cc_final: 0.8011 (ttm110) REVERT: T 64 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8879 (mm-30) REVERT: T 68 ARG cc_start: 0.9407 (ttp-170) cc_final: 0.8369 (ttp-170) REVERT: T 74 ASN cc_start: 0.9200 (m-40) cc_final: 0.8939 (m-40) REVERT: T 86 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8925 (ptmm) REVERT: T 104 MET cc_start: 0.9044 (tpp) cc_final: 0.8778 (tpp) REVERT: T 126 ASP cc_start: 0.9003 (t0) cc_final: 0.8684 (t70) REVERT: T 132 PHE cc_start: 0.9106 (t80) cc_final: 0.8768 (t80) REVERT: T 135 THR cc_start: 0.9228 (t) cc_final: 0.8899 (p) REVERT: T 136 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.7966 (p-80) REVERT: T 148 MET cc_start: 0.9427 (mtt) cc_final: 0.8831 (mtt) REVERT: U 29 GLN cc_start: 0.9146 (tp40) cc_final: 0.8865 (tp40) REVERT: U 42 ASP cc_start: 0.9146 (t0) cc_final: 0.8564 (t0) REVERT: U 44 ASP cc_start: 0.8277 (p0) cc_final: 0.8022 (p0) REVERT: U 63 ARG cc_start: 0.9453 (mtp-110) cc_final: 0.8388 (mtp-110) REVERT: U 64 GLU cc_start: 0.8454 (tp30) cc_final: 0.8081 (tm-30) REVERT: U 112 GLN cc_start: 0.9373 (tp40) cc_final: 0.9032 (tp40) REVERT: U 136 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.7736 (p-80) REVERT: U 156 HIS cc_start: 0.8947 (m90) cc_final: 0.8433 (m90) REVERT: V 9 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8145 (mmm160) REVERT: V 49 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8906 (tm-30) REVERT: V 57 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8379 (mm-30) REVERT: V 61 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8915 (mm-30) REVERT: V 63 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8928 (ttm110) REVERT: V 64 GLU cc_start: 0.9189 (tt0) cc_final: 0.8869 (pt0) REVERT: V 74 ASN cc_start: 0.9243 (m-40) cc_final: 0.8778 (t0) REVERT: V 84 ASP cc_start: 0.8888 (m-30) cc_final: 0.8683 (t0) REVERT: V 126 ASP cc_start: 0.8891 (t0) cc_final: 0.8554 (t0) REVERT: V 171 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8757 (tm-30) REVERT: V 172 ARG cc_start: 0.9026 (mmp80) cc_final: 0.8680 (mmp80) REVERT: W 15 ASP cc_start: 0.9108 (t0) cc_final: 0.8839 (t0) REVERT: W 29 GLN cc_start: 0.8946 (tp40) cc_final: 0.8383 (mm110) REVERT: W 42 ASP cc_start: 0.9251 (t0) cc_final: 0.8739 (t0) REVERT: W 58 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9333 (tp) REVERT: W 61 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8761 (tm-30) REVERT: W 68 ARG cc_start: 0.8846 (mtp180) cc_final: 0.8337 (mtp180) REVERT: W 124 ARG cc_start: 0.9115 (mmt90) cc_final: 0.8895 (mmt90) REVERT: W 126 ASP cc_start: 0.9439 (t0) cc_final: 0.8707 (t70) REVERT: W 136 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.7721 (p-80) REVERT: X 12 TYR cc_start: 0.9314 (t80) cc_final: 0.8660 (t80) REVERT: X 53 HIS cc_start: 0.9008 (t-90) cc_final: 0.8725 (t70) REVERT: X 63 ARG cc_start: 0.9327 (ttp80) cc_final: 0.9103 (ttp80) REVERT: X 74 ASN cc_start: 0.9269 (m-40) cc_final: 0.8837 (m-40) REVERT: X 93 TRP cc_start: 0.9201 (m100) cc_final: 0.8924 (m100) REVERT: X 126 ASP cc_start: 0.8837 (t0) cc_final: 0.8554 (t70) REVERT: X 172 ARG cc_start: 0.9247 (tpp-160) cc_final: 0.8851 (tpp80) outliers start: 124 outliers final: 95 residues processed: 1131 average time/residue: 0.6505 time to fit residues: 1149.3980 Evaluate side-chains 1112 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 999 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 73 GLN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 27 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 136 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 136 HIS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 141 GLU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 136 HIS Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain V residue 145 ILE Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 136 HIS Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 11 ASN Chi-restraints excluded: chain X residue 16 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 131 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 345 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 338 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 294 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN I 29 GLN J 111 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 GLN ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN O 111 ASN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 ASN ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 HIS ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN V 83 GLN W 75 GLN X 156 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053723 restraints weight = 120165.454| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.22 r_work: 0.2848 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33816 Z= 0.224 Angle : 0.800 13.840 45480 Z= 0.410 Chirality : 0.045 0.274 4872 Planarity : 0.005 0.068 5952 Dihedral : 5.360 51.717 4558 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 3.62 % Allowed : 28.28 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 4080 helix: 1.57 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -2.28 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 93 HIS 0.010 0.001 HIS C 151 PHE 0.041 0.002 PHE L 132 TYR 0.048 0.003 TYR X 40 ARG 0.015 0.001 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 2679) hydrogen bonds : angle 4.52453 ( 8037) covalent geometry : bond 0.00502 (33816) covalent geometry : angle 0.79999 (45480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21221.65 seconds wall clock time: 372 minutes 22.03 seconds (22342.03 seconds total)