Starting phenix.real_space_refine on Tue Aug 26 00:40:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bq5_44797/08_2025/9bq5_44797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bq5_44797/08_2025/9bq5_44797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bq5_44797/08_2025/9bq5_44797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bq5_44797/08_2025/9bq5_44797.map" model { file = "/net/cci-nas-00/data/ceres_data/9bq5_44797/08_2025/9bq5_44797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bq5_44797/08_2025/9bq5_44797.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.034 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 6334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 240 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33214 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: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "F" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "H" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "J" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "L" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "N" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "P" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "R" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "T" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "V" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "X" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Time building chain proxies: 7.60, per 1000 atoms: 0.23 Number of scatterers: 33214 At special positions: 0 Unit cell: (134.93, 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 6334 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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 78.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 13 through 43 Processing helix chain 'A' and resid 48 through 76 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 41 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 162 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 158 Processing helix chain 'C' and resid 159 through 162 removed outlier: 4.260A pdb=" N GLU C 162 " --> pdb=" O GLY C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'D' and resid 13 through 43 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 162 through 174 Processing helix chain 'E' and resid 13 through 41 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 158 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'F' and resid 13 through 43 removed outlier: 3.539A pdb=" N ASP F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 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 158 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 162 through 174 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 163 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 162 through 174 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 162 through 174 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 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 158 Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'M' and resid 13 through 43 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 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 158 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 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 158 Processing helix chain 'O' and resid 162 through 174 removed outlier: 3.673A pdb=" N GLY O 166 " --> pdb=" O GLU O 162 " (cutoff:3.500A) 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 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 158 Processing helix chain 'P' and resid 162 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 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 158 Processing helix chain 'R' and resid 162 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 41 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 158 Processing helix chain 'T' and resid 162 through 174 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 158 Processing helix chain 'U' and resid 162 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 163 through 174 Processing helix chain 'W' and resid 13 through 41 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 175 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 158 Processing helix chain 'X' and resid 163 through 175 2675 hydrogen bonds defined for protein. 8025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.40 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9504 1.33 - 1.45: 6316 1.45 - 1.58: 17802 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 33838 Sorted by residual: bond pdb=" CZ ARG J 157 " pdb=" NH2 ARG J 157 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" CZ ARG L 157 " pdb=" NH2 ARG L 157 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG E 157 " pdb=" NH2 ARG E 157 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" CZ ARG A 157 " pdb=" NH2 ARG A 157 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.11e+01 bond pdb=" CZ ARG H 157 " pdb=" NH2 ARG H 157 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.07e+01 ... (remaining 33833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 37354 2.37 - 4.75: 7664 4.75 - 7.12: 493 7.12 - 9.49: 11 9.49 - 11.87: 2 Bond angle restraints: 45524 Sorted by residual: angle pdb=" CA PHE W 170 " pdb=" CB PHE W 170 " pdb=" CG PHE W 170 " ideal model delta sigma weight residual 113.80 108.27 5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASP C 84 " pdb=" CB ASP C 84 " pdb=" CG ASP C 84 " ideal model delta sigma weight residual 112.60 118.05 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" CA PHE E 170 " pdb=" CB PHE E 170 " pdb=" CG PHE E 170 " ideal model delta sigma weight residual 113.80 108.44 5.36 1.00e+00 1.00e+00 2.88e+01 angle pdb=" CA PHE L 170 " pdb=" CB PHE L 170 " pdb=" CG PHE L 170 " ideal model delta sigma weight residual 113.80 108.44 5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" CB HIS I 151 " pdb=" CG HIS I 151 " pdb=" CD2 HIS I 151 " ideal model delta sigma weight residual 131.20 124.38 6.82 1.30e+00 5.92e-01 2.75e+01 ... (remaining 45519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 18425 17.95 - 35.89: 1482 35.89 - 53.84: 391 53.84 - 71.78: 119 71.78 - 89.72: 29 Dihedral angle restraints: 20446 sinusoidal: 8494 harmonic: 11952 Sorted by residual: dihedral pdb=" C LYS M 176 " pdb=" N LYS M 176 " pdb=" CA LYS M 176 " pdb=" CB LYS M 176 " ideal model delta harmonic sigma weight residual -122.60 -138.00 15.40 0 2.50e+00 1.60e-01 3.80e+01 dihedral pdb=" C LYS I 176 " pdb=" N LYS I 176 " pdb=" CA LYS I 176 " pdb=" CB LYS I 176 " ideal model delta harmonic sigma weight residual -122.60 -136.58 13.98 0 2.50e+00 1.60e-01 3.13e+01 dihedral pdb=" C LEU G 144 " pdb=" N LEU G 144 " pdb=" CA LEU G 144 " pdb=" CB LEU G 144 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 20443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3666 0.111 - 0.222: 1085 0.222 - 0.333: 103 0.333 - 0.444: 9 0.444 - 0.555: 9 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA LEU G 144 " pdb=" N LEU G 144 " pdb=" C LEU G 144 " pdb=" CB LEU G 144 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA LYS M 176 " pdb=" N LYS M 176 " pdb=" C LYS M 176 " pdb=" CB LYS M 176 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" CA LEU P 144 " pdb=" N LEU P 144 " pdb=" C LEU P 144 " pdb=" CB LEU P 144 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.38e+00 ... (remaining 4869 not shown) Planarity restraints: 5974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 34 " -0.137 2.00e-02 2.50e+03 7.79e-02 1.21e+02 pdb=" CG TYR C 34 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR C 34 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 TYR C 34 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR C 34 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR C 34 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR C 34 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 34 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 34 " 0.135 2.00e-02 2.50e+03 7.78e-02 1.21e+02 pdb=" CG TYR U 34 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR U 34 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR U 34 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR U 34 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR U 34 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR U 34 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR U 34 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 34 " -0.134 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR T 34 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR T 34 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR T 34 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR T 34 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR T 34 " 0.051 2.00e-02 2.50e+03 pdb=" CZ TYR T 34 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR T 34 " -0.122 2.00e-02 2.50e+03 ... (remaining 5971 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 16050 2.98 - 3.46: 40266 3.46 - 3.94: 66506 3.94 - 4.42: 74855 4.42 - 4.90: 119829 Nonbonded interactions: 317506 Sorted by model distance: nonbonded pdb=" OH TYR I 34 " pdb=" OE1 GLU I 107 " model vdw 2.503 3.040 nonbonded pdb=" OH TYR K 27 " pdb=" OE2 GLU K 141 " model vdw 2.528 3.040 nonbonded pdb=" OH TYR E 27 " pdb=" OE2 GLU E 141 " model vdw 2.531 3.040 nonbonded pdb=" OH TYR P 27 " pdb=" OE2 GLU P 141 " model vdw 2.532 3.040 nonbonded pdb=" OH TYR W 27 " pdb=" OE2 GLU W 141 " model vdw 2.533 3.040 ... (remaining 317501 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'D' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'E' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'F' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'G' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'H' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'I' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'J' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'K' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'L' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'M' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'N' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'O' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'P' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'Q' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'R' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'S' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'T' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'U' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'V' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'W' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'X' and (resid 5 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )))) } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.740 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 0.047 33838 Z= 0.720 Angle : 1.791 11.865 45524 Z= 1.208 Chirality : 0.096 0.555 4872 Planarity : 0.017 0.147 5974 Dihedral : 15.466 89.725 12766 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.08 % Favored : 97.60 % Rotamer: Outliers : 3.62 % Allowed : 4.57 % Favored : 91.81 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.12), residues: 4080 helix: 0.49 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : -1.57 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG E 172 TYR 0.137 0.027 TYR C 34 PHE 0.103 0.024 PHE K 41 TRP 0.046 0.018 TRP U 93 HIS 0.014 0.003 HIS Q 151 Details of bonding type rmsd covalent geometry : bond 0.01134 (33838) covalent geometry : angle 1.79098 (45524) hydrogen bonds : bond 0.09853 ( 2675) hydrogen bonds : angle 5.47530 ( 8025) *********************** 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 1823 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1697 time to evaluate : 1.334 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: C 146 LYS cc_start: 0.7731 (tptp) cc_final: 0.7502 (tptp) REVERT: D 53 HIS cc_start: 0.6691 (t-90) cc_final: 0.6382 (t-90) REVERT: D 104 MET cc_start: 0.6669 (mmm) cc_final: 0.6467 (mmm) REVERT: E 136 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7329 (OUTLIER) REVERT: E 176 LYS cc_start: 0.4505 (OUTLIER) cc_final: 0.4180 (tppt) REVERT: P 53 HIS cc_start: 0.6715 (t-90) cc_final: 0.6268 (t-90) REVERT: P 146 LYS cc_start: 0.7734 (tptp) cc_final: 0.7487 (tptp) REVERT: Q 146 LYS cc_start: 0.7776 (tptp) cc_final: 0.7532 (tptp) REVERT: R 62 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7440 (mmtm) REVERT: T 146 LYS cc_start: 0.7710 (tptp) cc_final: 0.7509 (tptp) REVERT: U 150 ASP cc_start: 0.6236 (m-30) cc_final: 0.6032 (m-30) REVERT: W 148 MET cc_start: 0.6904 (mtt) cc_final: 0.6644 (mtt) REVERT: X 107 GLU cc_start: 0.6049 (tp30) cc_final: 0.5716 (tp30) outliers start: 126 outliers final: 41 residues processed: 1725 average time/residue: 0.8848 time to fit residues: 1745.6485 Evaluate side-chains 1339 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 1296 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 15 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 15 ASP Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 15 ASP Chi-restraints excluded: chain V residue 107 GLU Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 29 GLN A 156 HIS B 7 GLN B 29 GLN C 7 GLN C 29 GLN C 156 HIS D 11 ASN D 29 GLN E 29 GLN F 7 GLN F 11 ASN F 156 HIS G 7 GLN G 29 GLN G 136 HIS G 156 HIS H 7 GLN H 156 HIS I 7 GLN I 156 HIS J 7 GLN J 29 GLN J 156 HIS K 7 GLN K 29 GLN L 7 GLN L 156 HIS M 29 GLN M 156 HIS N 7 GLN N 29 GLN O 156 HIS P 7 GLN P 29 GLN P 156 HIS Q 7 GLN Q 29 GLN Q 156 HIS R 7 GLN R 11 ASN R 29 GLN ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 GLN S 11 ASN S 29 GLN S 136 HIS S 156 HIS T 7 GLN T 29 GLN T 136 HIS U 7 GLN U 11 ASN U 29 GLN U 74 ASN U 156 HIS V 7 GLN V 11 ASN V 29 GLN W 7 GLN W 29 GLN W 156 HIS X 7 GLN X 29 GLN X 156 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080248 restraints weight = 58129.419| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.68 r_work: 0.2928 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33838 Z= 0.149 Angle : 0.625 11.609 45524 Z= 0.325 Chirality : 0.038 0.155 4872 Planarity : 0.004 0.037 5974 Dihedral : 7.615 87.860 4658 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.42 % Favored : 98.41 % Rotamer: Outliers : 3.76 % Allowed : 17.70 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.13), residues: 4080 helix: 2.18 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 56 TYR 0.030 0.002 TYR L 66 PHE 0.017 0.003 PHE T 132 TRP 0.009 0.002 TRP A 93 HIS 0.007 0.001 HIS M 128 Details of bonding type rmsd covalent geometry : bond 0.00330 (33838) covalent geometry : angle 0.62469 (45524) hydrogen bonds : bond 0.04235 ( 2675) hydrogen bonds : angle 3.81434 ( 8025) *********************** 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 1585 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1454 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8665 (tt0) cc_final: 0.8291 (tt0) REVERT: A 17 GLU cc_start: 0.8367 (tt0) cc_final: 0.8154 (tt0) REVERT: A 42 ASP cc_start: 0.8439 (t70) cc_final: 0.7861 (t70) REVERT: A 60 GLU cc_start: 0.8454 (tp30) cc_final: 0.8036 (tp30) REVERT: A 61 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 62 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8580 (mmtm) REVERT: A 64 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8187 (mm-30) REVERT: A 86 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8420 (mmmm) REVERT: A 107 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8456 (mm-30) REVERT: A 108 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8331 (mmmm) REVERT: A 141 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8331 (tp30) REVERT: A 144 LEU cc_start: 0.9025 (tp) cc_final: 0.8752 (tm) REVERT: A 147 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8178 (ttpp) REVERT: A 150 ASP cc_start: 0.8581 (m-30) cc_final: 0.8133 (m-30) REVERT: B 45 ASP cc_start: 0.8666 (p0) cc_final: 0.8071 (p0) REVERT: B 57 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 60 GLU cc_start: 0.8322 (tp30) cc_final: 0.8076 (mm-30) REVERT: B 61 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8301 (mm-30) REVERT: B 64 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7831 (mt-10) REVERT: B 84 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7679 (t70) REVERT: B 104 MET cc_start: 0.8660 (ttp) cc_final: 0.8312 (ttp) REVERT: B 112 GLN cc_start: 0.8760 (tp40) cc_final: 0.8247 (tp40) REVERT: B 116 ASP cc_start: 0.8707 (m-30) cc_final: 0.8189 (m-30) REVERT: B 147 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8247 (ttpp) REVERT: B 150 ASP cc_start: 0.8559 (m-30) cc_final: 0.8168 (m-30) REVERT: C 7 GLN cc_start: 0.8665 (pt0) cc_final: 0.8447 (pt0) REVERT: C 10 GLN cc_start: 0.8637 (tt0) cc_final: 0.8383 (tt0) REVERT: C 17 GLU cc_start: 0.8373 (tt0) cc_final: 0.8085 (tt0) REVERT: C 42 ASP cc_start: 0.8370 (t70) cc_final: 0.7772 (t70) REVERT: C 57 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8016 (mm-30) REVERT: C 60 GLU cc_start: 0.8237 (tp30) cc_final: 0.7952 (tp30) REVERT: C 61 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8053 (mm-30) REVERT: C 62 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8410 (mmtm) REVERT: C 104 MET cc_start: 0.8567 (ttp) cc_final: 0.8244 (ttp) REVERT: C 107 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8365 (mm-30) REVERT: C 116 ASP cc_start: 0.8796 (m-30) cc_final: 0.8555 (m-30) REVERT: C 135 THR cc_start: 0.9315 (m) cc_final: 0.9105 (p) REVERT: C 141 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8177 (tp30) REVERT: D 15 ASP cc_start: 0.8564 (p0) cc_final: 0.8167 (p0) REVERT: D 17 GLU cc_start: 0.8370 (tt0) cc_final: 0.8137 (tt0) REVERT: D 53 HIS cc_start: 0.8200 (t-90) cc_final: 0.7677 (t70) REVERT: D 57 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8170 (mt-10) REVERT: D 60 GLU cc_start: 0.8273 (tp30) cc_final: 0.8006 (tp30) REVERT: D 63 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7678 (ttm-80) REVERT: D 64 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 68 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7970 (mtm-85) REVERT: D 84 ASP cc_start: 0.8784 (m-30) cc_final: 0.8342 (m-30) REVERT: D 86 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8379 (tppt) REVERT: D 108 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8467 (mmmm) REVERT: D 116 ASP cc_start: 0.8762 (m-30) cc_final: 0.8531 (m-30) REVERT: D 124 ARG cc_start: 0.8950 (mmt-90) cc_final: 0.8662 (mmt-90) REVERT: D 143 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8606 (mtmm) REVERT: D 147 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8170 (ttpp) REVERT: D 162 GLU cc_start: 0.7278 (pm20) cc_final: 0.7042 (pm20) REVERT: D 167 GLU cc_start: 0.8466 (tt0) cc_final: 0.8251 (tt0) REVERT: E 17 GLU cc_start: 0.8475 (tt0) cc_final: 0.8118 (tt0) REVERT: E 49 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7396 (pp20) REVERT: E 61 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 68 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7928 (ttm110) REVERT: E 71 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8552 (tttm) REVERT: E 92 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7564 (tm-30) REVERT: E 116 ASP cc_start: 0.8739 (m-30) cc_final: 0.8527 (m-30) REVERT: E 136 HIS cc_start: 0.8655 (OUTLIER) cc_final: 0.7417 (p-80) REVERT: E 147 LYS cc_start: 0.8539 (ttpp) cc_final: 0.8316 (ttpt) REVERT: E 150 ASP cc_start: 0.8493 (m-30) cc_final: 0.8183 (m-30) REVERT: E 157 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7913 (ptp90) REVERT: E 165 LEU cc_start: 0.9230 (tp) cc_final: 0.9003 (tp) REVERT: E 167 GLU cc_start: 0.8355 (tt0) cc_final: 0.8097 (tt0) REVERT: E 171 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7434 (tm-30) REVERT: E 176 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6512 (mmtp) REVERT: F 17 GLU cc_start: 0.8395 (tt0) cc_final: 0.8113 (tt0) REVERT: F 57 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7794 (mt-10) REVERT: F 60 GLU cc_start: 0.8241 (tp30) cc_final: 0.7762 (tp30) REVERT: F 61 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: F 63 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7400 (ttm-80) REVERT: F 64 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7814 (mt-10) REVERT: F 84 ASP cc_start: 0.8276 (m-30) cc_final: 0.8075 (m-30) REVERT: F 86 LYS cc_start: 0.8651 (ptpp) cc_final: 0.8338 (mmmm) REVERT: F 87 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8261 (ptpp) REVERT: F 104 MET cc_start: 0.8616 (ttp) cc_final: 0.8260 (ttp) REVERT: F 107 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8426 (mm-30) REVERT: F 112 GLN cc_start: 0.8803 (tp40) cc_final: 0.8278 (tp-100) REVERT: F 116 ASP cc_start: 0.8760 (m-30) cc_final: 0.8227 (m-30) REVERT: F 135 THR cc_start: 0.9314 (m) cc_final: 0.9094 (t) REVERT: F 141 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8013 (mm-30) REVERT: F 147 LYS cc_start: 0.8527 (ttpp) cc_final: 0.8244 (ttpp) REVERT: G 10 GLN cc_start: 0.8615 (tt0) cc_final: 0.8264 (tt0) REVERT: G 17 GLU cc_start: 0.8399 (tt0) cc_final: 0.8120 (tt0) REVERT: G 61 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7916 (mm-30) REVERT: G 84 ASP cc_start: 0.8596 (m-30) cc_final: 0.8316 (m-30) REVERT: G 107 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8396 (tp30) REVERT: G 108 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8358 (mtmt) REVERT: G 141 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8710 (tp30) REVERT: G 150 ASP cc_start: 0.8592 (m-30) cc_final: 0.8123 (m-30) REVERT: G 167 GLU cc_start: 0.8495 (tt0) cc_final: 0.8282 (tt0) REVERT: H 57 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8067 (mm-30) REVERT: H 61 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8053 (mm-30) REVERT: H 64 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8264 (mm-30) REVERT: H 84 ASP cc_start: 0.8582 (m-30) cc_final: 0.8285 (m-30) REVERT: H 104 MET cc_start: 0.8705 (ttp) cc_final: 0.8328 (ttp) REVERT: H 109 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8782 (tttm) REVERT: H 116 ASP cc_start: 0.8720 (m-30) cc_final: 0.8507 (m-30) REVERT: H 140 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8299 (mm-30) REVERT: H 147 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8187 (ttpp) REVERT: H 162 GLU cc_start: 0.7522 (pm20) cc_final: 0.7301 (pm20) REVERT: I 22 SER cc_start: 0.9016 (m) cc_final: 0.8693 (p) REVERT: I 45 ASP cc_start: 0.8666 (p0) cc_final: 0.8264 (p0) REVERT: I 57 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8152 (mm-30) REVERT: I 60 GLU cc_start: 0.8360 (tp30) cc_final: 0.8070 (tp30) REVERT: I 61 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8092 (mm-30) REVERT: I 64 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8326 (mm-30) REVERT: I 81 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (mm) REVERT: I 84 ASP cc_start: 0.8680 (m-30) cc_final: 0.8397 (m-30) REVERT: I 86 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8376 (mmmm) REVERT: I 104 MET cc_start: 0.8537 (ttp) cc_final: 0.8303 (ttp) REVERT: I 116 ASP cc_start: 0.8691 (m-30) cc_final: 0.8480 (m-30) REVERT: I 147 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8278 (ttpp) REVERT: I 150 ASP cc_start: 0.8518 (m-30) cc_final: 0.8123 (m-30) REVERT: I 153 THR cc_start: 0.8903 (m) cc_final: 0.8675 (p) REVERT: J 15 ASP cc_start: 0.8605 (p0) cc_final: 0.8158 (p0) REVERT: J 57 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8121 (mm-30) REVERT: J 68 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8178 (ttm110) REVERT: J 86 LYS cc_start: 0.8782 (ptpp) cc_final: 0.8436 (mmmm) REVERT: J 87 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8360 (ptmm) REVERT: J 107 GLU cc_start: 0.8849 (tp30) cc_final: 0.8405 (tp30) REVERT: J 116 ASP cc_start: 0.8777 (m-30) cc_final: 0.8518 (m-30) REVERT: J 124 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8659 (mmt-90) REVERT: J 141 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8497 (tp30) REVERT: K 45 ASP cc_start: 0.8663 (p0) cc_final: 0.8399 (p0) REVERT: K 61 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7932 (mm-30) REVERT: K 68 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.7988 (ptp90) REVERT: K 84 ASP cc_start: 0.8272 (m-30) cc_final: 0.7816 (m-30) REVERT: K 87 LYS cc_start: 0.8683 (ptmm) cc_final: 0.8464 (ptmm) REVERT: K 92 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7497 (tm-30) REVERT: K 107 GLU cc_start: 0.8996 (tp30) cc_final: 0.8662 (tp30) REVERT: K 116 ASP cc_start: 0.8737 (m-30) cc_final: 0.8511 (m-30) REVERT: K 147 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8081 (ttpp) REVERT: K 150 ASP cc_start: 0.8400 (m-30) cc_final: 0.8113 (m-30) REVERT: K 167 GLU cc_start: 0.8428 (tt0) cc_final: 0.8216 (tt0) REVERT: L 45 ASP cc_start: 0.8823 (p0) cc_final: 0.8404 (p0) REVERT: L 57 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8077 (mm-30) REVERT: L 60 GLU cc_start: 0.8335 (tp30) cc_final: 0.7992 (tp30) REVERT: L 61 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: L 64 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7960 (mt-10) REVERT: L 84 ASP cc_start: 0.8751 (m-30) cc_final: 0.8380 (m-30) REVERT: L 86 LYS cc_start: 0.8746 (ptpp) cc_final: 0.8478 (mmmm) REVERT: L 104 MET cc_start: 0.8702 (ttp) cc_final: 0.8343 (ttp) REVERT: L 109 LYS cc_start: 0.9071 (tmmt) cc_final: 0.8784 (tttm) REVERT: L 116 ASP cc_start: 0.8744 (m-30) cc_final: 0.8490 (m-30) REVERT: L 143 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8563 (mtmm) REVERT: L 147 LYS cc_start: 0.8527 (ttpp) cc_final: 0.8186 (ttpp) REVERT: L 150 ASP cc_start: 0.8537 (m-30) cc_final: 0.8127 (m-30) REVERT: L 153 THR cc_start: 0.8894 (m) cc_final: 0.8667 (p) REVERT: M 9 ARG cc_start: 0.8379 (ttt180) cc_final: 0.7577 (ttt180) REVERT: M 57 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8212 (mm-30) REVERT: M 60 GLU cc_start: 0.8362 (tp30) cc_final: 0.8077 (tp30) REVERT: M 61 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7970 (mm-30) REVERT: M 64 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7952 (mt-10) REVERT: M 87 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8333 (ptmm) REVERT: M 104 MET cc_start: 0.8618 (ttp) cc_final: 0.8378 (ttp) REVERT: M 107 GLU cc_start: 0.8952 (tp30) cc_final: 0.8626 (tp30) REVERT: M 116 ASP cc_start: 0.8735 (m-30) cc_final: 0.8519 (m-30) REVERT: M 140 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8262 (mm-30) REVERT: M 147 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8183 (ttpt) REVERT: M 162 GLU cc_start: 0.7537 (pm20) cc_final: 0.7327 (pm20) REVERT: N 31 SER cc_start: 0.9040 (p) cc_final: 0.8828 (t) REVERT: N 43 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7757 (mtm180) REVERT: N 45 ASP cc_start: 0.8725 (p0) cc_final: 0.8400 (p0) REVERT: N 60 GLU cc_start: 0.8410 (tp30) cc_final: 0.7907 (tp30) REVERT: N 61 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8130 (mm-30) REVERT: N 63 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7384 (ttp-110) REVERT: N 79 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7535 (mmp80) REVERT: N 86 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8287 (mmmm) REVERT: N 104 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8358 (ttp) REVERT: N 107 GLU cc_start: 0.8906 (tp30) cc_final: 0.8614 (tp30) REVERT: N 116 ASP cc_start: 0.8734 (m-30) cc_final: 0.8499 (m-30) REVERT: N 147 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8070 (ttpp) REVERT: O 43 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7725 (mtm180) REVERT: O 45 ASP cc_start: 0.8643 (p0) cc_final: 0.8307 (p0) REVERT: O 49 GLU cc_start: 0.8113 (tp30) cc_final: 0.7840 (tp30) REVERT: O 61 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7902 (mm-30) REVERT: O 64 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7875 (mt-10) REVERT: O 79 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7602 (mmt180) REVERT: O 84 ASP cc_start: 0.8735 (m-30) cc_final: 0.8468 (m-30) REVERT: O 86 LYS cc_start: 0.8664 (ptpp) cc_final: 0.8423 (mmmm) REVERT: O 104 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8288 (ttp) REVERT: O 109 LYS cc_start: 0.9102 (tmmt) cc_final: 0.8820 (tttm) REVERT: O 116 ASP cc_start: 0.8775 (m-30) cc_final: 0.8547 (m-30) REVERT: O 140 GLU cc_start: 0.7871 (mp0) cc_final: 0.7203 (mp0) REVERT: O 147 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8188 (ttpp) REVERT: P 15 ASP cc_start: 0.8603 (p0) cc_final: 0.8333 (p0) REVERT: P 17 GLU cc_start: 0.8249 (tt0) cc_final: 0.8025 (tt0) REVERT: P 53 HIS cc_start: 0.8389 (t-90) cc_final: 0.8113 (t70) REVERT: P 57 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8105 (mm-30) REVERT: P 60 GLU cc_start: 0.8265 (tp30) cc_final: 0.7991 (tp30) REVERT: P 61 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8056 (mm-30) REVERT: P 62 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8660 (mmtm) REVERT: P 92 GLU cc_start: 0.7718 (pp20) cc_final: 0.7478 (tm-30) REVERT: P 101 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8477 (mppt) REVERT: P 104 MET cc_start: 0.8633 (ttp) cc_final: 0.8388 (ttp) REVERT: P 112 GLN cc_start: 0.8758 (tp40) cc_final: 0.8219 (tp-100) REVERT: P 116 ASP cc_start: 0.8763 (m-30) cc_final: 0.8251 (m-30) REVERT: P 124 ARG cc_start: 0.8892 (mmt-90) cc_final: 0.8654 (mmt-90) REVERT: P 131 ASP cc_start: 0.8584 (t70) cc_final: 0.8354 (t70) REVERT: P 135 THR cc_start: 0.9275 (m) cc_final: 0.9008 (p) REVERT: P 147 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8157 (ttpp) REVERT: P 167 GLU cc_start: 0.8511 (tt0) cc_final: 0.8231 (tt0) REVERT: Q 34 TYR cc_start: 0.9343 (m-80) cc_final: 0.9142 (m-10) REVERT: Q 61 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8049 (mm-30) REVERT: Q 104 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8253 (ttp) REVERT: Q 107 GLU cc_start: 0.8689 (tp30) cc_final: 0.8278 (tp30) REVERT: Q 116 ASP cc_start: 0.8734 (m-30) cc_final: 0.8504 (m-30) REVERT: Q 140 GLU cc_start: 0.7883 (mp0) cc_final: 0.7650 (mm-30) REVERT: R 10 GLN cc_start: 0.8626 (tt0) cc_final: 0.8214 (tt0) REVERT: R 57 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8171 (mm-30) REVERT: R 60 GLU cc_start: 0.8355 (tp30) cc_final: 0.7971 (tp30) REVERT: R 64 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8022 (mt-10) REVERT: R 84 ASP cc_start: 0.8741 (m-30) cc_final: 0.8523 (m-30) REVERT: R 104 MET cc_start: 0.8631 (ttp) cc_final: 0.8314 (ttp) REVERT: R 107 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: R 116 ASP cc_start: 0.8750 (m-30) cc_final: 0.8546 (m-30) REVERT: R 135 THR cc_start: 0.9204 (m) cc_final: 0.8961 (t) REVERT: S 10 GLN cc_start: 0.8667 (tt0) cc_final: 0.8287 (tt0) REVERT: S 17 GLU cc_start: 0.8316 (tt0) cc_final: 0.8028 (tt0) REVERT: S 31 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8924 (t) REVERT: S 45 ASP cc_start: 0.8724 (p0) cc_final: 0.8380 (p0) REVERT: S 49 GLU cc_start: 0.8539 (tt0) cc_final: 0.8203 (tp30) REVERT: S 60 GLU cc_start: 0.8381 (tp30) cc_final: 0.7774 (tp30) REVERT: S 64 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8008 (mm-30) REVERT: S 84 ASP cc_start: 0.8291 (m-30) cc_final: 0.8078 (m-30) REVERT: S 90 GLU cc_start: 0.8671 (pm20) cc_final: 0.8379 (pm20) REVERT: S 104 MET cc_start: 0.8656 (ttp) cc_final: 0.8329 (ttp) REVERT: S 107 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8438 (tp30) REVERT: S 116 ASP cc_start: 0.8742 (m-30) cc_final: 0.8515 (m-30) REVERT: S 136 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.7500 (p-80) REVERT: S 141 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8306 (tp30) REVERT: S 147 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8268 (ttpt) REVERT: S 150 ASP cc_start: 0.8537 (m-30) cc_final: 0.8107 (m-30) REVERT: S 167 GLU cc_start: 0.8507 (tt0) cc_final: 0.8285 (tt0) REVERT: T 104 MET cc_start: 0.8701 (ttp) cc_final: 0.8342 (ttp) REVERT: T 112 GLN cc_start: 0.8835 (tp40) cc_final: 0.8202 (tp-100) REVERT: T 116 ASP cc_start: 0.8778 (m-30) cc_final: 0.8223 (m-30) REVERT: T 136 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8355 (p90) REVERT: T 162 GLU cc_start: 0.7541 (pm20) cc_final: 0.7332 (pm20) REVERT: U 17 GLU cc_start: 0.8330 (tt0) cc_final: 0.8038 (tt0) REVERT: U 44 ASP cc_start: 0.8566 (p0) cc_final: 0.8345 (p0) REVERT: U 57 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8080 (mm-30) REVERT: U 61 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8063 (mm-30) REVERT: U 62 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8475 (mmtm) REVERT: U 84 ASP cc_start: 0.8801 (m-30) cc_final: 0.8461 (m-30) REVERT: U 86 LYS cc_start: 0.8718 (ptpp) cc_final: 0.8290 (mmmm) REVERT: U 104 MET cc_start: 0.8598 (ttp) cc_final: 0.8282 (ttp) REVERT: U 107 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8464 (tp30) REVERT: U 112 GLN cc_start: 0.8812 (tp40) cc_final: 0.8303 (tp-100) REVERT: U 116 ASP cc_start: 0.8782 (m-30) cc_final: 0.8282 (m-30) REVERT: U 147 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8152 (ttpp) REVERT: U 150 ASP cc_start: 0.8664 (m-30) cc_final: 0.8059 (m-30) REVERT: U 165 LEU cc_start: 0.9269 (tp) cc_final: 0.9069 (tm) REVERT: U 167 GLU cc_start: 0.8494 (tt0) cc_final: 0.8255 (tt0) REVERT: V 43 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7690 (mtm180) REVERT: V 45 ASP cc_start: 0.8708 (p0) cc_final: 0.8265 (p0) REVERT: V 57 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8174 (mm-30) REVERT: V 60 GLU cc_start: 0.8366 (tp30) cc_final: 0.7980 (tp30) REVERT: V 61 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: V 62 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8370 (mmtm) REVERT: V 64 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7885 (mt-10) REVERT: V 87 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8486 (ptpp) REVERT: V 107 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: V 112 GLN cc_start: 0.8791 (tp40) cc_final: 0.8239 (tp40) REVERT: V 135 THR cc_start: 0.9317 (m) cc_final: 0.9051 (t) REVERT: V 140 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8155 (mm-30) REVERT: V 147 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8251 (ttpp) REVERT: V 153 THR cc_start: 0.8905 (m) cc_final: 0.8674 (p) REVERT: W 45 ASP cc_start: 0.8793 (p0) cc_final: 0.8422 (p0) REVERT: W 57 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8112 (mm-30) REVERT: W 61 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8126 (mm-30) REVERT: W 68 ARG cc_start: 0.8298 (mtm110) cc_final: 0.8044 (mtm-85) REVERT: W 79 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7424 (mmt180) REVERT: W 86 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8342 (tppt) REVERT: W 104 MET cc_start: 0.8647 (ttp) cc_final: 0.8274 (ttp) REVERT: W 116 ASP cc_start: 0.8817 (m-30) cc_final: 0.8609 (m-30) REVERT: X 10 GLN cc_start: 0.8628 (tt0) cc_final: 0.8423 (tt0) REVERT: X 15 ASP cc_start: 0.8438 (p0) cc_final: 0.8174 (p0) REVERT: X 57 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8055 (mm-30) REVERT: X 84 ASP cc_start: 0.8730 (m-30) cc_final: 0.8377 (m-30) REVERT: X 116 ASP cc_start: 0.8768 (m-30) cc_final: 0.8513 (m-30) REVERT: X 124 ARG cc_start: 0.9004 (mmt-90) cc_final: 0.8767 (mmt-90) REVERT: X 135 THR cc_start: 0.9282 (m) cc_final: 0.9074 (t) REVERT: X 150 ASP cc_start: 0.8470 (m-30) cc_final: 0.8137 (m-30) outliers start: 131 outliers final: 28 residues processed: 1497 average time/residue: 0.8824 time to fit residues: 1519.2667 Evaluate side-chains 1351 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1298 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 101 LYS Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 107 GLU Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 265 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 337 optimal weight: 0.9980 chunk 316 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 309 optimal weight: 0.7980 chunk 394 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 11 ASN A 29 GLN B 11 ASN B 29 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN D 7 GLN D 29 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN E 74 ASN F 7 GLN F 156 HIS G 7 GLN G 11 ASN G 29 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN H 29 GLN H 111 ASN I 7 GLN I 29 GLN I 136 HIS J 29 GLN J 111 ASN K 29 GLN L 7 GLN L 111 ASN L 136 HIS M 7 GLN M 11 ASN M 29 GLN M 53 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN N 7 GLN N 29 GLN O 7 GLN O 74 ASN O 111 ASN O 136 HIS P 29 GLN Q 29 GLN Q 111 ASN Q 136 HIS R 7 GLN R 29 GLN R 74 ASN S 7 GLN S 136 HIS T 7 GLN T 29 GLN T 74 ASN T 136 HIS U 29 GLN V 7 GLN V 29 GLN W 7 GLN W 29 GLN X 7 GLN X 11 ASN X 29 GLN X 111 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.091538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080941 restraints weight = 58188.356| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.68 r_work: 0.2952 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33838 Z= 0.136 Angle : 0.587 10.135 45524 Z= 0.304 Chirality : 0.037 0.154 4872 Planarity : 0.004 0.036 5974 Dihedral : 7.163 88.727 4624 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.54 % Favored : 98.31 % Rotamer: Outliers : 3.30 % Allowed : 21.67 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.13), residues: 4080 helix: 2.62 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.38 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 56 TYR 0.025 0.002 TYR R 66 PHE 0.022 0.002 PHE T 132 TRP 0.005 0.001 TRP A 93 HIS 0.015 0.001 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00301 (33838) covalent geometry : angle 0.58672 (45524) hydrogen bonds : bond 0.03667 ( 2675) hydrogen bonds : angle 3.63666 ( 8025) *********************** 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 1536 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1421 time to evaluate : 1.429 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: A 57 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 60 GLU cc_start: 0.8433 (tp30) cc_final: 0.7966 (tp30) REVERT: A 61 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 64 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8181 (mt-10) REVERT: A 86 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8452 (tppt) REVERT: A 87 LYS cc_start: 0.8811 (ptpp) cc_final: 0.8384 (ptpp) REVERT: A 91 ASP cc_start: 0.8554 (m-30) cc_final: 0.8292 (OUTLIER) REVERT: A 107 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8435 (mm-30) REVERT: A 108 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8366 (mmmm) REVERT: A 112 GLN cc_start: 0.8740 (tp40) cc_final: 0.8165 (tp-100) REVERT: A 116 ASP cc_start: 0.8721 (m-30) cc_final: 0.8290 (m-30) REVERT: A 144 LEU cc_start: 0.9102 (tp) cc_final: 0.8831 (tm) REVERT: A 147 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8232 (ttpp) REVERT: A 148 MET cc_start: 0.8658 (mtt) cc_final: 0.8385 (mtt) REVERT: A 150 ASP cc_start: 0.8447 (m-30) cc_final: 0.8181 (m-30) REVERT: B 17 GLU cc_start: 0.8392 (tt0) cc_final: 0.8026 (tt0) REVERT: B 45 ASP cc_start: 0.8508 (p0) cc_final: 0.8012 (p0) REVERT: B 61 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8357 (mm-30) REVERT: B 64 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7965 (mt-10) REVERT: B 84 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7492 (t70) REVERT: B 86 LYS cc_start: 0.8650 (ptpp) cc_final: 0.8123 (mmmm) REVERT: B 90 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8526 (mm-30) REVERT: B 104 MET cc_start: 0.8551 (ttp) cc_final: 0.8155 (ttp) REVERT: B 108 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8413 (mmmm) REVERT: B 112 GLN cc_start: 0.8800 (tp40) cc_final: 0.8132 (tp40) REVERT: B 116 ASP cc_start: 0.8735 (m-30) cc_final: 0.8195 (m-30) REVERT: B 140 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 147 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8239 (ttpp) REVERT: B 150 ASP cc_start: 0.8372 (m-30) cc_final: 0.8091 (m-30) REVERT: C 10 GLN cc_start: 0.8633 (tt0) cc_final: 0.8426 (tt0) REVERT: C 17 GLU cc_start: 0.8369 (tt0) cc_final: 0.8077 (tt0) REVERT: C 42 ASP cc_start: 0.8415 (t70) cc_final: 0.7824 (t70) REVERT: C 49 GLU cc_start: 0.8086 (tp30) cc_final: 0.7873 (tp30) REVERT: C 57 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8093 (mm-30) REVERT: C 60 GLU cc_start: 0.8324 (tp30) cc_final: 0.8041 (tp30) REVERT: C 61 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8038 (mm-30) REVERT: C 64 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8002 (mt-10) REVERT: C 86 LYS cc_start: 0.8890 (tppt) cc_final: 0.8673 (tppt) REVERT: C 87 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8425 (ptmm) REVERT: C 101 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8362 (mtmm) REVERT: C 104 MET cc_start: 0.8522 (ttp) cc_final: 0.8188 (ttp) REVERT: C 116 ASP cc_start: 0.8795 (m-30) cc_final: 0.8532 (m-30) REVERT: C 140 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7758 (mp0) REVERT: C 147 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8223 (ttpp) REVERT: D 15 ASP cc_start: 0.8480 (p0) cc_final: 0.8142 (p0) REVERT: D 53 HIS cc_start: 0.8179 (t-90) cc_final: 0.7611 (t70) REVERT: D 57 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7759 (mt-10) REVERT: D 61 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8105 (mm-30) REVERT: D 64 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8123 (mm-30) REVERT: D 84 ASP cc_start: 0.8736 (m-30) cc_final: 0.8431 (m-30) REVERT: D 86 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8401 (tppt) REVERT: D 112 GLN cc_start: 0.8803 (tp40) cc_final: 0.8111 (tp-100) REVERT: D 116 ASP cc_start: 0.8771 (m-30) cc_final: 0.8196 (m-30) REVERT: D 124 ARG cc_start: 0.8829 (mmt-90) cc_final: 0.8584 (mmt-90) REVERT: D 147 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8214 (ttpp) REVERT: D 162 GLU cc_start: 0.7473 (pm20) cc_final: 0.7208 (pm20) REVERT: D 167 GLU cc_start: 0.8456 (tt0) cc_final: 0.8224 (tt0) REVERT: E 7 GLN cc_start: 0.8866 (pt0) cc_final: 0.8663 (pt0) REVERT: E 17 GLU cc_start: 0.8428 (tt0) cc_final: 0.8149 (tt0) REVERT: E 57 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7804 (mt-10) REVERT: E 61 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7915 (mm-30) REVERT: E 68 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7968 (ttm110) REVERT: E 84 ASP cc_start: 0.8671 (m-30) cc_final: 0.8442 (m-30) REVERT: E 92 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 107 GLU cc_start: 0.8978 (tp30) cc_final: 0.8723 (mm-30) REVERT: E 112 GLN cc_start: 0.8799 (tp40) cc_final: 0.8233 (tp-100) REVERT: E 116 ASP cc_start: 0.8720 (m-30) cc_final: 0.8149 (m-30) REVERT: E 136 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.7331 (p-80) REVERT: E 141 GLU cc_start: 0.8889 (tp30) cc_final: 0.8650 (tp30) REVERT: E 147 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8116 (ttpp) REVERT: E 150 ASP cc_start: 0.8444 (m-30) cc_final: 0.8124 (m-30) REVERT: E 157 ARG cc_start: 0.8311 (mtm110) cc_final: 0.8025 (ptp90) REVERT: E 171 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8285 (tm-30) REVERT: F 17 GLU cc_start: 0.8395 (tt0) cc_final: 0.8109 (tt0) REVERT: F 60 GLU cc_start: 0.8258 (tp30) cc_final: 0.7777 (tp30) REVERT: F 61 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: F 63 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7365 (ttm-80) REVERT: F 84 ASP cc_start: 0.8301 (m-30) cc_final: 0.8085 (m-30) REVERT: F 86 LYS cc_start: 0.8578 (ptpp) cc_final: 0.8298 (mmmm) REVERT: F 104 MET cc_start: 0.8643 (ttp) cc_final: 0.8251 (ttp) REVERT: F 107 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8272 (mm-30) REVERT: F 112 GLN cc_start: 0.8813 (tp40) cc_final: 0.8134 (tp-100) REVERT: F 116 ASP cc_start: 0.8768 (m-30) cc_final: 0.8270 (m-30) REVERT: F 141 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8020 (mm-30) REVERT: F 147 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8312 (ttpp) REVERT: G 61 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7878 (mm-30) REVERT: G 84 ASP cc_start: 0.8641 (m-30) cc_final: 0.8408 (m-30) REVERT: G 101 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8478 (ttmm) REVERT: G 150 ASP cc_start: 0.8399 (m-30) cc_final: 0.8094 (m-30) REVERT: H 15 ASP cc_start: 0.8585 (p0) cc_final: 0.8324 (p0) REVERT: H 42 ASP cc_start: 0.8317 (t70) cc_final: 0.7895 (t70) REVERT: H 61 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8096 (mm-30) REVERT: H 64 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7871 (mt-10) REVERT: H 84 ASP cc_start: 0.8504 (m-30) cc_final: 0.8293 (m-30) REVERT: H 87 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8412 (ptmm) REVERT: H 104 MET cc_start: 0.8535 (ttp) cc_final: 0.8180 (ttp) REVERT: H 116 ASP cc_start: 0.8735 (m-30) cc_final: 0.8512 (m-30) REVERT: H 140 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8165 (mm-30) REVERT: H 147 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8258 (ttpp) REVERT: H 148 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8584 (mtt) REVERT: H 162 GLU cc_start: 0.7714 (pm20) cc_final: 0.7458 (pm20) REVERT: I 45 ASP cc_start: 0.8492 (p0) cc_final: 0.8137 (p0) REVERT: I 60 GLU cc_start: 0.8390 (tp30) cc_final: 0.8064 (tp30) REVERT: I 61 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8093 (mm-30) REVERT: I 64 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7910 (mt-10) REVERT: I 81 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8305 (mm) REVERT: I 83 GLN cc_start: 0.8821 (mm110) cc_final: 0.8508 (mm-40) REVERT: I 84 ASP cc_start: 0.8617 (m-30) cc_final: 0.8391 (m-30) REVERT: I 104 MET cc_start: 0.8546 (ttp) cc_final: 0.8243 (ttp) REVERT: I 112 GLN cc_start: 0.8785 (tp40) cc_final: 0.8105 (tp40) REVERT: I 116 ASP cc_start: 0.8727 (m-30) cc_final: 0.8183 (m-30) REVERT: I 140 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8223 (mm-30) REVERT: I 147 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8352 (ttpp) REVERT: I 150 ASP cc_start: 0.8513 (m-30) cc_final: 0.8313 (m-30) REVERT: J 15 ASP cc_start: 0.8392 (p0) cc_final: 0.8057 (p0) REVERT: J 22 SER cc_start: 0.8989 (m) cc_final: 0.8676 (p) REVERT: J 57 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8097 (mm-30) REVERT: J 61 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7738 (mm-30) REVERT: J 64 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7937 (mt-10) REVERT: J 86 LYS cc_start: 0.8733 (ptpp) cc_final: 0.8470 (mmmm) REVERT: J 108 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8326 (mmmm) REVERT: J 116 ASP cc_start: 0.8753 (m-30) cc_final: 0.8469 (m-30) REVERT: J 124 ARG cc_start: 0.8848 (mmt-90) cc_final: 0.8601 (mmt-90) REVERT: J 140 GLU cc_start: 0.7774 (mp0) cc_final: 0.7495 (mm-30) REVERT: J 147 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8331 (ttpp) REVERT: K 10 GLN cc_start: 0.8620 (tt0) cc_final: 0.8401 (tt0) REVERT: K 17 GLU cc_start: 0.8292 (tt0) cc_final: 0.8092 (tt0) REVERT: K 34 TYR cc_start: 0.9315 (m-10) cc_final: 0.8828 (m-10) REVERT: K 45 ASP cc_start: 0.8475 (p0) cc_final: 0.7909 (p0) REVERT: K 61 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7967 (mm-30) REVERT: K 63 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7608 (ttm-80) REVERT: K 68 ARG cc_start: 0.8416 (ptp-110) cc_final: 0.8001 (ptp90) REVERT: K 84 ASP cc_start: 0.8386 (m-30) cc_final: 0.8023 (m-30) REVERT: K 107 GLU cc_start: 0.8907 (tp30) cc_final: 0.8422 (tp30) REVERT: K 112 GLN cc_start: 0.8809 (tp40) cc_final: 0.8130 (tp-100) REVERT: K 116 ASP cc_start: 0.8769 (m-30) cc_final: 0.8255 (m-30) REVERT: K 135 THR cc_start: 0.9226 (m) cc_final: 0.8984 (t) REVERT: K 147 LYS cc_start: 0.8339 (ttpp) cc_final: 0.8065 (ttpp) REVERT: K 150 ASP cc_start: 0.8364 (m-30) cc_final: 0.8031 (m-30) REVERT: K 153 THR cc_start: 0.8822 (m) cc_final: 0.8619 (p) REVERT: K 167 GLU cc_start: 0.8425 (tt0) cc_final: 0.8170 (tt0) REVERT: L 45 ASP cc_start: 0.8711 (p0) cc_final: 0.8330 (p0) REVERT: L 60 GLU cc_start: 0.8422 (tp30) cc_final: 0.8129 (tp30) REVERT: L 61 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: L 64 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8250 (mm-30) REVERT: L 90 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8386 (mm-30) REVERT: L 104 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8216 (ttp) REVERT: L 109 LYS cc_start: 0.9048 (tmmt) cc_final: 0.8766 (tttm) REVERT: L 112 GLN cc_start: 0.8798 (tp40) cc_final: 0.8033 (tp40) REVERT: L 116 ASP cc_start: 0.8753 (m-30) cc_final: 0.8106 (m-30) REVERT: L 140 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8186 (mm-30) REVERT: L 147 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8271 (ttpp) REVERT: L 148 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8706 (mtm) REVERT: L 150 ASP cc_start: 0.8417 (m-30) cc_final: 0.8170 (m-30) REVERT: L 167 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8187 (tt0) REVERT: M 9 ARG cc_start: 0.8344 (ttt180) cc_final: 0.7512 (ttt180) REVERT: M 49 GLU cc_start: 0.8166 (tp30) cc_final: 0.7853 (tp30) REVERT: M 57 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8216 (mm-30) REVERT: M 60 GLU cc_start: 0.8372 (tp30) cc_final: 0.8030 (tp30) REVERT: M 61 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8027 (mm-30) REVERT: M 64 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7918 (mt-10) REVERT: M 98 ASP cc_start: 0.8429 (m-30) cc_final: 0.8103 (p0) REVERT: M 101 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8059 (mppt) REVERT: M 112 GLN cc_start: 0.8796 (tp40) cc_final: 0.8077 (tp40) REVERT: M 116 ASP cc_start: 0.8758 (m-30) cc_final: 0.8131 (m-30) REVERT: M 140 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8141 (mm-30) REVERT: M 162 GLU cc_start: 0.7571 (pm20) cc_final: 0.7368 (pm20) REVERT: N 17 GLU cc_start: 0.8448 (tt0) cc_final: 0.8184 (tt0) REVERT: N 43 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7873 (mtm180) REVERT: N 45 ASP cc_start: 0.8566 (p0) cc_final: 0.8156 (p0) REVERT: N 49 GLU cc_start: 0.8152 (tp30) cc_final: 0.7914 (tp30) REVERT: N 60 GLU cc_start: 0.8411 (tp30) cc_final: 0.7992 (tp30) REVERT: N 61 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8178 (mm-30) REVERT: N 64 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8044 (mt-10) REVERT: N 79 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7399 (mmt180) REVERT: N 86 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8454 (mmmm) REVERT: N 104 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7810 (ttp) REVERT: N 107 GLU cc_start: 0.8867 (tp30) cc_final: 0.8349 (tp30) REVERT: N 112 GLN cc_start: 0.8765 (tp40) cc_final: 0.8088 (tp40) REVERT: N 116 ASP cc_start: 0.8742 (m-30) cc_final: 0.8133 (m-30) REVERT: N 140 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8128 (mm-30) REVERT: N 141 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8254 (tp30) REVERT: N 147 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8094 (ttpp) REVERT: N 171 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8349 (tm-30) REVERT: N 172 ARG cc_start: 0.8930 (mmm160) cc_final: 0.8684 (mmm160) REVERT: O 43 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7851 (mtm180) REVERT: O 45 ASP cc_start: 0.8489 (p0) cc_final: 0.8134 (p0) REVERT: O 49 GLU cc_start: 0.8130 (tp30) cc_final: 0.7924 (tp30) REVERT: O 61 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7888 (mm-30) REVERT: O 64 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7893 (mt-10) REVERT: O 79 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7509 (mmt180) REVERT: O 84 ASP cc_start: 0.8678 (m-30) cc_final: 0.8403 (m-30) REVERT: O 109 LYS cc_start: 0.9033 (tmmt) cc_final: 0.8757 (tttm) REVERT: O 116 ASP cc_start: 0.8774 (m-30) cc_final: 0.8490 (m-30) REVERT: O 140 GLU cc_start: 0.8031 (mp0) cc_final: 0.7782 (mm-30) REVERT: O 147 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8171 (ttpp) REVERT: O 148 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8751 (mtm) REVERT: P 15 ASP cc_start: 0.8461 (p0) cc_final: 0.8224 (p0) REVERT: P 22 SER cc_start: 0.8975 (m) cc_final: 0.8689 (p) REVERT: P 53 HIS cc_start: 0.8410 (t-90) cc_final: 0.8032 (t70) REVERT: P 57 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8134 (mm-30) REVERT: P 60 GLU cc_start: 0.8313 (tp30) cc_final: 0.8073 (tp30) REVERT: P 61 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8106 (mm-30) REVERT: P 86 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8365 (tppt) REVERT: P 101 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8328 (mppt) REVERT: P 104 MET cc_start: 0.8643 (ttp) cc_final: 0.8345 (ttp) REVERT: P 107 GLU cc_start: 0.9054 (tp30) cc_final: 0.8844 (tp30) REVERT: P 112 GLN cc_start: 0.8797 (tp40) cc_final: 0.8082 (tp-100) REVERT: P 116 ASP cc_start: 0.8762 (m-30) cc_final: 0.8257 (m-30) REVERT: P 124 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.8600 (mmt-90) REVERT: P 131 ASP cc_start: 0.8542 (t70) cc_final: 0.8287 (t0) REVERT: P 135 THR cc_start: 0.9222 (m) cc_final: 0.8989 (p) REVERT: P 141 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8196 (tp30) REVERT: P 147 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8204 (ttpp) REVERT: P 162 GLU cc_start: 0.7626 (pm20) cc_final: 0.7372 (pm20) REVERT: P 167 GLU cc_start: 0.8522 (tt0) cc_final: 0.8288 (tt0) REVERT: Q 61 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7939 (mm-30) REVERT: Q 64 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7986 (mt-10) REVERT: Q 104 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8121 (ttp) REVERT: Q 116 ASP cc_start: 0.8762 (m-30) cc_final: 0.8471 (m-30) REVERT: Q 140 GLU cc_start: 0.8064 (mp0) cc_final: 0.7704 (mm-30) REVERT: R 34 TYR cc_start: 0.9204 (m-10) cc_final: 0.8966 (m-10) REVERT: R 60 GLU cc_start: 0.8434 (tp30) cc_final: 0.8081 (tp30) REVERT: R 61 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7816 (mm-30) REVERT: R 64 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8104 (mt-10) REVERT: R 107 GLU cc_start: 0.8333 (tp30) cc_final: 0.8128 (tp30) REVERT: R 116 ASP cc_start: 0.8782 (m-30) cc_final: 0.8481 (m-30) REVERT: R 135 THR cc_start: 0.9214 (m) cc_final: 0.8972 (t) REVERT: R 148 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8785 (mtm) REVERT: S 45 ASP cc_start: 0.8619 (p0) cc_final: 0.8365 (p0) REVERT: S 49 GLU cc_start: 0.8509 (tt0) cc_final: 0.8157 (tp30) REVERT: S 60 GLU cc_start: 0.8403 (tp30) cc_final: 0.7960 (tp30) REVERT: S 61 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7778 (mm-30) REVERT: S 84 ASP cc_start: 0.8349 (m-30) cc_final: 0.8109 (m-30) REVERT: S 104 MET cc_start: 0.8631 (ttp) cc_final: 0.8226 (ttp) REVERT: S 107 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8073 (mm-30) REVERT: S 112 GLN cc_start: 0.8771 (tp40) cc_final: 0.8095 (tp-100) REVERT: S 116 ASP cc_start: 0.8740 (m-30) cc_final: 0.8240 (m-30) REVERT: S 136 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8161 (p-80) REVERT: S 140 GLU cc_start: 0.7939 (mp0) cc_final: 0.7209 (mp0) REVERT: T 45 ASP cc_start: 0.8574 (p0) cc_final: 0.8279 (p0) REVERT: T 104 MET cc_start: 0.8627 (ttp) cc_final: 0.8253 (ttp) REVERT: T 112 GLN cc_start: 0.8828 (tp40) cc_final: 0.8059 (tp-100) REVERT: T 116 ASP cc_start: 0.8778 (m-30) cc_final: 0.8198 (m-30) REVERT: T 162 GLU cc_start: 0.7600 (pm20) cc_final: 0.7345 (pm20) REVERT: U 17 GLU cc_start: 0.8306 (tt0) cc_final: 0.7948 (tt0) REVERT: U 45 ASP cc_start: 0.8704 (p0) cc_final: 0.8499 (p0) REVERT: U 49 GLU cc_start: 0.8180 (tp30) cc_final: 0.7878 (tp30) REVERT: U 57 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8094 (mm-30) REVERT: U 61 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8179 (mm-30) REVERT: U 63 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7847 (ttm-80) REVERT: U 83 GLN cc_start: 0.8897 (mm110) cc_final: 0.8667 (mm-40) REVERT: U 104 MET cc_start: 0.8562 (ttp) cc_final: 0.8118 (ttp) REVERT: U 112 GLN cc_start: 0.8797 (tp40) cc_final: 0.8050 (tp-100) REVERT: U 116 ASP cc_start: 0.8774 (m-30) cc_final: 0.8244 (m-30) REVERT: U 135 THR cc_start: 0.9262 (m) cc_final: 0.8999 (t) REVERT: U 141 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8270 (tp30) REVERT: U 147 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8249 (ttpp) REVERT: U 150 ASP cc_start: 0.8365 (m-30) cc_final: 0.8144 (m-30) REVERT: U 167 GLU cc_start: 0.8486 (tt0) cc_final: 0.8146 (tt0) REVERT: V 43 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7873 (mtm180) REVERT: V 45 ASP cc_start: 0.8589 (p0) cc_final: 0.8223 (p0) REVERT: V 57 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8233 (mm-30) REVERT: V 60 GLU cc_start: 0.8412 (tp30) cc_final: 0.8118 (tp30) REVERT: V 61 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: V 64 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7906 (mt-10) REVERT: V 87 LYS cc_start: 0.8762 (ptpp) cc_final: 0.8491 (ptpp) REVERT: V 107 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8584 (tp30) REVERT: V 112 GLN cc_start: 0.8766 (tp40) cc_final: 0.8213 (tp40) REVERT: V 135 THR cc_start: 0.9298 (m) cc_final: 0.9036 (t) REVERT: V 140 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7870 (mp0) REVERT: V 147 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8270 (ttpp) REVERT: V 153 THR cc_start: 0.8887 (m) cc_final: 0.8618 (p) REVERT: W 17 GLU cc_start: 0.8451 (tt0) cc_final: 0.8192 (tt0) REVERT: W 22 SER cc_start: 0.9059 (m) cc_final: 0.8753 (p) REVERT: W 57 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8111 (mm-30) REVERT: W 61 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8055 (mm-30) REVERT: W 64 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8082 (mt-10) REVERT: W 79 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7448 (mmt180) REVERT: W 86 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8349 (mmpt) REVERT: W 90 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8443 (mm-30) REVERT: W 92 GLU cc_start: 0.7573 (pp20) cc_final: 0.7263 (tm-30) REVERT: W 104 MET cc_start: 0.8624 (ttp) cc_final: 0.8102 (ttp) REVERT: W 107 GLU cc_start: 0.8878 (tp30) cc_final: 0.8503 (mm-30) REVERT: W 108 LYS cc_start: 0.8395 (mtmt) cc_final: 0.8150 (mmmm) REVERT: W 116 ASP cc_start: 0.8835 (m-30) cc_final: 0.8614 (m-30) REVERT: W 140 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7846 (mp0) REVERT: W 141 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8253 (tp30) REVERT: W 147 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8208 (ttpp) REVERT: W 162 GLU cc_start: 0.7518 (pm20) cc_final: 0.7310 (pm20) REVERT: W 167 GLU cc_start: 0.8371 (tt0) cc_final: 0.8123 (tt0) REVERT: X 15 ASP cc_start: 0.8271 (p0) cc_final: 0.8070 (p0) REVERT: X 61 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7782 (mm-30) REVERT: X 64 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7945 (mt-10) REVERT: X 116 ASP cc_start: 0.8780 (m-30) cc_final: 0.8472 (m-30) REVERT: X 124 ARG cc_start: 0.8935 (mmt-90) cc_final: 0.8677 (mmt-90) REVERT: X 150 ASP cc_start: 0.8441 (m-30) cc_final: 0.8070 (m-30) outliers start: 115 outliers final: 38 residues processed: 1455 average time/residue: 0.9747 time to fit residues: 1621.8191 Evaluate side-chains 1372 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 1314 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain L residue 148 MET Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 148 MET Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 101 LYS Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 107 GLU Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 72 MET Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 151 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 394 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 29 GLN A 74 ASN B 29 GLN B 74 ASN C 75 GLN D 7 GLN F 7 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 GLN G 29 GLN G 75 GLN H 7 GLN H 136 HIS I 7 GLN J 136 HIS K 7 GLN K 11 ASN K 73 GLN L 7 GLN L 29 GLN M 136 HIS N 7 GLN N 11 ASN N 29 GLN N 74 ASN N 136 HIS O 7 GLN O 29 GLN P 74 ASN Q 11 ASN Q 29 GLN R 29 GLN R 136 HIS S 29 GLN S 136 HIS T 29 GLN ** T 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 GLN U 29 GLN V 74 ASN W 7 GLN W 29 GLN ** X 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075760 restraints weight = 58564.392| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.63 r_work: 0.2881 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 33838 Z= 0.276 Angle : 0.648 9.622 45524 Z= 0.328 Chirality : 0.042 0.171 4872 Planarity : 0.005 0.042 5974 Dihedral : 7.112 89.633 4617 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.37 % Favored : 98.48 % Rotamer: Outliers : 3.51 % Allowed : 22.56 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.13), residues: 4080 helix: 2.42 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.07 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 63 TYR 0.022 0.002 TYR F 66 PHE 0.022 0.003 PHE F 41 TRP 0.006 0.001 TRP D 93 HIS 0.010 0.001 HIS S 136 Details of bonding type rmsd covalent geometry : bond 0.00609 (33838) covalent geometry : angle 0.64810 (45524) hydrogen bonds : bond 0.04603 ( 2675) hydrogen bonds : angle 3.82369 ( 8025) *********************** 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 1467 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1345 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8473 (tp30) cc_final: 0.8056 (tp30) REVERT: A 60 GLU cc_start: 0.8842 (tp30) cc_final: 0.8527 (tp30) REVERT: A 61 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8334 (mm-30) REVERT: A 64 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8607 (mt-10) REVERT: A 86 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8532 (tppt) REVERT: A 104 MET cc_start: 0.9142 (tpp) cc_final: 0.8886 (tpp) REVERT: A 147 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8696 (ttpp) REVERT: A 150 ASP cc_start: 0.8770 (m-30) cc_final: 0.8548 (m-30) REVERT: B 45 ASP cc_start: 0.8803 (p0) cc_final: 0.8530 (p0) REVERT: B 60 GLU cc_start: 0.8854 (tp30) cc_final: 0.8337 (tp30) REVERT: B 64 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8356 (mt-10) REVERT: B 84 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8016 (t70) REVERT: B 104 MET cc_start: 0.8968 (ttp) cc_final: 0.8611 (ttp) REVERT: B 116 ASP cc_start: 0.8962 (m-30) cc_final: 0.8740 (m-30) REVERT: B 147 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8695 (ttpp) REVERT: C 10 GLN cc_start: 0.9017 (tt0) cc_final: 0.8802 (tt0) REVERT: C 42 ASP cc_start: 0.8770 (t70) cc_final: 0.8290 (t70) REVERT: C 57 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8482 (mm-30) REVERT: C 60 GLU cc_start: 0.8753 (tp30) cc_final: 0.8445 (tp30) REVERT: C 61 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8623 (mm-30) REVERT: C 64 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8345 (mt-10) REVERT: C 104 MET cc_start: 0.8907 (ttp) cc_final: 0.8536 (ttp) REVERT: C 116 ASP cc_start: 0.8959 (m-30) cc_final: 0.8730 (m-30) REVERT: C 140 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8233 (mp0) REVERT: C 141 GLU cc_start: 0.9104 (tp30) cc_final: 0.8709 (tp30) REVERT: C 147 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8694 (ttpp) REVERT: D 42 ASP cc_start: 0.8713 (t70) cc_final: 0.8213 (t70) REVERT: D 53 HIS cc_start: 0.8582 (t-90) cc_final: 0.8065 (t70) REVERT: D 57 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8477 (mt-10) REVERT: D 61 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8680 (mm-30) REVERT: D 64 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8534 (mm-30) REVERT: D 86 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8672 (tppt) REVERT: D 104 MET cc_start: 0.9051 (mmm) cc_final: 0.8840 (tpp) REVERT: D 116 ASP cc_start: 0.9014 (m-30) cc_final: 0.8793 (m-30) REVERT: D 147 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8651 (ttpp) REVERT: D 162 GLU cc_start: 0.7765 (pm20) cc_final: 0.7419 (pm20) REVERT: D 167 GLU cc_start: 0.8673 (tt0) cc_final: 0.8418 (tt0) REVERT: E 68 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8710 (ttm110) REVERT: E 104 MET cc_start: 0.9097 (mmm) cc_final: 0.8833 (tpp) REVERT: E 107 GLU cc_start: 0.9266 (tp30) cc_final: 0.9066 (mm-30) REVERT: E 116 ASP cc_start: 0.8998 (m-30) cc_final: 0.8781 (m-30) REVERT: F 57 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8191 (mt-10) REVERT: F 61 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: F 104 MET cc_start: 0.9059 (ttp) cc_final: 0.8685 (ttp) REVERT: F 107 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8792 (mm-30) REVERT: F 116 ASP cc_start: 0.8968 (m-30) cc_final: 0.8757 (m-30) REVERT: F 141 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8674 (mm-30) REVERT: F 147 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8751 (ttpp) REVERT: G 49 GLU cc_start: 0.8438 (tp30) cc_final: 0.8122 (tp30) REVERT: G 61 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8437 (mm-30) REVERT: G 84 ASP cc_start: 0.8924 (m-30) cc_final: 0.8706 (m-30) REVERT: G 150 ASP cc_start: 0.8724 (m-30) cc_final: 0.8517 (m-30) REVERT: H 61 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8597 (mm-30) REVERT: H 64 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8555 (mm-30) REVERT: H 84 ASP cc_start: 0.8847 (m-30) cc_final: 0.8591 (m-30) REVERT: H 90 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8558 (mm-30) REVERT: H 104 MET cc_start: 0.9040 (ttp) cc_final: 0.8700 (ttp) REVERT: H 116 ASP cc_start: 0.8934 (m-30) cc_final: 0.8714 (m-30) REVERT: H 140 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8384 (mm-30) REVERT: H 147 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8750 (ttpp) REVERT: H 148 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.8840 (mtt) REVERT: H 162 GLU cc_start: 0.7876 (pm20) cc_final: 0.7580 (pm20) REVERT: I 60 GLU cc_start: 0.8740 (tp30) cc_final: 0.8380 (tp30) REVERT: I 61 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8625 (mm-30) REVERT: I 64 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8485 (mm-30) REVERT: I 92 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7699 (tm-30) REVERT: I 104 MET cc_start: 0.8941 (ttp) cc_final: 0.8705 (ttp) REVERT: I 108 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8823 (mmmm) REVERT: I 116 ASP cc_start: 0.8964 (m-30) cc_final: 0.8736 (m-30) REVERT: I 147 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8764 (ttpp) REVERT: J 61 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8330 (mm-30) REVERT: J 64 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8299 (mt-10) REVERT: J 84 ASP cc_start: 0.8874 (m-30) cc_final: 0.8664 (m-30) REVERT: J 108 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8727 (mtmt) REVERT: J 116 ASP cc_start: 0.8941 (m-30) cc_final: 0.8705 (m-30) REVERT: J 140 GLU cc_start: 0.8140 (mp0) cc_final: 0.7819 (mm-30) REVERT: J 143 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8824 (mtmm) REVERT: J 147 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8706 (ttpp) REVERT: J 157 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: K 45 ASP cc_start: 0.8786 (p0) cc_final: 0.8345 (p0) REVERT: K 60 GLU cc_start: 0.8668 (tp30) cc_final: 0.8333 (tp30) REVERT: K 61 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8459 (mm-30) REVERT: K 63 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8130 (ttp-110) REVERT: K 68 ARG cc_start: 0.8836 (ptp-110) cc_final: 0.8474 (ptp90) REVERT: K 84 ASP cc_start: 0.8698 (m-30) cc_final: 0.8340 (m-30) REVERT: K 107 GLU cc_start: 0.9150 (tp30) cc_final: 0.8662 (tp30) REVERT: K 116 ASP cc_start: 0.8997 (m-30) cc_final: 0.8769 (m-30) REVERT: K 147 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8665 (ttpp) REVERT: K 167 GLU cc_start: 0.8760 (tt0) cc_final: 0.8530 (tt0) REVERT: L 45 ASP cc_start: 0.8864 (p0) cc_final: 0.8457 (p0) REVERT: L 60 GLU cc_start: 0.8844 (tp30) cc_final: 0.8459 (tp30) REVERT: L 61 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8616 (mm-30) REVERT: L 64 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8351 (mt-10) REVERT: L 104 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8702 (ttp) REVERT: L 116 ASP cc_start: 0.8994 (m-30) cc_final: 0.8760 (m-30) REVERT: L 148 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8816 (mtt) REVERT: M 49 GLU cc_start: 0.8498 (tp30) cc_final: 0.8162 (tp30) REVERT: M 60 GLU cc_start: 0.8769 (tp30) cc_final: 0.8434 (tp30) REVERT: M 61 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8570 (mm-30) REVERT: M 64 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8272 (mt-10) REVERT: M 101 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8603 (mtpt) REVERT: M 116 ASP cc_start: 0.8933 (m-30) cc_final: 0.8706 (m-30) REVERT: M 140 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8459 (mm-30) REVERT: M 147 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8633 (ttpp) REVERT: M 162 GLU cc_start: 0.7666 (pm20) cc_final: 0.7421 (pm20) REVERT: N 45 ASP cc_start: 0.8790 (p0) cc_final: 0.8589 (p0) REVERT: N 60 GLU cc_start: 0.8791 (tp30) cc_final: 0.8349 (tp30) REVERT: N 61 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8650 (mm-30) REVERT: N 79 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7847 (mmt-90) REVERT: N 86 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8694 (mmmm) REVERT: N 92 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7858 (tm-30) REVERT: N 104 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8569 (ttp) REVERT: N 107 GLU cc_start: 0.9025 (tp30) cc_final: 0.8752 (tp30) REVERT: N 116 ASP cc_start: 0.8934 (m-30) cc_final: 0.8679 (m-30) REVERT: N 140 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8390 (mm-30) REVERT: N 141 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8718 (tp30) REVERT: N 147 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8627 (ttpp) REVERT: O 49 GLU cc_start: 0.8522 (tp30) cc_final: 0.8299 (tp30) REVERT: O 61 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8463 (mm-30) REVERT: O 64 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8302 (mt-10) REVERT: O 79 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7980 (mmt-90) REVERT: O 116 ASP cc_start: 0.8962 (m-30) cc_final: 0.8736 (m-30) REVERT: O 140 GLU cc_start: 0.8268 (mp0) cc_final: 0.8051 (mm-30) REVERT: O 147 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8692 (ttpp) REVERT: O 148 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8952 (mtt) REVERT: P 53 HIS cc_start: 0.8693 (t-90) cc_final: 0.8336 (t70) REVERT: P 60 GLU cc_start: 0.8724 (tp30) cc_final: 0.8463 (tp30) REVERT: P 61 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8589 (mm-30) REVERT: P 64 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8305 (mt-10) REVERT: P 86 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8684 (tppt) REVERT: P 104 MET cc_start: 0.9007 (ttp) cc_final: 0.8662 (ttp) REVERT: P 116 ASP cc_start: 0.9018 (m-30) cc_final: 0.8802 (m-30) REVERT: P 147 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8708 (ttpp) REVERT: Q 61 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8445 (mm-30) REVERT: Q 64 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8292 (mt-10) REVERT: Q 104 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8709 (ttp) REVERT: Q 116 ASP cc_start: 0.8947 (m-30) cc_final: 0.8726 (m-30) REVERT: Q 140 GLU cc_start: 0.8343 (mp0) cc_final: 0.7810 (mp0) REVERT: Q 162 GLU cc_start: 0.7844 (pm20) cc_final: 0.7589 (pm20) REVERT: R 45 ASP cc_start: 0.8941 (p0) cc_final: 0.8710 (p0) REVERT: R 60 GLU cc_start: 0.8840 (tp30) cc_final: 0.8358 (tp30) REVERT: R 61 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8308 (mm-30) REVERT: R 62 LYS cc_start: 0.8998 (mmpt) cc_final: 0.8771 (mmpt) REVERT: R 64 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8465 (mt-10) REVERT: R 107 GLU cc_start: 0.8918 (tp30) cc_final: 0.8654 (tp30) REVERT: R 116 ASP cc_start: 0.8960 (m-30) cc_final: 0.8737 (m-30) REVERT: R 147 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8774 (ttpp) REVERT: R 148 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8987 (mtm) REVERT: R 162 GLU cc_start: 0.7639 (pm20) cc_final: 0.7429 (pm20) REVERT: S 49 GLU cc_start: 0.8912 (tt0) cc_final: 0.8690 (tp30) REVERT: S 60 GLU cc_start: 0.8672 (tp30) cc_final: 0.8371 (tp30) REVERT: S 84 ASP cc_start: 0.8797 (m-30) cc_final: 0.8543 (m-30) REVERT: S 104 MET cc_start: 0.9051 (ttp) cc_final: 0.8636 (ttp) REVERT: S 107 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8827 (tp30) REVERT: S 116 ASP cc_start: 0.8946 (m-30) cc_final: 0.8728 (m-30) REVERT: S 136 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8777 (p90) REVERT: S 147 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8735 (ttpp) REVERT: T 104 MET cc_start: 0.9017 (ttp) cc_final: 0.8649 (ttp) REVERT: T 116 ASP cc_start: 0.8979 (m-30) cc_final: 0.8752 (m-30) REVERT: T 136 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.7801 (p90) REVERT: T 162 GLU cc_start: 0.7724 (pm20) cc_final: 0.7413 (pm20) REVERT: U 45 ASP cc_start: 0.8881 (p0) cc_final: 0.8668 (p0) REVERT: U 49 GLU cc_start: 0.8540 (tp30) cc_final: 0.8192 (tp30) REVERT: U 61 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8581 (mm-30) REVERT: U 104 MET cc_start: 0.9028 (ttp) cc_final: 0.8644 (ttp) REVERT: U 107 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8816 (mm-30) REVERT: U 116 ASP cc_start: 0.8952 (m-30) cc_final: 0.8720 (m-30) REVERT: U 141 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8421 (tp30) REVERT: U 147 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8721 (ttpp) REVERT: U 162 GLU cc_start: 0.7709 (pm20) cc_final: 0.7379 (pm20) REVERT: U 167 GLU cc_start: 0.8820 (tt0) cc_final: 0.8482 (tt0) REVERT: V 60 GLU cc_start: 0.8810 (tp30) cc_final: 0.8402 (tp30) REVERT: V 64 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8358 (mt-10) REVERT: V 87 LYS cc_start: 0.9006 (ptpp) cc_final: 0.8736 (ptpp) REVERT: V 140 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8152 (mp0) REVERT: V 141 GLU cc_start: 0.9059 (tp30) cc_final: 0.8774 (tp30) REVERT: V 147 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8784 (ttpp) REVERT: V 167 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8418 (tt0) REVERT: W 61 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8575 (mm-30) REVERT: W 64 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8421 (mt-10) REVERT: W 79 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7936 (mmt180) REVERT: W 84 ASP cc_start: 0.8925 (m-30) cc_final: 0.8725 (m-30) REVERT: W 104 MET cc_start: 0.8979 (ttp) cc_final: 0.8582 (ttp) REVERT: W 107 GLU cc_start: 0.9195 (tp30) cc_final: 0.8972 (mm-30) REVERT: W 116 ASP cc_start: 0.9013 (m-30) cc_final: 0.8807 (m-30) REVERT: W 140 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8156 (mp0) REVERT: W 141 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8636 (tp30) REVERT: W 147 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8704 (ttpp) REVERT: W 148 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.8855 (mtt) REVERT: W 162 GLU cc_start: 0.7716 (pm20) cc_final: 0.7470 (pm20) REVERT: W 167 GLU cc_start: 0.8671 (tt0) cc_final: 0.8428 (tt0) REVERT: X 107 GLU cc_start: 0.9197 (tp30) cc_final: 0.8813 (mm-30) REVERT: X 116 ASP cc_start: 0.9008 (m-30) cc_final: 0.8805 (m-30) REVERT: X 167 GLU cc_start: 0.8734 (tt0) cc_final: 0.8513 (tt0) outliers start: 122 outliers final: 51 residues processed: 1375 average time/residue: 0.9045 time to fit residues: 1423.7117 Evaluate side-chains 1312 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1242 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 7 GLN Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 157 ARG Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain L residue 148 MET Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 148 MET Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 255 optimal weight: 5.9990 chunk 363 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 340 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 29 GLN C 75 GLN C 136 HIS D 7 GLN D 10 GLN E 7 GLN E 11 ASN F 7 GLN G 7 GLN G 29 GLN G 75 GLN I 7 GLN J 29 GLN K 7 GLN L 7 GLN L 29 GLN O 7 GLN Q 29 GLN Q 156 HIS S 7 GLN S 10 GLN S 136 HIS T 29 GLN ** T 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 GLN V 156 HIS W 29 GLN X 111 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.078268 restraints weight = 58672.176| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.62 r_work: 0.2933 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33838 Z= 0.184 Angle : 0.615 11.014 45524 Z= 0.314 Chirality : 0.039 0.201 4872 Planarity : 0.004 0.041 5974 Dihedral : 6.920 89.405 4608 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.50 % Favored : 98.36 % Rotamer: Outliers : 3.16 % Allowed : 24.54 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.13), residues: 4080 helix: 2.48 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.06 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 56 TYR 0.025 0.002 TYR E 66 PHE 0.021 0.002 PHE S 137 TRP 0.006 0.001 TRP A 93 HIS 0.008 0.001 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00414 (33838) covalent geometry : angle 0.61459 (45524) hydrogen bonds : bond 0.03967 ( 2675) hydrogen bonds : angle 3.75428 ( 8025) *********************** 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 1470 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1360 time to evaluate : 1.312 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: A 42 ASP cc_start: 0.8563 (t70) cc_final: 0.8122 (t70) REVERT: A 49 GLU cc_start: 0.8291 (tp30) cc_final: 0.7921 (tp30) REVERT: A 60 GLU cc_start: 0.8656 (tp30) cc_final: 0.8323 (tp30) REVERT: A 61 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 86 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8593 (tppt) REVERT: A 108 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8807 (mmmm) REVERT: A 147 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8617 (ttpp) REVERT: A 150 ASP cc_start: 0.8563 (m-30) cc_final: 0.8303 (m-30) REVERT: B 45 ASP cc_start: 0.8679 (p0) cc_final: 0.8283 (p0) REVERT: B 60 GLU cc_start: 0.8664 (tp30) cc_final: 0.8121 (tp30) REVERT: B 61 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 64 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8187 (mt-10) REVERT: B 86 LYS cc_start: 0.8864 (mtpm) cc_final: 0.8378 (mmmm) REVERT: B 104 MET cc_start: 0.8874 (ttp) cc_final: 0.8527 (ttp) REVERT: B 116 ASP cc_start: 0.8846 (m-30) cc_final: 0.8569 (m-30) REVERT: B 143 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8896 (mtmm) REVERT: B 147 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8649 (ttpp) REVERT: C 42 ASP cc_start: 0.8602 (t70) cc_final: 0.8091 (t70) REVERT: C 60 GLU cc_start: 0.8549 (tp30) cc_final: 0.8284 (tp30) REVERT: C 86 LYS cc_start: 0.8927 (tppt) cc_final: 0.8590 (tppt) REVERT: C 104 MET cc_start: 0.8876 (ttp) cc_final: 0.8453 (ttp) REVERT: C 107 GLU cc_start: 0.8909 (tp30) cc_final: 0.8310 (mm-30) REVERT: C 116 ASP cc_start: 0.8850 (m-30) cc_final: 0.8602 (m-30) REVERT: C 140 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 141 GLU cc_start: 0.8742 (tp30) cc_final: 0.8240 (tp30) REVERT: C 147 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8644 (ttpp) REVERT: D 15 ASP cc_start: 0.8506 (p0) cc_final: 0.8174 (p0) REVERT: D 42 ASP cc_start: 0.8554 (t70) cc_final: 0.8048 (t70) REVERT: D 53 HIS cc_start: 0.8442 (t-90) cc_final: 0.7818 (t70) REVERT: D 57 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 61 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8429 (mm-30) REVERT: D 64 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8298 (mm-30) REVERT: D 87 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8268 (ttmm) REVERT: D 104 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8704 (tpp) REVERT: D 107 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8527 (mm-30) REVERT: D 116 ASP cc_start: 0.8883 (m-30) cc_final: 0.8657 (m-30) REVERT: D 124 ARG cc_start: 0.8905 (mmt-90) cc_final: 0.8680 (mmt-90) REVERT: D 147 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8616 (ttpp) REVERT: D 162 GLU cc_start: 0.7642 (pm20) cc_final: 0.7371 (pm20) REVERT: D 167 GLU cc_start: 0.8448 (tt0) cc_final: 0.8186 (tt0) REVERT: E 42 ASP cc_start: 0.8406 (t70) cc_final: 0.7972 (t70) REVERT: E 107 GLU cc_start: 0.9041 (tp30) cc_final: 0.8791 (tp30) REVERT: E 108 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8791 (mmmm) REVERT: E 116 ASP cc_start: 0.8835 (m-30) cc_final: 0.8604 (m-30) REVERT: F 17 GLU cc_start: 0.8672 (tt0) cc_final: 0.8446 (tt0) REVERT: F 57 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7928 (mt-10) REVERT: F 60 GLU cc_start: 0.8483 (tp30) cc_final: 0.8060 (tp30) REVERT: F 104 MET cc_start: 0.8788 (ttp) cc_final: 0.8403 (ttp) REVERT: F 107 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8367 (mm-30) REVERT: F 116 ASP cc_start: 0.8847 (m-30) cc_final: 0.8558 (m-30) REVERT: F 147 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8677 (ttpp) REVERT: G 42 ASP cc_start: 0.8467 (t70) cc_final: 0.8185 (t70) REVERT: G 49 GLU cc_start: 0.8208 (tp30) cc_final: 0.7974 (tp30) REVERT: G 61 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8187 (mm-30) REVERT: G 84 ASP cc_start: 0.8750 (m-30) cc_final: 0.8540 (m-30) REVERT: H 42 ASP cc_start: 0.8462 (t70) cc_final: 0.8035 (t70) REVERT: H 61 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8446 (mm-30) REVERT: H 64 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8303 (mm-30) REVERT: H 68 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8375 (ttm110) REVERT: H 104 MET cc_start: 0.8786 (ttp) cc_final: 0.8530 (ttp) REVERT: H 116 ASP cc_start: 0.8851 (m-30) cc_final: 0.8620 (m-30) REVERT: H 140 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8144 (mp0) REVERT: H 147 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8612 (ttpp) REVERT: H 162 GLU cc_start: 0.7766 (pm20) cc_final: 0.7520 (pm20) REVERT: I 49 GLU cc_start: 0.8225 (tp30) cc_final: 0.8020 (tp30) REVERT: I 60 GLU cc_start: 0.8565 (tp30) cc_final: 0.8233 (tp30) REVERT: I 61 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8334 (mm-30) REVERT: I 64 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8231 (mt-10) REVERT: I 84 ASP cc_start: 0.8756 (m-30) cc_final: 0.8542 (m-30) REVERT: I 104 MET cc_start: 0.8887 (ttp) cc_final: 0.8568 (ttp) REVERT: I 108 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8789 (mmmm) REVERT: I 116 ASP cc_start: 0.8829 (m-30) cc_final: 0.8548 (m-30) REVERT: I 143 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8883 (mtmm) REVERT: I 147 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8682 (ttpp) REVERT: J 61 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8137 (mm-30) REVERT: J 64 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8204 (mt-10) REVERT: J 116 ASP cc_start: 0.8860 (m-30) cc_final: 0.8628 (m-30) REVERT: J 140 GLU cc_start: 0.7932 (mp0) cc_final: 0.7401 (mp0) REVERT: J 143 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8923 (mtmm) REVERT: J 147 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8542 (ttpp) REVERT: J 157 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7759 (ptp-170) REVERT: K 45 ASP cc_start: 0.8678 (p0) cc_final: 0.8361 (p0) REVERT: K 60 GLU cc_start: 0.8498 (tp30) cc_final: 0.8191 (tp30) REVERT: K 61 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8144 (mm-30) REVERT: K 63 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7988 (ttp-110) REVERT: K 68 ARG cc_start: 0.8736 (ptp-110) cc_final: 0.8404 (ptp90) REVERT: K 84 ASP cc_start: 0.8582 (m-30) cc_final: 0.8256 (m-30) REVERT: K 86 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8561 (mmmm) REVERT: K 116 ASP cc_start: 0.8860 (m-30) cc_final: 0.8572 (m-30) REVERT: K 147 LYS cc_start: 0.8883 (ttpp) cc_final: 0.8589 (ttpp) REVERT: L 45 ASP cc_start: 0.8775 (p0) cc_final: 0.8231 (p0) REVERT: L 60 GLU cc_start: 0.8617 (tp30) cc_final: 0.8346 (tp30) REVERT: L 64 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8319 (mt-10) REVERT: L 101 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8576 (mtpt) REVERT: L 104 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8428 (ttp) REVERT: L 116 ASP cc_start: 0.8874 (m-30) cc_final: 0.8647 (m-30) REVERT: L 140 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8038 (mp0) REVERT: L 147 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8610 (ttpp) REVERT: L 167 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8150 (tt0) REVERT: M 42 ASP cc_start: 0.8516 (t70) cc_final: 0.7998 (t70) REVERT: M 49 GLU cc_start: 0.8324 (tp30) cc_final: 0.8017 (tp30) REVERT: M 60 GLU cc_start: 0.8593 (tp30) cc_final: 0.8272 (tp30) REVERT: M 61 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8467 (mm-30) REVERT: M 64 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8180 (mt-10) REVERT: M 101 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8541 (mtpt) REVERT: M 116 ASP cc_start: 0.8844 (m-30) cc_final: 0.8624 (m-30) REVERT: M 140 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8214 (mm-30) REVERT: M 143 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8933 (mtmm) REVERT: M 147 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8479 (ttpp) REVERT: M 150 ASP cc_start: 0.8539 (m-30) cc_final: 0.8240 (m-30) REVERT: N 17 GLU cc_start: 0.8678 (tt0) cc_final: 0.8442 (tt0) REVERT: N 34 TYR cc_start: 0.9417 (m-10) cc_final: 0.9141 (m-10) REVERT: N 43 ARG cc_start: 0.8578 (mtm180) cc_final: 0.8283 (mtm180) REVERT: N 45 ASP cc_start: 0.8689 (p0) cc_final: 0.8286 (p0) REVERT: N 60 GLU cc_start: 0.8551 (tp30) cc_final: 0.8190 (tp30) REVERT: N 61 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8502 (mm-30) REVERT: N 64 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8279 (mt-10) REVERT: N 79 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7838 (mmp80) REVERT: N 84 ASP cc_start: 0.8779 (m-30) cc_final: 0.8502 (m-30) REVERT: N 86 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8622 (mmmm) REVERT: N 92 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7527 (tm-30) REVERT: N 104 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8498 (ttp) REVERT: N 107 GLU cc_start: 0.8757 (tp30) cc_final: 0.8242 (tp30) REVERT: N 116 ASP cc_start: 0.8845 (m-30) cc_final: 0.8607 (m-30) REVERT: N 140 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8148 (mm-30) REVERT: N 141 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8547 (tp30) REVERT: N 147 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8530 (ttpp) REVERT: O 34 TYR cc_start: 0.9474 (m-10) cc_final: 0.9221 (m-10) REVERT: O 43 ARG cc_start: 0.8332 (mtm180) cc_final: 0.8123 (mtm180) REVERT: O 45 ASP cc_start: 0.8589 (p0) cc_final: 0.8328 (p0) REVERT: O 49 GLU cc_start: 0.8227 (tp30) cc_final: 0.8003 (tp30) REVERT: O 61 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8239 (mm-30) REVERT: O 64 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8296 (mt-10) REVERT: O 79 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7840 (mmt-90) REVERT: O 116 ASP cc_start: 0.8836 (m-30) cc_final: 0.8618 (m-30) REVERT: O 140 GLU cc_start: 0.8094 (mp0) cc_final: 0.7537 (mp0) REVERT: O 147 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8619 (ttpp) REVERT: P 15 ASP cc_start: 0.8589 (p0) cc_final: 0.8298 (p0) REVERT: P 22 SER cc_start: 0.9313 (m) cc_final: 0.9024 (p) REVERT: P 42 ASP cc_start: 0.8495 (t70) cc_final: 0.8112 (t70) REVERT: P 61 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8410 (mm-30) REVERT: P 64 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8233 (mt-10) REVERT: P 86 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8572 (tppt) REVERT: P 104 MET cc_start: 0.8842 (ttp) cc_final: 0.8466 (ttp) REVERT: P 116 ASP cc_start: 0.8857 (m-30) cc_final: 0.8569 (m-30) REVERT: P 147 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8605 (ttpp) REVERT: Q 34 TYR cc_start: 0.9465 (m-10) cc_final: 0.9240 (m-10) REVERT: Q 61 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8183 (mm-30) REVERT: Q 64 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8159 (mt-10) REVERT: Q 104 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8520 (ttp) REVERT: Q 116 ASP cc_start: 0.8831 (m-30) cc_final: 0.8611 (m-30) REVERT: Q 140 GLU cc_start: 0.8128 (mp0) cc_final: 0.7572 (mp0) REVERT: Q 144 LEU cc_start: 0.9065 (tp) cc_final: 0.8789 (tm) REVERT: Q 162 GLU cc_start: 0.7780 (pm20) cc_final: 0.7551 (pm20) REVERT: R 42 ASP cc_start: 0.8590 (t70) cc_final: 0.7971 (t70) REVERT: R 49 GLU cc_start: 0.8225 (tp30) cc_final: 0.7984 (tp30) REVERT: R 57 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8427 (mm-30) REVERT: R 60 GLU cc_start: 0.8636 (tp30) cc_final: 0.8194 (tp30) REVERT: R 61 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8164 (mm-30) REVERT: R 62 LYS cc_start: 0.8862 (mmpt) cc_final: 0.8649 (mmpt) REVERT: R 107 GLU cc_start: 0.8700 (tp30) cc_final: 0.8430 (mm-30) REVERT: R 116 ASP cc_start: 0.8852 (m-30) cc_final: 0.8627 (m-30) REVERT: R 147 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8652 (ttpp) REVERT: R 148 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8956 (mtm) REVERT: R 162 GLU cc_start: 0.7535 (pm20) cc_final: 0.7301 (pm20) REVERT: R 167 GLU cc_start: 0.8568 (tt0) cc_final: 0.8259 (tt0) REVERT: S 42 ASP cc_start: 0.8448 (t70) cc_final: 0.7973 (t70) REVERT: S 84 ASP cc_start: 0.8753 (m-30) cc_final: 0.8519 (m-30) REVERT: S 86 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8659 (tppt) REVERT: S 104 MET cc_start: 0.8789 (ttp) cc_final: 0.8440 (ttp) REVERT: S 116 ASP cc_start: 0.8806 (m-30) cc_final: 0.8577 (m-30) REVERT: S 147 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8658 (ttpp) REVERT: T 45 ASP cc_start: 0.8603 (p0) cc_final: 0.8377 (p0) REVERT: T 104 MET cc_start: 0.8865 (ttp) cc_final: 0.8460 (ttp) REVERT: T 116 ASP cc_start: 0.8806 (m-30) cc_final: 0.8557 (m-30) REVERT: T 162 GLU cc_start: 0.7606 (pm20) cc_final: 0.7390 (pm20) REVERT: U 42 ASP cc_start: 0.8437 (t70) cc_final: 0.8046 (t70) REVERT: U 49 GLU cc_start: 0.8313 (tp30) cc_final: 0.7958 (tp30) REVERT: U 61 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8422 (mm-30) REVERT: U 64 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8314 (mt-10) REVERT: U 104 MET cc_start: 0.8805 (ttp) cc_final: 0.8417 (ttp) REVERT: U 107 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8525 (mm-30) REVERT: U 116 ASP cc_start: 0.8819 (m-30) cc_final: 0.8585 (m-30) REVERT: U 147 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8655 (ttpp) REVERT: U 162 GLU cc_start: 0.7564 (pm20) cc_final: 0.7247 (pm20) REVERT: U 167 GLU cc_start: 0.8610 (tt0) cc_final: 0.8265 (tt0) REVERT: V 43 ARG cc_start: 0.8510 (mtm180) cc_final: 0.8273 (mtm180) REVERT: V 45 ASP cc_start: 0.8678 (p0) cc_final: 0.8398 (p0) REVERT: V 60 GLU cc_start: 0.8644 (tp30) cc_final: 0.8264 (tp30) REVERT: V 61 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7975 (mm-30) REVERT: V 64 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8319 (mt-10) REVERT: V 87 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8730 (ptpp) REVERT: V 140 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8014 (mp0) REVERT: V 147 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8658 (ttpp) REVERT: W 22 SER cc_start: 0.9319 (m) cc_final: 0.9026 (p) REVERT: W 61 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8403 (mm-30) REVERT: W 64 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8332 (mt-10) REVERT: W 79 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7879 (mmt-90) REVERT: W 104 MET cc_start: 0.8817 (ttp) cc_final: 0.8400 (ttp) REVERT: W 108 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8687 (mmmm) REVERT: W 116 ASP cc_start: 0.8863 (m-30) cc_final: 0.8643 (m-30) REVERT: W 140 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8024 (mp0) REVERT: W 147 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8632 (ttpp) REVERT: W 162 GLU cc_start: 0.7584 (pm20) cc_final: 0.7375 (pm20) REVERT: W 167 GLU cc_start: 0.8469 (tt0) cc_final: 0.8204 (tt0) REVERT: X 15 ASP cc_start: 0.8467 (p0) cc_final: 0.8180 (p0) REVERT: X 64 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8351 (mt-10) REVERT: X 84 ASP cc_start: 0.8835 (m-30) cc_final: 0.8541 (m-30) REVERT: X 86 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8649 (tppt) REVERT: X 112 GLN cc_start: 0.9102 (tp40) cc_final: 0.8369 (tp-100) REVERT: X 116 ASP cc_start: 0.8888 (m-30) cc_final: 0.8325 (m-30) REVERT: X 124 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8726 (mmt-90) REVERT: X 140 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8013 (mp0) REVERT: X 147 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8568 (ttpp) REVERT: X 167 GLU cc_start: 0.8517 (tt0) cc_final: 0.8302 (tt0) outliers start: 110 outliers final: 53 residues processed: 1390 average time/residue: 0.9079 time to fit residues: 1442.5318 Evaluate side-chains 1297 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1233 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 7 GLN Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 157 ARG Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain S residue 72 MET Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 155 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 240 optimal weight: 0.9980 chunk 326 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 375 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 10 GLN B 7 GLN C 111 ASN D 7 GLN E 7 GLN F 7 GLN G 7 GLN G 29 GLN H 7 GLN I 7 GLN K 7 GLN L 7 GLN L 29 GLN M 7 GLN N 7 GLN O 7 GLN O 10 GLN O 111 ASN P 53 HIS Q 29 GLN R 10 GLN S 7 GLN U 7 GLN W 7 GLN W 29 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079704 restraints weight = 58258.915| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.60 r_work: 0.2970 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33838 Z= 0.160 Angle : 0.615 10.578 45524 Z= 0.315 Chirality : 0.038 0.179 4872 Planarity : 0.004 0.044 5974 Dihedral : 6.773 89.288 4608 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.57 % Favored : 98.28 % Rotamer: Outliers : 3.19 % Allowed : 25.14 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.13), residues: 4080 helix: 2.54 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.01 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 63 TYR 0.025 0.002 TYR D 66 PHE 0.020 0.002 PHE T 137 TRP 0.005 0.001 TRP R 93 HIS 0.006 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00362 (33838) covalent geometry : angle 0.61550 (45524) hydrogen bonds : bond 0.03655 ( 2675) hydrogen bonds : angle 3.71729 ( 8025) *********************** 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 1441 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1330 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8546 (t70) cc_final: 0.8038 (t70) REVERT: A 49 GLU cc_start: 0.8327 (tp30) cc_final: 0.8009 (tp30) REVERT: A 60 GLU cc_start: 0.8531 (tp30) cc_final: 0.8257 (tp30) REVERT: A 61 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 86 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8676 (tppt) REVERT: A 104 MET cc_start: 0.9033 (tpp) cc_final: 0.8665 (tpp) REVERT: A 108 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8793 (mmmm) REVERT: A 147 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8583 (ttpp) REVERT: A 150 ASP cc_start: 0.8546 (m-30) cc_final: 0.8288 (m-30) REVERT: B 45 ASP cc_start: 0.8624 (p0) cc_final: 0.8383 (p0) REVERT: B 61 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 63 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: B 64 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8252 (mt-10) REVERT: B 86 LYS cc_start: 0.8821 (mtpm) cc_final: 0.8347 (mmmm) REVERT: B 104 MET cc_start: 0.8834 (ttp) cc_final: 0.8485 (ttp) REVERT: B 116 ASP cc_start: 0.8850 (m-30) cc_final: 0.8567 (m-30) REVERT: B 143 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8878 (mtmm) REVERT: B 147 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8635 (ttpp) REVERT: C 42 ASP cc_start: 0.8619 (t70) cc_final: 0.8014 (t70) REVERT: C 60 GLU cc_start: 0.8565 (tp30) cc_final: 0.8188 (tp30) REVERT: C 68 ARG cc_start: 0.8748 (ptp90) cc_final: 0.8445 (ptp90) REVERT: C 86 LYS cc_start: 0.8924 (tppt) cc_final: 0.8593 (tppt) REVERT: C 104 MET cc_start: 0.8815 (ttp) cc_final: 0.8380 (ttp) REVERT: C 112 GLN cc_start: 0.9053 (tp40) cc_final: 0.8224 (tp-100) REVERT: C 116 ASP cc_start: 0.8867 (m-30) cc_final: 0.8340 (m-30) REVERT: C 140 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8027 (mp0) REVERT: C 147 LYS cc_start: 0.8882 (ttpp) cc_final: 0.8545 (ttpp) REVERT: D 15 ASP cc_start: 0.8379 (p0) cc_final: 0.8110 (p0) REVERT: D 22 SER cc_start: 0.9316 (m) cc_final: 0.9019 (p) REVERT: D 42 ASP cc_start: 0.8530 (t70) cc_final: 0.8170 (t70) REVERT: D 45 ASP cc_start: 0.8446 (p0) cc_final: 0.8125 (p0) REVERT: D 60 GLU cc_start: 0.8536 (tp30) cc_final: 0.8304 (tp30) REVERT: D 61 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8264 (mm-30) REVERT: D 64 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8256 (mm-30) REVERT: D 116 ASP cc_start: 0.8880 (m-30) cc_final: 0.8647 (m-30) REVERT: D 140 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7999 (pp20) REVERT: D 147 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8606 (ttpp) REVERT: D 162 GLU cc_start: 0.7643 (pm20) cc_final: 0.7379 (pm20) REVERT: D 167 GLU cc_start: 0.8474 (tt0) cc_final: 0.8195 (tt0) REVERT: E 17 GLU cc_start: 0.8479 (tt0) cc_final: 0.8193 (tt0) REVERT: E 42 ASP cc_start: 0.8398 (t70) cc_final: 0.7766 (t70) REVERT: E 86 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8546 (mmmm) REVERT: E 108 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8737 (mmmm) REVERT: E 116 ASP cc_start: 0.8850 (m-30) cc_final: 0.8525 (m-30) REVERT: F 61 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8045 (mm-30) REVERT: F 104 MET cc_start: 0.8717 (ttp) cc_final: 0.8335 (ttp) REVERT: F 107 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8666 (tp30) REVERT: F 116 ASP cc_start: 0.8815 (m-30) cc_final: 0.8517 (m-30) REVERT: F 147 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8647 (ttpp) REVERT: G 42 ASP cc_start: 0.8451 (t70) cc_final: 0.8066 (t70) REVERT: G 49 GLU cc_start: 0.8190 (tp30) cc_final: 0.7969 (tp30) REVERT: G 61 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8275 (mm-30) REVERT: G 84 ASP cc_start: 0.8721 (m-30) cc_final: 0.8510 (m-30) REVERT: G 86 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8421 (tppt) REVERT: H 15 ASP cc_start: 0.8671 (p0) cc_final: 0.8078 (p0) REVERT: H 42 ASP cc_start: 0.8414 (t70) cc_final: 0.8049 (t70) REVERT: H 60 GLU cc_start: 0.8611 (tp30) cc_final: 0.8291 (tp30) REVERT: H 61 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8426 (mm-30) REVERT: H 64 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8351 (mt-10) REVERT: H 68 ARG cc_start: 0.8587 (ttm110) cc_final: 0.8373 (ttm110) REVERT: H 74 ASN cc_start: 0.9106 (m-40) cc_final: 0.8487 (m110) REVERT: H 104 MET cc_start: 0.8669 (ttp) cc_final: 0.8386 (tpp) REVERT: H 116 ASP cc_start: 0.8837 (m-30) cc_final: 0.8548 (m-30) REVERT: H 124 ARG cc_start: 0.8624 (mmt-90) cc_final: 0.8345 (mtp85) REVERT: H 140 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8086 (mp0) REVERT: H 147 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8588 (ttpp) REVERT: H 162 GLU cc_start: 0.7721 (pm20) cc_final: 0.7513 (pm20) REVERT: I 7 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: I 49 GLU cc_start: 0.8260 (tp30) cc_final: 0.8024 (tp30) REVERT: I 60 GLU cc_start: 0.8528 (tp30) cc_final: 0.8245 (tp30) REVERT: I 61 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8289 (mm-30) REVERT: I 64 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8272 (mt-10) REVERT: I 81 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8722 (mm) REVERT: I 84 ASP cc_start: 0.8737 (m-30) cc_final: 0.8510 (m-30) REVERT: I 104 MET cc_start: 0.8891 (ttp) cc_final: 0.8602 (ttp) REVERT: I 108 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8735 (mmmm) REVERT: I 116 ASP cc_start: 0.8813 (m-30) cc_final: 0.8505 (m-30) REVERT: I 140 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7996 (mp0) REVERT: I 143 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8880 (mtpt) REVERT: I 147 LYS cc_start: 0.8967 (ttpp) cc_final: 0.8637 (ttpp) REVERT: J 61 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8227 (mm-30) REVERT: J 64 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8357 (mt-10) REVERT: J 116 ASP cc_start: 0.8858 (m-30) cc_final: 0.8600 (m-30) REVERT: J 140 GLU cc_start: 0.7900 (mp0) cc_final: 0.7359 (mp0) REVERT: J 143 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8850 (mtmm) REVERT: J 147 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8521 (ttpp) REVERT: J 172 ARG cc_start: 0.9239 (mmm160) cc_final: 0.8959 (mmm160) REVERT: K 10 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8792 (tt0) REVERT: K 45 ASP cc_start: 0.8600 (p0) cc_final: 0.8270 (p0) REVERT: K 61 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8117 (mm-30) REVERT: K 68 ARG cc_start: 0.8674 (ptp-110) cc_final: 0.8359 (ptp90) REVERT: K 84 ASP cc_start: 0.8580 (m-30) cc_final: 0.8213 (m-30) REVERT: K 86 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8612 (mmmm) REVERT: K 112 GLN cc_start: 0.9060 (tp40) cc_final: 0.8291 (tp-100) REVERT: K 116 ASP cc_start: 0.8858 (m-30) cc_final: 0.8348 (m-30) REVERT: K 140 GLU cc_start: 0.8415 (pp20) cc_final: 0.8199 (pp20) REVERT: K 147 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8567 (ttpp) REVERT: L 45 ASP cc_start: 0.8710 (p0) cc_final: 0.8186 (p0) REVERT: L 49 GLU cc_start: 0.8275 (tp30) cc_final: 0.8040 (tp30) REVERT: L 60 GLU cc_start: 0.8564 (tp30) cc_final: 0.8280 (tp30) REVERT: L 61 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8142 (mm-30) REVERT: L 64 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8300 (mt-10) REVERT: L 87 LYS cc_start: 0.9090 (ptmm) cc_final: 0.8822 (ptmm) REVERT: L 101 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8460 (mtpt) REVERT: L 104 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8450 (ttp) REVERT: L 116 ASP cc_start: 0.8887 (m-30) cc_final: 0.8567 (m-30) REVERT: L 140 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8033 (mp0) REVERT: L 147 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8582 (ttpp) REVERT: M 42 ASP cc_start: 0.8501 (t70) cc_final: 0.8015 (t70) REVERT: M 49 GLU cc_start: 0.8314 (tp30) cc_final: 0.8025 (tp30) REVERT: M 60 GLU cc_start: 0.8568 (tp30) cc_final: 0.8262 (tp30) REVERT: M 61 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8444 (mm-30) REVERT: M 64 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8320 (mt-10) REVERT: M 101 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8307 (mppt) REVERT: M 116 ASP cc_start: 0.8850 (m-30) cc_final: 0.8587 (m-30) REVERT: M 140 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8141 (mm-30) REVERT: M 150 ASP cc_start: 0.8498 (m-30) cc_final: 0.8199 (m-30) REVERT: N 34 TYR cc_start: 0.9396 (m-10) cc_final: 0.9106 (m-10) REVERT: N 43 ARG cc_start: 0.8493 (mtm180) cc_final: 0.8151 (mtm180) REVERT: N 45 ASP cc_start: 0.8649 (p0) cc_final: 0.8239 (p0) REVERT: N 49 GLU cc_start: 0.8295 (tp30) cc_final: 0.8025 (tp30) REVERT: N 60 GLU cc_start: 0.8561 (tp30) cc_final: 0.8172 (tp30) REVERT: N 61 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8460 (mm-30) REVERT: N 64 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8129 (mt-10) REVERT: N 79 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7767 (mmp80) REVERT: N 84 ASP cc_start: 0.8763 (m-30) cc_final: 0.8470 (m-30) REVERT: N 86 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8599 (mmmm) REVERT: N 104 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8460 (ttp) REVERT: N 116 ASP cc_start: 0.8834 (m-30) cc_final: 0.8523 (m-30) REVERT: N 140 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8105 (mm-30) REVERT: N 147 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8513 (ttpp) REVERT: O 45 ASP cc_start: 0.8499 (p0) cc_final: 0.8141 (p0) REVERT: O 49 GLU cc_start: 0.8204 (tp30) cc_final: 0.7971 (tp30) REVERT: O 61 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8224 (mm-30) REVERT: O 64 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8303 (mt-10) REVERT: O 79 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7826 (mmp80) REVERT: O 116 ASP cc_start: 0.8866 (m-30) cc_final: 0.8606 (m-30) REVERT: O 140 GLU cc_start: 0.8061 (mp0) cc_final: 0.7539 (mp0) REVERT: O 147 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8523 (ttpp) REVERT: P 17 GLU cc_start: 0.8488 (tt0) cc_final: 0.8225 (tt0) REVERT: P 22 SER cc_start: 0.9277 (m) cc_final: 0.9001 (p) REVERT: P 45 ASP cc_start: 0.8873 (p0) cc_final: 0.8642 (p0) REVERT: P 61 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8398 (mm-30) REVERT: P 64 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8352 (mt-10) REVERT: P 86 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8640 (tppt) REVERT: P 104 MET cc_start: 0.8690 (ttp) cc_final: 0.8403 (ttp) REVERT: P 107 GLU cc_start: 0.9049 (tp30) cc_final: 0.8790 (mm-30) REVERT: P 112 GLN cc_start: 0.9079 (tp40) cc_final: 0.8247 (tp-100) REVERT: P 116 ASP cc_start: 0.8875 (m-30) cc_final: 0.8290 (m-30) REVERT: P 141 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8369 (mm-30) REVERT: P 147 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8569 (ttpp) REVERT: P 162 GLU cc_start: 0.7734 (pm20) cc_final: 0.7464 (pm20) REVERT: P 167 GLU cc_start: 0.8555 (tt0) cc_final: 0.8306 (tt0) REVERT: Q 34 TYR cc_start: 0.9430 (m-10) cc_final: 0.9195 (m-10) REVERT: Q 45 ASP cc_start: 0.8841 (p0) cc_final: 0.8584 (p0) REVERT: Q 61 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8225 (mm-30) REVERT: Q 64 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8284 (mt-10) REVERT: Q 104 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8436 (ttp) REVERT: Q 116 ASP cc_start: 0.8866 (m-30) cc_final: 0.8553 (m-30) REVERT: Q 140 GLU cc_start: 0.8189 (mp0) cc_final: 0.7617 (mp0) REVERT: Q 162 GLU cc_start: 0.7744 (pm20) cc_final: 0.7506 (pm20) REVERT: R 42 ASP cc_start: 0.8592 (t70) cc_final: 0.7909 (t70) REVERT: R 45 ASP cc_start: 0.8798 (p0) cc_final: 0.8520 (p0) REVERT: R 49 GLU cc_start: 0.8190 (tp30) cc_final: 0.7952 (tp30) REVERT: R 60 GLU cc_start: 0.8528 (tp30) cc_final: 0.8224 (tp30) REVERT: R 61 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8166 (mm-30) REVERT: R 116 ASP cc_start: 0.8874 (m-30) cc_final: 0.8629 (m-30) REVERT: R 147 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8618 (ttpp) REVERT: R 148 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8980 (mtm) REVERT: R 162 GLU cc_start: 0.7570 (pm20) cc_final: 0.7332 (pm20) REVERT: S 42 ASP cc_start: 0.8507 (t70) cc_final: 0.7993 (t70) REVERT: S 74 ASN cc_start: 0.9053 (m-40) cc_final: 0.8441 (m110) REVERT: S 84 ASP cc_start: 0.8629 (m-30) cc_final: 0.8404 (m-30) REVERT: S 91 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: S 104 MET cc_start: 0.8703 (ttp) cc_final: 0.8358 (ttp) REVERT: S 116 ASP cc_start: 0.8844 (m-30) cc_final: 0.8553 (m-30) REVERT: S 147 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8557 (ttpp) REVERT: S 162 GLU cc_start: 0.7517 (mp0) cc_final: 0.7161 (pm20) REVERT: T 104 MET cc_start: 0.8782 (ttp) cc_final: 0.8378 (ttp) REVERT: T 112 GLN cc_start: 0.9127 (tp40) cc_final: 0.8358 (tp-100) REVERT: T 116 ASP cc_start: 0.8840 (m-30) cc_final: 0.8252 (m-30) REVERT: T 140 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7930 (mp0) REVERT: T 162 GLU cc_start: 0.7653 (pm20) cc_final: 0.7417 (pm20) REVERT: U 42 ASP cc_start: 0.8353 (t70) cc_final: 0.8012 (t70) REVERT: U 49 GLU cc_start: 0.8297 (tp30) cc_final: 0.7975 (tp30) REVERT: U 61 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8337 (mm-30) REVERT: U 64 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8196 (mt-10) REVERT: U 104 MET cc_start: 0.8609 (ttp) cc_final: 0.8192 (ttp) REVERT: U 116 ASP cc_start: 0.8824 (m-30) cc_final: 0.8520 (m-30) REVERT: U 147 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8611 (ttpp) REVERT: V 43 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8218 (mtm180) REVERT: V 45 ASP cc_start: 0.8645 (p0) cc_final: 0.8325 (p0) REVERT: V 60 GLU cc_start: 0.8637 (tp30) cc_final: 0.8330 (tp30) REVERT: V 61 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7917 (mm-30) REVERT: V 64 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8279 (mt-10) REVERT: V 84 ASP cc_start: 0.8757 (m-30) cc_final: 0.8537 (m-30) REVERT: V 86 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8694 (mmpt) REVERT: V 87 LYS cc_start: 0.9007 (ptpp) cc_final: 0.8784 (ptpp) REVERT: V 140 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7941 (mp0) REVERT: V 147 LYS cc_start: 0.8962 (ttpp) cc_final: 0.8614 (ttpp) REVERT: W 57 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8428 (mm-30) REVERT: W 61 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8310 (mm-30) REVERT: W 64 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8374 (mt-10) REVERT: W 79 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7943 (mmt-90) REVERT: W 104 MET cc_start: 0.8753 (ttp) cc_final: 0.8309 (ttp) REVERT: W 107 GLU cc_start: 0.8983 (tp30) cc_final: 0.8586 (tp30) REVERT: W 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8598 (m-30) REVERT: W 140 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7987 (mp0) REVERT: W 147 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8617 (ttpp) REVERT: W 162 GLU cc_start: 0.7586 (pm20) cc_final: 0.7362 (pm20) REVERT: W 167 GLU cc_start: 0.8476 (tt0) cc_final: 0.8164 (tt0) REVERT: X 15 ASP cc_start: 0.8365 (p0) cc_final: 0.8145 (p0) REVERT: X 45 ASP cc_start: 0.8784 (p0) cc_final: 0.8561 (p0) REVERT: X 60 GLU cc_start: 0.8636 (tp30) cc_final: 0.8235 (mm-30) REVERT: X 64 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8289 (mt-10) REVERT: X 84 ASP cc_start: 0.8828 (m-30) cc_final: 0.8490 (m-30) REVERT: X 87 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8295 (ttmm) REVERT: X 107 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8516 (mm-30) REVERT: X 109 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8873 (tttm) REVERT: X 112 GLN cc_start: 0.9084 (tp40) cc_final: 0.8285 (tp-100) REVERT: X 116 ASP cc_start: 0.8865 (m-30) cc_final: 0.8298 (m-30) REVERT: X 140 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8061 (mp0) REVERT: X 141 GLU cc_start: 0.8517 (tp30) cc_final: 0.8305 (mm-30) REVERT: X 147 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8475 (ttpp) REVERT: X 167 GLU cc_start: 0.8476 (tt0) cc_final: 0.8275 (tt0) outliers start: 111 outliers final: 58 residues processed: 1363 average time/residue: 0.9538 time to fit residues: 1486.8166 Evaluate side-chains 1328 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1257 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 7 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 10 GLN Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain S residue 72 MET Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 158 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 358 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 7 GLN D 7 GLN D 136 HIS E 7 GLN F 7 GLN F 10 GLN G 7 GLN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN H 7 GLN I 7 GLN I 10 GLN K 7 GLN L 7 GLN M 7 GLN N 7 GLN O 7 GLN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 HIS Q 29 GLN S 7 GLN U 7 GLN V 136 HIS ** W 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 136 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077971 restraints weight = 58614.115| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.61 r_work: 0.2931 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 33838 Z= 0.209 Angle : 0.647 10.332 45524 Z= 0.329 Chirality : 0.040 0.178 4872 Planarity : 0.004 0.043 5974 Dihedral : 6.733 86.266 4608 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.50 % Favored : 98.43 % Rotamer: Outliers : 3.10 % Allowed : 26.01 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.13), residues: 4080 helix: 2.49 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.99 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 63 TYR 0.025 0.002 TYR E 66 PHE 0.020 0.002 PHE T 137 TRP 0.005 0.001 TRP D 93 HIS 0.007 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00470 (33838) covalent geometry : angle 0.64676 (45524) hydrogen bonds : bond 0.03973 ( 2675) hydrogen bonds : angle 3.78473 ( 8025) *********************** 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 1389 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1281 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8350 (tp30) cc_final: 0.8032 (tp30) REVERT: A 60 GLU cc_start: 0.8570 (tp30) cc_final: 0.8266 (tp30) REVERT: A 61 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 86 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8640 (tppt) REVERT: A 108 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8801 (mmmm) REVERT: A 147 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8672 (ttmm) REVERT: A 150 ASP cc_start: 0.8574 (m-30) cc_final: 0.8316 (m-30) REVERT: B 45 ASP cc_start: 0.8647 (p0) cc_final: 0.8409 (p0) REVERT: B 61 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 64 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8286 (mt-10) REVERT: B 86 LYS cc_start: 0.8779 (mtpm) cc_final: 0.8343 (mmmm) REVERT: B 104 MET cc_start: 0.8861 (ttp) cc_final: 0.8517 (ttp) REVERT: B 116 ASP cc_start: 0.8844 (m-30) cc_final: 0.8533 (m-30) REVERT: B 140 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7994 (mp0) REVERT: B 147 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8674 (ttpp) REVERT: B 172 ARG cc_start: 0.9322 (mmm160) cc_final: 0.9116 (mmm160) REVERT: C 42 ASP cc_start: 0.8619 (t70) cc_final: 0.8116 (t70) REVERT: C 49 GLU cc_start: 0.8316 (tp30) cc_final: 0.8113 (tp30) REVERT: C 60 GLU cc_start: 0.8477 (tp30) cc_final: 0.8182 (tp30) REVERT: C 68 ARG cc_start: 0.8784 (ptp90) cc_final: 0.8252 (ptp90) REVERT: C 104 MET cc_start: 0.8852 (ttp) cc_final: 0.8566 (ttp) REVERT: C 116 ASP cc_start: 0.8882 (m-30) cc_final: 0.8630 (m-30) REVERT: C 140 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8090 (mp0) REVERT: C 147 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8661 (ttpp) REVERT: D 42 ASP cc_start: 0.8602 (t70) cc_final: 0.8102 (t70) REVERT: D 60 GLU cc_start: 0.8566 (tp30) cc_final: 0.8072 (tp30) REVERT: D 61 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8256 (mm-30) REVERT: D 63 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: D 116 ASP cc_start: 0.8860 (m-30) cc_final: 0.8614 (m-30) REVERT: D 124 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8591 (mmt-90) REVERT: D 140 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8189 (pp20) REVERT: D 147 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8588 (ttpp) REVERT: D 162 GLU cc_start: 0.7645 (pm20) cc_final: 0.7385 (pm20) REVERT: D 167 GLU cc_start: 0.8488 (tt0) cc_final: 0.8199 (tt0) REVERT: E 17 GLU cc_start: 0.8537 (tt0) cc_final: 0.8333 (tt0) REVERT: E 86 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8533 (tppt) REVERT: E 107 GLU cc_start: 0.8971 (tp30) cc_final: 0.8758 (mm-30) REVERT: E 108 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8819 (mmmm) REVERT: E 116 ASP cc_start: 0.8843 (m-30) cc_final: 0.8592 (m-30) REVERT: F 60 GLU cc_start: 0.8435 (tp30) cc_final: 0.7995 (pt0) REVERT: F 61 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7988 (mm-30) REVERT: F 104 MET cc_start: 0.8784 (ttp) cc_final: 0.8402 (ttp) REVERT: F 107 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8414 (mm-30) REVERT: F 116 ASP cc_start: 0.8832 (m-30) cc_final: 0.8516 (m-30) REVERT: F 141 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8549 (tp30) REVERT: F 147 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8690 (ttpp) REVERT: G 42 ASP cc_start: 0.8496 (t70) cc_final: 0.8236 (t70) REVERT: G 45 ASP cc_start: 0.8800 (p0) cc_final: 0.8538 (p0) REVERT: G 49 GLU cc_start: 0.8253 (tp30) cc_final: 0.8050 (tp30) REVERT: G 61 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8299 (mm-30) REVERT: G 84 ASP cc_start: 0.8743 (m-30) cc_final: 0.8505 (m-30) REVERT: G 86 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8476 (tppt) REVERT: G 162 GLU cc_start: 0.7606 (pm20) cc_final: 0.7390 (pm20) REVERT: H 42 ASP cc_start: 0.8472 (t70) cc_final: 0.8153 (t70) REVERT: H 49 GLU cc_start: 0.8228 (tp30) cc_final: 0.7954 (tp30) REVERT: H 61 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8407 (mm-30) REVERT: H 64 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8324 (mt-10) REVERT: H 68 ARG cc_start: 0.8646 (ttm110) cc_final: 0.8408 (ttm110) REVERT: H 84 ASP cc_start: 0.8695 (m-30) cc_final: 0.8472 (m-30) REVERT: H 104 MET cc_start: 0.8708 (ttp) cc_final: 0.8411 (tpp) REVERT: H 116 ASP cc_start: 0.8838 (m-30) cc_final: 0.8583 (m-30) REVERT: H 124 ARG cc_start: 0.8766 (mmt-90) cc_final: 0.8529 (mmt-90) REVERT: H 140 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8134 (mp0) REVERT: H 147 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8591 (ttpp) REVERT: H 162 GLU cc_start: 0.7751 (pm20) cc_final: 0.7509 (pm20) REVERT: I 49 GLU cc_start: 0.8235 (tp30) cc_final: 0.8003 (tp30) REVERT: I 60 GLU cc_start: 0.8565 (tp30) cc_final: 0.8291 (tp30) REVERT: I 61 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8362 (mm-30) REVERT: I 64 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8316 (mt-10) REVERT: I 84 ASP cc_start: 0.8723 (m-30) cc_final: 0.8521 (m-30) REVERT: I 104 MET cc_start: 0.8852 (ttp) cc_final: 0.8583 (ttp) REVERT: I 116 ASP cc_start: 0.8822 (m-30) cc_final: 0.8513 (m-30) REVERT: I 140 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7967 (mp0) REVERT: I 172 ARG cc_start: 0.9279 (mmm160) cc_final: 0.9045 (mmm160) REVERT: J 15 ASP cc_start: 0.8777 (p0) cc_final: 0.8378 (p0) REVERT: J 49 GLU cc_start: 0.8279 (tp30) cc_final: 0.7998 (tp30) REVERT: J 61 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8278 (mm-30) REVERT: J 64 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8359 (mt-10) REVERT: J 86 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8669 (mmpt) REVERT: J 116 ASP cc_start: 0.8845 (m-30) cc_final: 0.8588 (m-30) REVERT: J 124 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8487 (mtp85) REVERT: J 140 GLU cc_start: 0.7955 (mp0) cc_final: 0.7435 (mp0) REVERT: J 143 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8929 (mtmm) REVERT: J 147 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8586 (ttpp) REVERT: K 10 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8838 (tt0) REVERT: K 45 ASP cc_start: 0.8611 (p0) cc_final: 0.8389 (p0) REVERT: K 61 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8220 (mm-30) REVERT: K 68 ARG cc_start: 0.8738 (ptp-110) cc_final: 0.8410 (ptp90) REVERT: K 84 ASP cc_start: 0.8615 (m-30) cc_final: 0.8251 (m-30) REVERT: K 86 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8653 (mmmm) REVERT: K 116 ASP cc_start: 0.8868 (m-30) cc_final: 0.8570 (m-30) REVERT: K 140 GLU cc_start: 0.8397 (pp20) cc_final: 0.8123 (pp20) REVERT: K 147 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8638 (ttpp) REVERT: L 7 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: L 10 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: L 45 ASP cc_start: 0.8726 (p0) cc_final: 0.8467 (p0) REVERT: L 49 GLU cc_start: 0.8283 (tp30) cc_final: 0.7997 (tp30) REVERT: L 60 GLU cc_start: 0.8561 (tp30) cc_final: 0.8261 (tp30) REVERT: L 61 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8193 (mm-30) REVERT: L 101 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8493 (mtpt) REVERT: L 104 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8363 (ttp) REVERT: L 116 ASP cc_start: 0.8873 (m-30) cc_final: 0.8623 (m-30) REVERT: L 140 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8008 (mp0) REVERT: L 147 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8500 (ttpp) REVERT: M 42 ASP cc_start: 0.8485 (t70) cc_final: 0.8044 (t70) REVERT: M 49 GLU cc_start: 0.8340 (tp30) cc_final: 0.8022 (tp30) REVERT: M 60 GLU cc_start: 0.8582 (tp30) cc_final: 0.8256 (tp30) REVERT: M 64 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8327 (mt-10) REVERT: M 101 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8507 (mtpt) REVERT: M 116 ASP cc_start: 0.8819 (m-30) cc_final: 0.8575 (m-30) REVERT: M 140 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8235 (mm-30) REVERT: M 147 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8515 (ttpp) REVERT: N 7 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8870 (pt0) REVERT: N 43 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8143 (mtm180) REVERT: N 45 ASP cc_start: 0.8636 (p0) cc_final: 0.8197 (p0) REVERT: N 60 GLU cc_start: 0.8585 (tp30) cc_final: 0.8284 (tp30) REVERT: N 64 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8271 (mt-10) REVERT: N 79 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7743 (mmp80) REVERT: N 86 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8605 (mmmm) REVERT: N 87 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8214 (ttmm) REVERT: N 104 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8434 (ttp) REVERT: N 116 ASP cc_start: 0.8850 (m-30) cc_final: 0.8596 (m-30) REVERT: N 140 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8143 (mm-30) REVERT: N 147 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8615 (ttpp) REVERT: O 45 ASP cc_start: 0.8664 (p0) cc_final: 0.8445 (p0) REVERT: O 49 GLU cc_start: 0.8256 (tp30) cc_final: 0.8028 (tp30) REVERT: O 61 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8194 (mm-30) REVERT: O 64 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8343 (mt-10) REVERT: O 79 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7820 (mmp80) REVERT: O 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8618 (m-30) REVERT: O 140 GLU cc_start: 0.8138 (mp0) cc_final: 0.7622 (mp0) REVERT: O 147 LYS cc_start: 0.8917 (ttpt) cc_final: 0.8565 (ttpp) REVERT: P 15 ASP cc_start: 0.8760 (p0) cc_final: 0.8137 (p0) REVERT: P 17 GLU cc_start: 0.8566 (tt0) cc_final: 0.8252 (tt0) REVERT: P 22 SER cc_start: 0.9297 (m) cc_final: 0.9013 (p) REVERT: P 57 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8483 (mm-30) REVERT: P 60 GLU cc_start: 0.8613 (tp30) cc_final: 0.8189 (tp30) REVERT: P 61 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8434 (mm-30) REVERT: P 63 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8070 (ttm-80) REVERT: P 86 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8632 (tppt) REVERT: P 104 MET cc_start: 0.8758 (ttp) cc_final: 0.8396 (ttp) REVERT: P 116 ASP cc_start: 0.8868 (m-30) cc_final: 0.8565 (m-30) REVERT: P 147 LYS cc_start: 0.8990 (ttpt) cc_final: 0.8627 (ttpp) REVERT: P 162 GLU cc_start: 0.7726 (pm20) cc_final: 0.7447 (pm20) REVERT: P 167 GLU cc_start: 0.8535 (tt0) cc_final: 0.8312 (tt0) REVERT: Q 34 TYR cc_start: 0.9482 (m-10) cc_final: 0.9207 (m-10) REVERT: Q 49 GLU cc_start: 0.8165 (tp30) cc_final: 0.7887 (tp30) REVERT: Q 61 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8192 (mm-30) REVERT: Q 64 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8188 (mt-10) REVERT: Q 104 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8517 (ttp) REVERT: Q 116 ASP cc_start: 0.8851 (m-30) cc_final: 0.8521 (m-30) REVERT: Q 140 GLU cc_start: 0.8192 (mp0) cc_final: 0.7672 (mp0) REVERT: Q 144 LEU cc_start: 0.9048 (tp) cc_final: 0.8631 (tm) REVERT: Q 162 GLU cc_start: 0.7732 (pm20) cc_final: 0.7462 (pm20) REVERT: R 42 ASP cc_start: 0.8597 (t70) cc_final: 0.8244 (t70) REVERT: R 57 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8487 (mm-30) REVERT: R 60 GLU cc_start: 0.8546 (tp30) cc_final: 0.8338 (tp30) REVERT: R 61 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8256 (mm-30) REVERT: R 86 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8617 (mmpt) REVERT: R 107 GLU cc_start: 0.8864 (tp30) cc_final: 0.8501 (mm-30) REVERT: R 116 ASP cc_start: 0.8887 (m-30) cc_final: 0.8639 (m-30) REVERT: R 147 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8673 (ttpp) REVERT: R 148 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8981 (mtm) REVERT: R 162 GLU cc_start: 0.7621 (pm20) cc_final: 0.7378 (pm20) REVERT: R 167 GLU cc_start: 0.8608 (tt0) cc_final: 0.8244 (tt0) REVERT: S 22 SER cc_start: 0.9303 (m) cc_final: 0.9014 (p) REVERT: S 42 ASP cc_start: 0.8536 (t70) cc_final: 0.8044 (t70) REVERT: S 104 MET cc_start: 0.8807 (ttp) cc_final: 0.8420 (ttp) REVERT: S 116 ASP cc_start: 0.8781 (m-30) cc_final: 0.8533 (m-30) REVERT: S 147 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8600 (ttpp) REVERT: S 162 GLU cc_start: 0.7622 (mp0) cc_final: 0.7284 (pm20) REVERT: T 68 ARG cc_start: 0.8801 (ptp90) cc_final: 0.8292 (ptp90) REVERT: T 104 MET cc_start: 0.8847 (ttp) cc_final: 0.8496 (ttp) REVERT: T 116 ASP cc_start: 0.8829 (m-30) cc_final: 0.8567 (m-30) REVERT: T 140 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7955 (mp0) REVERT: T 162 GLU cc_start: 0.7690 (pm20) cc_final: 0.7395 (pm20) REVERT: U 42 ASP cc_start: 0.8466 (t70) cc_final: 0.8112 (t70) REVERT: U 49 GLU cc_start: 0.8338 (tp30) cc_final: 0.8013 (tp30) REVERT: U 61 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8356 (mm-30) REVERT: U 64 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8234 (mt-10) REVERT: U 104 MET cc_start: 0.8630 (ttp) cc_final: 0.8263 (ttp) REVERT: U 116 ASP cc_start: 0.8843 (m-30) cc_final: 0.8521 (m-30) REVERT: U 147 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8665 (ttpp) REVERT: V 43 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8239 (mtm180) REVERT: V 45 ASP cc_start: 0.8642 (p0) cc_final: 0.8309 (p0) REVERT: V 49 GLU cc_start: 0.8267 (tp30) cc_final: 0.7988 (tp30) REVERT: V 60 GLU cc_start: 0.8626 (tp30) cc_final: 0.8297 (tp30) REVERT: V 61 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8082 (mm-30) REVERT: V 64 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8309 (mt-10) REVERT: V 86 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8693 (mmpt) REVERT: V 108 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8832 (mmmm) REVERT: V 140 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7962 (mp0) REVERT: V 147 LYS cc_start: 0.9005 (ttpp) cc_final: 0.8621 (ttpp) REVERT: W 61 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8356 (mm-30) REVERT: W 64 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8338 (mt-10) REVERT: W 79 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8004 (mmt-90) REVERT: W 87 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8465 (ttmm) REVERT: W 104 MET cc_start: 0.8804 (ttp) cc_final: 0.8400 (ttp) REVERT: W 116 ASP cc_start: 0.8845 (m-30) cc_final: 0.8603 (m-30) REVERT: W 140 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8055 (mp0) REVERT: W 147 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8601 (ttpp) REVERT: W 162 GLU cc_start: 0.7646 (pm20) cc_final: 0.7428 (pm20) REVERT: X 64 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8197 (mt-10) REVERT: X 108 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8803 (mmmm) REVERT: X 109 LYS cc_start: 0.9256 (ttmt) cc_final: 0.8914 (tttm) REVERT: X 116 ASP cc_start: 0.8881 (m-30) cc_final: 0.8640 (m-30) REVERT: X 140 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7999 (mp0) outliers start: 108 outliers final: 43 residues processed: 1313 average time/residue: 0.8427 time to fit residues: 1267.4077 Evaluate side-chains 1283 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 1227 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 10 GLN Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 GLN Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 7 GLN Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 244 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 303 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN D 7 GLN E 7 GLN F 7 GLN F 136 HIS G 7 GLN G 10 GLN G 29 GLN I 75 GLN K 7 GLN L 7 GLN M 7 GLN N 7 GLN O 7 GLN O 10 GLN P 53 HIS Q 29 GLN S 7 GLN W 7 GLN ** W 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 136 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081757 restraints weight = 58436.738| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.62 r_work: 0.3003 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33838 Z= 0.146 Angle : 0.632 10.151 45524 Z= 0.324 Chirality : 0.039 0.184 4872 Planarity : 0.004 0.046 5974 Dihedral : 6.305 89.609 4602 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 2.47 % Allowed : 27.70 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.13), residues: 4080 helix: 2.63 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.07 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 63 TYR 0.025 0.002 TYR K 66 PHE 0.016 0.002 PHE T 137 TRP 0.004 0.001 TRP D 93 HIS 0.007 0.001 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00335 (33838) covalent geometry : angle 0.63192 (45524) hydrogen bonds : bond 0.03473 ( 2675) hydrogen bonds : angle 3.74400 ( 8025) *********************** 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 1395 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1309 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8581 (pm20) REVERT: A 42 ASP cc_start: 0.8510 (t70) cc_final: 0.7939 (t70) REVERT: A 49 GLU cc_start: 0.8266 (tp30) cc_final: 0.8006 (tp30) REVERT: A 60 GLU cc_start: 0.8498 (tp30) cc_final: 0.8175 (tp30) REVERT: A 61 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8166 (mm-30) REVERT: A 84 ASP cc_start: 0.8614 (m-30) cc_final: 0.8334 (m-30) REVERT: A 104 MET cc_start: 0.8901 (tpp) cc_final: 0.8594 (tpp) REVERT: A 108 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8774 (mmmm) REVERT: A 147 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8627 (ttmm) REVERT: A 150 ASP cc_start: 0.8538 (m-30) cc_final: 0.8293 (m-30) REVERT: B 45 ASP cc_start: 0.8605 (p0) cc_final: 0.8335 (p0) REVERT: B 61 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7981 (mm-30) REVERT: B 86 LYS cc_start: 0.8746 (mtpm) cc_final: 0.8288 (mmmm) REVERT: B 104 MET cc_start: 0.8827 (ttp) cc_final: 0.8435 (ttp) REVERT: B 112 GLN cc_start: 0.9078 (tp40) cc_final: 0.8271 (tp-100) REVERT: B 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8271 (m-30) REVERT: B 140 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7961 (mp0) REVERT: B 143 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8924 (mtmm) REVERT: B 147 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8632 (ttpp) REVERT: B 172 ARG cc_start: 0.9297 (mmm160) cc_final: 0.9084 (mmm160) REVERT: C 42 ASP cc_start: 0.8538 (t70) cc_final: 0.8079 (t70) REVERT: C 60 GLU cc_start: 0.8465 (tp30) cc_final: 0.8154 (tp30) REVERT: C 68 ARG cc_start: 0.8721 (ptp90) cc_final: 0.8232 (ptp90) REVERT: C 104 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8199 (ttp) REVERT: C 112 GLN cc_start: 0.9062 (tp40) cc_final: 0.8331 (tp40) REVERT: C 116 ASP cc_start: 0.8909 (m-30) cc_final: 0.8490 (m-30) REVERT: C 140 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8084 (mp0) REVERT: C 147 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8643 (ttpp) REVERT: D 22 SER cc_start: 0.9306 (m) cc_final: 0.9017 (p) REVERT: D 42 ASP cc_start: 0.8549 (t70) cc_final: 0.8046 (t70) REVERT: D 45 ASP cc_start: 0.8590 (p0) cc_final: 0.8378 (p0) REVERT: D 61 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8141 (mm-30) REVERT: D 64 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8018 (mt-10) REVERT: D 112 GLN cc_start: 0.9081 (tp40) cc_final: 0.8229 (tp-100) REVERT: D 116 ASP cc_start: 0.8887 (m-30) cc_final: 0.8366 (m-30) REVERT: D 140 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8170 (pp20) REVERT: D 147 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8541 (ttpp) REVERT: D 162 GLU cc_start: 0.7671 (pm20) cc_final: 0.7349 (pm20) REVERT: E 17 GLU cc_start: 0.8391 (tt0) cc_final: 0.8190 (tt0) REVERT: E 42 ASP cc_start: 0.8339 (t70) cc_final: 0.7649 (t70) REVERT: E 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8537 (m-30) REVERT: E 141 GLU cc_start: 0.8948 (tp30) cc_final: 0.8575 (tp30) REVERT: F 61 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8109 (mm-30) REVERT: F 68 ARG cc_start: 0.8790 (ptp90) cc_final: 0.8540 (ptp90) REVERT: F 104 MET cc_start: 0.8583 (ttp) cc_final: 0.8232 (ttp) REVERT: F 108 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8715 (mmmm) REVERT: F 112 GLN cc_start: 0.9105 (tp40) cc_final: 0.8266 (tp-100) REVERT: F 116 ASP cc_start: 0.8824 (m-30) cc_final: 0.8263 (m-30) REVERT: F 147 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8636 (ttpp) REVERT: G 42 ASP cc_start: 0.8423 (t70) cc_final: 0.8179 (t70) REVERT: G 45 ASP cc_start: 0.8718 (p0) cc_final: 0.8509 (p0) REVERT: G 61 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8263 (mm-30) REVERT: G 84 ASP cc_start: 0.8686 (m-30) cc_final: 0.8481 (m-30) REVERT: H 34 TYR cc_start: 0.9423 (m-10) cc_final: 0.9221 (m-10) REVERT: H 42 ASP cc_start: 0.8405 (t70) cc_final: 0.8136 (t70) REVERT: H 49 GLU cc_start: 0.8213 (tp30) cc_final: 0.7968 (tp30) REVERT: H 61 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8392 (mm-30) REVERT: H 64 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8276 (mt-10) REVERT: H 112 GLN cc_start: 0.9047 (tp40) cc_final: 0.8171 (tp-100) REVERT: H 116 ASP cc_start: 0.8845 (m-30) cc_final: 0.8273 (m-30) REVERT: H 140 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8103 (mp0) REVERT: H 147 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8508 (ttpp) REVERT: H 162 GLU cc_start: 0.7697 (pm20) cc_final: 0.7466 (pm20) REVERT: I 49 GLU cc_start: 0.8184 (tp30) cc_final: 0.7958 (tp30) REVERT: I 60 GLU cc_start: 0.8535 (tp30) cc_final: 0.8177 (tp30) REVERT: I 61 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8276 (mm-30) REVERT: I 84 ASP cc_start: 0.8726 (m-30) cc_final: 0.8497 (m-30) REVERT: I 86 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8504 (tppt) REVERT: I 91 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8698 (m-30) REVERT: I 104 MET cc_start: 0.8758 (ttp) cc_final: 0.8422 (ttp) REVERT: I 108 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8647 (mmmm) REVERT: I 112 GLN cc_start: 0.9075 (tp40) cc_final: 0.8243 (tp-100) REVERT: I 116 ASP cc_start: 0.8802 (m-30) cc_final: 0.8230 (m-30) REVERT: J 15 ASP cc_start: 0.8652 (p0) cc_final: 0.8271 (p0) REVERT: J 49 GLU cc_start: 0.8238 (tp30) cc_final: 0.8002 (tp30) REVERT: J 61 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8138 (mm-30) REVERT: J 68 ARG cc_start: 0.8753 (ptp90) cc_final: 0.8376 (ptp90) REVERT: J 86 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8672 (mmpt) REVERT: J 116 ASP cc_start: 0.8880 (m-30) cc_final: 0.8559 (m-30) REVERT: J 140 GLU cc_start: 0.8059 (mp0) cc_final: 0.7505 (mp0) REVERT: J 143 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8847 (mtmm) REVERT: J 147 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8462 (ttpp) REVERT: K 7 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8877 (pt0) REVERT: K 10 GLN cc_start: 0.9019 (tt0) cc_final: 0.8791 (tt0) REVERT: K 42 ASP cc_start: 0.8379 (t70) cc_final: 0.7842 (t70) REVERT: K 45 ASP cc_start: 0.8563 (p0) cc_final: 0.8339 (p0) REVERT: K 61 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8200 (mm-30) REVERT: K 68 ARG cc_start: 0.8652 (ptp-110) cc_final: 0.8356 (ptp90) REVERT: K 84 ASP cc_start: 0.8591 (m-30) cc_final: 0.8217 (m-30) REVERT: K 86 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8583 (tppt) REVERT: K 112 GLN cc_start: 0.9067 (tp40) cc_final: 0.8271 (tp-100) REVERT: K 116 ASP cc_start: 0.8875 (m-30) cc_final: 0.8488 (m-30) REVERT: K 140 GLU cc_start: 0.8428 (pp20) cc_final: 0.8131 (pp20) REVERT: K 143 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8868 (mtmm) REVERT: K 147 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8568 (ttpp) REVERT: L 7 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8866 (pt0) REVERT: L 45 ASP cc_start: 0.8649 (p0) cc_final: 0.8344 (p0) REVERT: L 49 GLU cc_start: 0.8262 (tp30) cc_final: 0.7968 (tp30) REVERT: L 84 ASP cc_start: 0.8674 (m-30) cc_final: 0.8228 (m-30) REVERT: L 101 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8417 (mppt) REVERT: L 104 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8149 (ttp) REVERT: L 116 ASP cc_start: 0.8895 (m-30) cc_final: 0.8572 (m-30) REVERT: L 140 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8026 (mp0) REVERT: L 147 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8514 (ttpp) REVERT: M 42 ASP cc_start: 0.8438 (t70) cc_final: 0.7973 (t70) REVERT: M 49 GLU cc_start: 0.8252 (tp30) cc_final: 0.8002 (tp30) REVERT: M 60 GLU cc_start: 0.8600 (tp30) cc_final: 0.8250 (tp30) REVERT: M 68 ARG cc_start: 0.8787 (ptp90) cc_final: 0.8453 (ptp90) REVERT: M 84 ASP cc_start: 0.8711 (m-30) cc_final: 0.8453 (m-30) REVERT: M 86 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8657 (tppt) REVERT: M 98 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (p0) REVERT: M 101 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8347 (mppt) REVERT: M 116 ASP cc_start: 0.8863 (m-30) cc_final: 0.8561 (m-30) REVERT: M 140 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7965 (mp0) REVERT: M 143 LYS cc_start: 0.9111 (mtmm) cc_final: 0.8878 (mtmm) REVERT: M 172 ARG cc_start: 0.9207 (mmm160) cc_final: 0.8876 (mmm160) REVERT: N 43 ARG cc_start: 0.8345 (mtm180) cc_final: 0.8077 (mtm180) REVERT: N 45 ASP cc_start: 0.8604 (p0) cc_final: 0.8207 (p0) REVERT: N 49 GLU cc_start: 0.8287 (tp30) cc_final: 0.7991 (tp30) REVERT: N 60 GLU cc_start: 0.8545 (tp30) cc_final: 0.8154 (tp30) REVERT: N 61 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8156 (mm-30) REVERT: N 68 ARG cc_start: 0.8751 (ptp90) cc_final: 0.8389 (ptp90) REVERT: N 79 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7743 (mmp80) REVERT: N 86 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8551 (mmmm) REVERT: N 87 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8087 (ttmm) REVERT: N 104 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: N 116 ASP cc_start: 0.8861 (m-30) cc_final: 0.8540 (m-30) REVERT: N 140 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7953 (mp0) REVERT: N 147 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8531 (ttpp) REVERT: O 34 TYR cc_start: 0.9420 (m-10) cc_final: 0.9163 (m-10) REVERT: O 45 ASP cc_start: 0.8700 (p0) cc_final: 0.8363 (p0) REVERT: O 61 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8168 (mm-30) REVERT: O 64 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8295 (mt-10) REVERT: O 79 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7740 (mmp80) REVERT: O 86 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8643 (mmpt) REVERT: O 107 GLU cc_start: 0.8466 (tp30) cc_final: 0.8194 (tp30) REVERT: O 116 ASP cc_start: 0.8887 (m-30) cc_final: 0.8573 (m-30) REVERT: O 140 GLU cc_start: 0.8248 (mp0) cc_final: 0.7655 (mp0) REVERT: O 147 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8409 (ttpp) REVERT: P 15 ASP cc_start: 0.8711 (p0) cc_final: 0.8158 (p0) REVERT: P 22 SER cc_start: 0.9253 (m) cc_final: 0.8980 (p) REVERT: P 42 ASP cc_start: 0.8356 (t70) cc_final: 0.8001 (t70) REVERT: P 61 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8316 (mm-30) REVERT: P 84 ASP cc_start: 0.8699 (m-30) cc_final: 0.8449 (m-30) REVERT: P 86 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8589 (tppt) REVERT: P 112 GLN cc_start: 0.9071 (tp40) cc_final: 0.8231 (tp-100) REVERT: P 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8355 (m-30) REVERT: P 147 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8593 (ttpp) REVERT: Q 60 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8379 (mm-30) REVERT: Q 61 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8228 (mm-30) REVERT: Q 74 ASN cc_start: 0.9122 (m-40) cc_final: 0.8487 (m110) REVERT: Q 104 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8405 (ttp) REVERT: Q 112 GLN cc_start: 0.9051 (tp40) cc_final: 0.8204 (tp-100) REVERT: Q 116 ASP cc_start: 0.8877 (m-30) cc_final: 0.8290 (m-30) REVERT: Q 140 GLU cc_start: 0.8088 (mp0) cc_final: 0.7451 (mp0) REVERT: Q 141 GLU cc_start: 0.8695 (tp30) cc_final: 0.8311 (tp30) REVERT: Q 162 GLU cc_start: 0.7754 (pm20) cc_final: 0.7478 (pm20) REVERT: R 42 ASP cc_start: 0.8521 (t70) cc_final: 0.7977 (t70) REVERT: R 60 GLU cc_start: 0.8511 (tp30) cc_final: 0.8216 (tp30) REVERT: R 61 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8165 (mm-30) REVERT: R 86 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8582 (mmpt) REVERT: R 116 ASP cc_start: 0.8885 (m-30) cc_final: 0.8569 (m-30) REVERT: R 147 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8588 (ttpp) REVERT: R 148 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8987 (mtm) REVERT: R 162 GLU cc_start: 0.7534 (pm20) cc_final: 0.7263 (pm20) REVERT: S 22 SER cc_start: 0.9285 (m) cc_final: 0.9004 (p) REVERT: S 42 ASP cc_start: 0.8478 (t70) cc_final: 0.7885 (t70) REVERT: S 68 ARG cc_start: 0.8760 (ptp90) cc_final: 0.8415 (ptp90) REVERT: S 86 LYS cc_start: 0.8859 (tppt) cc_final: 0.8433 (mmpt) REVERT: S 116 ASP cc_start: 0.8819 (m-30) cc_final: 0.8525 (m-30) REVERT: S 147 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8474 (ttpp) REVERT: S 162 GLU cc_start: 0.7463 (mp0) cc_final: 0.7128 (pm20) REVERT: T 42 ASP cc_start: 0.8397 (t70) cc_final: 0.7998 (t70) REVERT: T 68 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8286 (ptp90) REVERT: T 74 ASN cc_start: 0.9096 (m-40) cc_final: 0.8885 (m110) REVERT: T 104 MET cc_start: 0.8755 (ttp) cc_final: 0.8334 (ttp) REVERT: T 112 GLN cc_start: 0.9140 (tp40) cc_final: 0.8375 (tp-100) REVERT: T 116 ASP cc_start: 0.8828 (m-30) cc_final: 0.8319 (m-30) REVERT: T 140 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7922 (mp0) REVERT: T 162 GLU cc_start: 0.7716 (pm20) cc_final: 0.7436 (pm20) REVERT: U 42 ASP cc_start: 0.8325 (t70) cc_final: 0.7984 (t70) REVERT: U 49 GLU cc_start: 0.8330 (tp30) cc_final: 0.8017 (tp30) REVERT: U 61 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8377 (mm-30) REVERT: U 64 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8332 (mt-10) REVERT: U 104 MET cc_start: 0.8543 (ttp) cc_final: 0.8203 (ttp) REVERT: U 116 ASP cc_start: 0.8836 (m-30) cc_final: 0.8556 (m-30) REVERT: U 147 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8641 (ttpp) REVERT: V 45 ASP cc_start: 0.8582 (p0) cc_final: 0.8218 (p0) REVERT: V 60 GLU cc_start: 0.8596 (tp30) cc_final: 0.8287 (tp30) REVERT: V 61 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8133 (mm-30) REVERT: V 84 ASP cc_start: 0.8606 (m-30) cc_final: 0.8273 (m-30) REVERT: V 107 GLU cc_start: 0.8905 (tp30) cc_final: 0.8677 (tp30) REVERT: V 112 GLN cc_start: 0.8988 (tp40) cc_final: 0.8672 (tp-100) REVERT: V 116 ASP cc_start: 0.8683 (m-30) cc_final: 0.8424 (m-30) REVERT: V 135 THR cc_start: 0.9382 (m) cc_final: 0.9167 (t) REVERT: V 140 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7956 (mp0) REVERT: V 167 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7965 (tt0) REVERT: W 42 ASP cc_start: 0.8458 (t70) cc_final: 0.7927 (t70) REVERT: W 61 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8391 (mm-30) REVERT: W 64 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8325 (mt-10) REVERT: W 79 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7856 (mmt-90) REVERT: W 87 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8389 (ttmm) REVERT: W 104 MET cc_start: 0.8705 (ttp) cc_final: 0.8423 (tpp) REVERT: W 116 ASP cc_start: 0.8875 (m-30) cc_final: 0.8571 (m-30) REVERT: W 135 THR cc_start: 0.9405 (m) cc_final: 0.9198 (t) REVERT: W 140 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8070 (mp0) REVERT: W 147 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8587 (ttpp) REVERT: W 162 GLU cc_start: 0.7645 (pm20) cc_final: 0.7426 (pm20) REVERT: W 167 GLU cc_start: 0.8393 (tt0) cc_final: 0.8180 (tt0) REVERT: X 60 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8354 (mm-30) REVERT: X 68 ARG cc_start: 0.8739 (ptp90) cc_final: 0.8368 (ptp90) REVERT: X 84 ASP cc_start: 0.8783 (m-30) cc_final: 0.8543 (m-30) REVERT: X 109 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8856 (tttm) REVERT: X 112 GLN cc_start: 0.9070 (tp40) cc_final: 0.8238 (tp-100) REVERT: X 116 ASP cc_start: 0.8874 (m-30) cc_final: 0.8358 (m-30) REVERT: X 140 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8024 (mp0) REVERT: X 167 GLU cc_start: 0.8473 (tt0) cc_final: 0.8273 (tt0) outliers start: 86 outliers final: 40 residues processed: 1336 average time/residue: 0.8817 time to fit residues: 1349.3021 Evaluate side-chains 1283 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1228 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain S residue 72 MET Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 123 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 371 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 387 optimal weight: 9.9990 chunk 344 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 7 GLN D 7 GLN D 156 HIS E 7 GLN F 7 GLN F 75 GLN G 7 GLN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 GLN J 7 GLN K 7 GLN K 136 HIS L 7 GLN M 7 GLN N 7 GLN N 111 ASN O 7 GLN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 HIS P 136 HIS Q 111 ASN S 7 GLN T 10 GLN U 7 GLN U 136 HIS V 7 GLN V 10 GLN ** W 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.081257 restraints weight = 58137.844| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.63 r_work: 0.2994 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33838 Z= 0.164 Angle : 0.660 10.306 45524 Z= 0.338 Chirality : 0.040 0.228 4872 Planarity : 0.004 0.053 5974 Dihedral : 6.256 85.353 4600 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 2.27 % Allowed : 28.94 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.13), residues: 4080 helix: 2.56 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.06 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 63 TYR 0.026 0.002 TYR U 66 PHE 0.016 0.002 PHE T 137 TRP 0.005 0.001 TRP D 93 HIS 0.007 0.001 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00377 (33838) covalent geometry : angle 0.66045 (45524) hydrogen bonds : bond 0.03597 ( 2675) hydrogen bonds : angle 3.81176 ( 8025) *********************** 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 1347 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1268 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8705 (pm20) REVERT: A 22 SER cc_start: 0.9282 (m) cc_final: 0.8947 (p) REVERT: A 49 GLU cc_start: 0.8295 (tp30) cc_final: 0.8042 (tp30) REVERT: A 61 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 86 LYS cc_start: 0.8878 (tppt) cc_final: 0.8538 (mmpt) REVERT: A 108 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8773 (mmmm) REVERT: A 147 LYS cc_start: 0.8877 (ttpp) cc_final: 0.8619 (ttmm) REVERT: A 150 ASP cc_start: 0.8559 (m-30) cc_final: 0.8270 (m-30) REVERT: B 45 ASP cc_start: 0.8599 (p0) cc_final: 0.8329 (p0) REVERT: B 60 GLU cc_start: 0.8417 (tp30) cc_final: 0.8132 (tp30) REVERT: B 86 LYS cc_start: 0.8751 (mtpm) cc_final: 0.8294 (mmmm) REVERT: B 104 MET cc_start: 0.8795 (ttp) cc_final: 0.8423 (ttp) REVERT: B 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8552 (m-30) REVERT: B 140 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7967 (mp0) REVERT: B 143 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8912 (mtmm) REVERT: B 147 LYS cc_start: 0.8896 (ttpp) cc_final: 0.8623 (ttpp) REVERT: B 172 ARG cc_start: 0.9293 (mmm160) cc_final: 0.9087 (mmm160) REVERT: C 42 ASP cc_start: 0.8570 (t70) cc_final: 0.8068 (t70) REVERT: C 60 GLU cc_start: 0.8479 (tp30) cc_final: 0.8245 (tp30) REVERT: C 68 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8256 (ptp90) REVERT: C 104 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8187 (ttp) REVERT: C 112 GLN cc_start: 0.9082 (tp40) cc_final: 0.8320 (tp40) REVERT: C 116 ASP cc_start: 0.8903 (m-30) cc_final: 0.8480 (m-30) REVERT: C 140 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8044 (mp0) REVERT: C 147 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8646 (ttpp) REVERT: D 15 ASP cc_start: 0.8698 (p0) cc_final: 0.8233 (p0) REVERT: D 22 SER cc_start: 0.9293 (m) cc_final: 0.9012 (p) REVERT: D 42 ASP cc_start: 0.8581 (t70) cc_final: 0.8096 (t70) REVERT: D 60 GLU cc_start: 0.8576 (tp30) cc_final: 0.8108 (tp30) REVERT: D 61 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8151 (mm-30) REVERT: D 63 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.8125 (ttm-80) REVERT: D 101 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8592 (mppt) REVERT: D 107 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8469 (mm-30) REVERT: D 112 GLN cc_start: 0.9057 (tp40) cc_final: 0.8208 (tp-100) REVERT: D 116 ASP cc_start: 0.8886 (m-30) cc_final: 0.8408 (m-30) REVERT: D 140 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8230 (pp20) REVERT: D 162 GLU cc_start: 0.7639 (pm20) cc_final: 0.7294 (pm20) REVERT: D 167 GLU cc_start: 0.8431 (tt0) cc_final: 0.8133 (tt0) REVERT: E 17 GLU cc_start: 0.8411 (tt0) cc_final: 0.8206 (tt0) REVERT: E 42 ASP cc_start: 0.8367 (t70) cc_final: 0.7683 (t70) REVERT: E 57 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 86 LYS cc_start: 0.8868 (tppt) cc_final: 0.8458 (mmpt) REVERT: E 87 LYS cc_start: 0.9064 (ptmm) cc_final: 0.8864 (ptmm) REVERT: E 116 ASP cc_start: 0.8874 (m-30) cc_final: 0.8555 (m-30) REVERT: F 17 GLU cc_start: 0.8339 (tt0) cc_final: 0.8125 (tt0) REVERT: F 60 GLU cc_start: 0.8313 (tp30) cc_final: 0.7909 (pt0) REVERT: F 68 ARG cc_start: 0.8776 (ptp90) cc_final: 0.8566 (ptp90) REVERT: F 107 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8657 (tp30) REVERT: F 108 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8761 (mmmm) REVERT: F 116 ASP cc_start: 0.8819 (m-30) cc_final: 0.8547 (m-30) REVERT: F 147 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8638 (ttpp) REVERT: G 42 ASP cc_start: 0.8491 (t70) cc_final: 0.8106 (t70) REVERT: G 61 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8204 (mm-30) REVERT: G 84 ASP cc_start: 0.8680 (m-30) cc_final: 0.8460 (m-30) REVERT: G 87 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8810 (ptmm) REVERT: G 144 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9072 (tm) REVERT: H 15 ASP cc_start: 0.8671 (p0) cc_final: 0.8343 (p0) REVERT: H 42 ASP cc_start: 0.8431 (t70) cc_final: 0.8177 (t70) REVERT: H 49 GLU cc_start: 0.8149 (tp30) cc_final: 0.7920 (tp30) REVERT: H 61 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8381 (mm-30) REVERT: H 64 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8297 (mt-10) REVERT: H 84 ASP cc_start: 0.8719 (m-30) cc_final: 0.8434 (m-30) REVERT: H 86 LYS cc_start: 0.8621 (ptpp) cc_final: 0.8245 (ptmm) REVERT: H 109 LYS cc_start: 0.9116 (ttpp) cc_final: 0.8864 (pttt) REVERT: H 116 ASP cc_start: 0.8834 (m-30) cc_final: 0.8523 (m-30) REVERT: H 124 ARG cc_start: 0.8384 (mtp85) cc_final: 0.8169 (ptp-110) REVERT: H 140 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8070 (mp0) REVERT: H 147 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8378 (ttpp) REVERT: H 150 ASP cc_start: 0.8503 (m-30) cc_final: 0.8300 (m-30) REVERT: H 162 GLU cc_start: 0.7668 (pm20) cc_final: 0.7439 (pm20) REVERT: I 7 GLN cc_start: 0.8788 (pm20) cc_final: 0.8326 (pm20) REVERT: I 60 GLU cc_start: 0.8350 (tp30) cc_final: 0.8141 (tp30) REVERT: I 61 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8288 (mm-30) REVERT: I 86 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8528 (tppt) REVERT: I 108 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8572 (mmmm) REVERT: I 116 ASP cc_start: 0.8798 (m-30) cc_final: 0.8518 (m-30) REVERT: I 143 LYS cc_start: 0.9098 (mtmm) cc_final: 0.8889 (mtmm) REVERT: I 147 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8458 (ttpp) REVERT: J 15 ASP cc_start: 0.8654 (p0) cc_final: 0.8326 (p0) REVERT: J 49 GLU cc_start: 0.8264 (tp30) cc_final: 0.7995 (tp30) REVERT: J 61 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8235 (mm-30) REVERT: J 68 ARG cc_start: 0.8751 (ptp90) cc_final: 0.8429 (ptp90) REVERT: J 108 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8739 (mmmm) REVERT: J 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8525 (m-30) REVERT: J 140 GLU cc_start: 0.7982 (mp0) cc_final: 0.7472 (mp0) REVERT: J 147 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8531 (ttpp) REVERT: K 7 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8796 (pt0) REVERT: K 10 GLN cc_start: 0.9011 (tt0) cc_final: 0.8786 (tt0) REVERT: K 34 TYR cc_start: 0.9399 (m-10) cc_final: 0.9192 (m-10) REVERT: K 42 ASP cc_start: 0.8392 (t70) cc_final: 0.7863 (t70) REVERT: K 45 ASP cc_start: 0.8590 (p0) cc_final: 0.8360 (p0) REVERT: K 61 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8225 (mm-30) REVERT: K 68 ARG cc_start: 0.8683 (ptp-110) cc_final: 0.8377 (ptp90) REVERT: K 84 ASP cc_start: 0.8616 (m-30) cc_final: 0.8266 (m-30) REVERT: K 86 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8604 (mmpt) REVERT: K 112 GLN cc_start: 0.9085 (tp40) cc_final: 0.8245 (tp-100) REVERT: K 116 ASP cc_start: 0.8841 (m-30) cc_final: 0.8349 (m-30) REVERT: K 140 GLU cc_start: 0.8463 (pp20) cc_final: 0.8159 (pp20) REVERT: K 143 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8862 (mtmm) REVERT: K 147 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8580 (ttpp) REVERT: L 45 ASP cc_start: 0.8632 (p0) cc_final: 0.8423 (p0) REVERT: L 49 GLU cc_start: 0.8276 (tp30) cc_final: 0.7979 (tp30) REVERT: L 84 ASP cc_start: 0.8757 (m-30) cc_final: 0.8393 (m-30) REVERT: L 86 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8601 (mmmm) REVERT: L 101 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8460 (mtpt) REVERT: L 116 ASP cc_start: 0.8892 (m-30) cc_final: 0.8542 (m-30) REVERT: L 140 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8049 (mp0) REVERT: L 144 LEU cc_start: 0.8977 (tp) cc_final: 0.8398 (tm) REVERT: L 147 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8401 (ttpp) REVERT: M 42 ASP cc_start: 0.8483 (t70) cc_final: 0.7949 (t70) REVERT: M 49 GLU cc_start: 0.8190 (tp30) cc_final: 0.7943 (tp30) REVERT: M 68 ARG cc_start: 0.8781 (ptp90) cc_final: 0.8496 (ptp90) REVERT: M 84 ASP cc_start: 0.8743 (m-30) cc_final: 0.8375 (m-30) REVERT: M 86 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8659 (tppt) REVERT: M 98 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8305 (p0) REVERT: M 101 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8326 (mppt) REVERT: M 116 ASP cc_start: 0.8856 (m-30) cc_final: 0.8526 (m-30) REVERT: M 140 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7989 (mp0) REVERT: M 143 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8913 (mtmm) REVERT: M 172 ARG cc_start: 0.9206 (mmm160) cc_final: 0.8869 (mmm160) REVERT: N 45 ASP cc_start: 0.8590 (p0) cc_final: 0.8365 (p0) REVERT: N 49 GLU cc_start: 0.8334 (tp30) cc_final: 0.8044 (tp30) REVERT: N 60 GLU cc_start: 0.8390 (tp30) cc_final: 0.8144 (tp30) REVERT: N 68 ARG cc_start: 0.8734 (ptp90) cc_final: 0.8417 (ptp90) REVERT: N 79 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7680 (mmp80) REVERT: N 84 ASP cc_start: 0.8712 (m-30) cc_final: 0.8368 (m-30) REVERT: N 86 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8562 (mmmm) REVERT: N 116 ASP cc_start: 0.8863 (m-30) cc_final: 0.8540 (m-30) REVERT: N 140 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7947 (mp0) REVERT: O 34 TYR cc_start: 0.9454 (m-10) cc_final: 0.9222 (m-10) REVERT: O 61 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8138 (mm-30) REVERT: O 64 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8293 (mt-10) REVERT: O 79 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7760 (mmp80) REVERT: O 86 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8599 (mmpt) REVERT: O 116 ASP cc_start: 0.8870 (m-30) cc_final: 0.8543 (m-30) REVERT: O 140 GLU cc_start: 0.8291 (mp0) cc_final: 0.7722 (mp0) REVERT: O 147 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8465 (ttpp) REVERT: P 15 ASP cc_start: 0.8573 (p0) cc_final: 0.8344 (p0) REVERT: P 22 SER cc_start: 0.9259 (m) cc_final: 0.8982 (p) REVERT: P 42 ASP cc_start: 0.8422 (t70) cc_final: 0.8002 (t70) REVERT: P 45 ASP cc_start: 0.8728 (p0) cc_final: 0.8523 (p0) REVERT: P 61 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8304 (mm-30) REVERT: P 84 ASP cc_start: 0.8732 (m-30) cc_final: 0.8493 (m-30) REVERT: P 86 LYS cc_start: 0.8772 (mmmm) cc_final: 0.8535 (tppt) REVERT: P 112 GLN cc_start: 0.9055 (tp40) cc_final: 0.8172 (tp-100) REVERT: P 116 ASP cc_start: 0.8829 (m-30) cc_final: 0.8318 (m-30) REVERT: P 147 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8445 (ttpp) REVERT: Q 49 GLU cc_start: 0.8186 (tp30) cc_final: 0.7952 (tp30) REVERT: Q 61 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8122 (mm-30) REVERT: Q 74 ASN cc_start: 0.9125 (m-40) cc_final: 0.8510 (m110) REVERT: Q 116 ASP cc_start: 0.8886 (m-30) cc_final: 0.8558 (m-30) REVERT: Q 162 GLU cc_start: 0.7741 (pm20) cc_final: 0.7458 (pm20) REVERT: R 60 GLU cc_start: 0.8516 (tp30) cc_final: 0.8210 (tp30) REVERT: R 61 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8116 (mm-30) REVERT: R 86 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8571 (mmpt) REVERT: R 116 ASP cc_start: 0.8880 (m-30) cc_final: 0.8570 (m-30) REVERT: R 147 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8603 (ttpp) REVERT: R 148 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8993 (mtm) REVERT: R 162 GLU cc_start: 0.7591 (pm20) cc_final: 0.7329 (pm20) REVERT: S 22 SER cc_start: 0.9280 (m) cc_final: 0.8974 (p) REVERT: S 42 ASP cc_start: 0.8443 (t70) cc_final: 0.7968 (t70) REVERT: S 49 GLU cc_start: 0.8280 (tp30) cc_final: 0.8052 (tp30) REVERT: S 68 ARG cc_start: 0.8771 (ptp90) cc_final: 0.8432 (ptp90) REVERT: S 86 LYS cc_start: 0.8862 (tppt) cc_final: 0.8460 (mmpt) REVERT: S 116 ASP cc_start: 0.8828 (m-30) cc_final: 0.8520 (m-30) REVERT: S 147 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8500 (ttpp) REVERT: S 150 ASP cc_start: 0.8442 (m-30) cc_final: 0.8216 (m-30) REVERT: S 162 GLU cc_start: 0.7463 (mp0) cc_final: 0.7132 (pm20) REVERT: T 49 GLU cc_start: 0.8280 (tp30) cc_final: 0.8025 (tp30) REVERT: T 63 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8203 (ttp-110) REVERT: T 68 ARG cc_start: 0.8748 (ptp90) cc_final: 0.8323 (ptp90) REVERT: T 104 MET cc_start: 0.8775 (ttp) cc_final: 0.8459 (tpp) REVERT: T 112 GLN cc_start: 0.9146 (tp40) cc_final: 0.8350 (tp-100) REVERT: T 116 ASP cc_start: 0.8830 (m-30) cc_final: 0.8309 (m-30) REVERT: T 140 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8007 (mp0) REVERT: T 162 GLU cc_start: 0.7675 (pm20) cc_final: 0.7422 (pm20) REVERT: U 42 ASP cc_start: 0.8365 (t70) cc_final: 0.8002 (t70) REVERT: U 49 GLU cc_start: 0.8348 (tp30) cc_final: 0.8074 (tp30) REVERT: U 57 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8198 (mm-30) REVERT: U 60 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8352 (mm-30) REVERT: U 61 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8438 (mm-30) REVERT: U 107 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8609 (mm-30) REVERT: U 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8564 (m-30) REVERT: U 147 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8632 (ttpp) REVERT: U 162 GLU cc_start: 0.7419 (pm20) cc_final: 0.7068 (pm20) REVERT: U 167 GLU cc_start: 0.8589 (tt0) cc_final: 0.8257 (tt0) REVERT: V 45 ASP cc_start: 0.8712 (p0) cc_final: 0.8423 (p0) REVERT: V 49 GLU cc_start: 0.8297 (tp30) cc_final: 0.7998 (tp30) REVERT: V 60 GLU cc_start: 0.8485 (tp30) cc_final: 0.8208 (tp30) REVERT: V 61 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8043 (mm-30) REVERT: V 112 GLN cc_start: 0.8996 (tp40) cc_final: 0.8625 (tp-100) REVERT: V 116 ASP cc_start: 0.8696 (m-30) cc_final: 0.8394 (m-30) REVERT: V 140 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8115 (mp0) REVERT: V 148 MET cc_start: 0.9233 (tpp) cc_final: 0.9023 (mtm) REVERT: W 45 ASP cc_start: 0.8868 (p0) cc_final: 0.8619 (p0) REVERT: W 61 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8313 (mm-30) REVERT: W 64 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8261 (mt-10) REVERT: W 79 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7758 (mmp80) REVERT: W 104 MET cc_start: 0.8679 (ttp) cc_final: 0.8394 (tpp) REVERT: W 116 ASP cc_start: 0.8858 (m-30) cc_final: 0.8576 (m-30) REVERT: W 147 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8586 (ttpp) REVERT: W 162 GLU cc_start: 0.7696 (pm20) cc_final: 0.7467 (pm20) REVERT: X 15 ASP cc_start: 0.8613 (p0) cc_final: 0.8243 (p0) REVERT: X 63 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8127 (ttm-80) REVERT: X 68 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8426 (ptp90) REVERT: X 84 ASP cc_start: 0.8788 (m-30) cc_final: 0.8562 (m-30) REVERT: X 112 GLN cc_start: 0.9030 (tp40) cc_final: 0.8197 (tp-100) REVERT: X 116 ASP cc_start: 0.8907 (m-30) cc_final: 0.8504 (m-30) outliers start: 79 outliers final: 43 residues processed: 1293 average time/residue: 0.8859 time to fit residues: 1311.3115 Evaluate side-chains 1262 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 1208 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 7 GLN Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain S residue 7 GLN Chi-restraints excluded: chain S residue 72 MET Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 7 GLN Chi-restraints excluded: chain V residue 7 GLN Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 83 optimal weight: 10.0000 chunk 169 optimal weight: 0.0070 chunk 252 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 396 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 275 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 7 GLN B 75 GLN D 7 GLN D 75 GLN F 7 GLN F 75 GLN G 7 GLN G 156 HIS H 7 GLN I 74 ASN K 7 GLN L 7 GLN M 7 GLN N 7 GLN O 7 GLN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 HIS S 7 GLN U 7 GLN V 7 GLN W 7 GLN W 74 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083620 restraints weight = 58857.693| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.67 r_work: 0.3050 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33838 Z= 0.140 Angle : 0.667 10.246 45524 Z= 0.343 Chirality : 0.040 0.198 4872 Planarity : 0.005 0.057 5974 Dihedral : 6.131 82.051 4598 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 1.95 % Allowed : 30.60 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.13), residues: 4080 helix: 2.61 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.07 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 63 TYR 0.027 0.002 TYR U 66 PHE 0.016 0.002 PHE T 132 TRP 0.005 0.001 TRP B 93 HIS 0.007 0.001 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00324 (33838) covalent geometry : angle 0.66748 (45524) hydrogen bonds : bond 0.03363 ( 2675) hydrogen bonds : angle 3.79222 ( 8025) ********************** 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 1379 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1311 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.9234 (m) cc_final: 0.8907 (p) REVERT: A 49 GLU cc_start: 0.8211 (tp30) cc_final: 0.8005 (tp30) REVERT: A 61 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 86 LYS cc_start: 0.8803 (tppt) cc_final: 0.8463 (mmpt) REVERT: A 104 MET cc_start: 0.8953 (tpp) cc_final: 0.8647 (mmm) REVERT: A 112 GLN cc_start: 0.8868 (tp40) cc_final: 0.8563 (tp-100) REVERT: A 116 ASP cc_start: 0.8616 (m-30) cc_final: 0.8398 (m-30) REVERT: A 147 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8549 (ttmm) REVERT: A 150 ASP cc_start: 0.8596 (m-30) cc_final: 0.8251 (m-30) REVERT: B 42 ASP cc_start: 0.8395 (t70) cc_final: 0.7733 (t70) REVERT: B 45 ASP cc_start: 0.8520 (p0) cc_final: 0.8255 (p0) REVERT: B 60 GLU cc_start: 0.8330 (tp30) cc_final: 0.7897 (tp30) REVERT: B 86 LYS cc_start: 0.8721 (mtpm) cc_final: 0.8223 (mmmm) REVERT: B 104 MET cc_start: 0.8680 (ttp) cc_final: 0.8314 (ttt) REVERT: B 112 GLN cc_start: 0.9012 (tp40) cc_final: 0.8118 (tp-100) REVERT: B 116 ASP cc_start: 0.8862 (m-30) cc_final: 0.8427 (m-30) REVERT: B 140 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7964 (mp0) REVERT: B 147 LYS cc_start: 0.8812 (ttpp) cc_final: 0.8535 (ttpp) REVERT: C 42 ASP cc_start: 0.8598 (t70) cc_final: 0.8110 (t70) REVERT: C 68 ARG cc_start: 0.8693 (ptp90) cc_final: 0.8208 (ptp90) REVERT: C 101 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8551 (mppt) REVERT: C 104 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8397 (tpp) REVERT: C 112 GLN cc_start: 0.9017 (tp40) cc_final: 0.8317 (mm-40) REVERT: C 116 ASP cc_start: 0.8916 (m-30) cc_final: 0.8711 (m-30) REVERT: C 140 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8013 (mp0) REVERT: C 147 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8516 (ttpp) REVERT: D 7 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8931 (pt0) REVERT: D 22 SER cc_start: 0.9240 (m) cc_final: 0.8980 (p) REVERT: D 42 ASP cc_start: 0.8580 (t70) cc_final: 0.8074 (t70) REVERT: D 61 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8122 (mm-30) REVERT: D 64 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8175 (mt-10) REVERT: D 112 GLN cc_start: 0.9030 (tp40) cc_final: 0.8132 (tp-100) REVERT: D 116 ASP cc_start: 0.8887 (m-30) cc_final: 0.8476 (m-30) REVERT: D 162 GLU cc_start: 0.7645 (pm20) cc_final: 0.7360 (pm20) REVERT: D 167 GLU cc_start: 0.8434 (tt0) cc_final: 0.8166 (tt0) REVERT: E 42 ASP cc_start: 0.8304 (t70) cc_final: 0.7558 (t70) REVERT: E 45 ASP cc_start: 0.8628 (p0) cc_final: 0.8317 (p0) REVERT: E 57 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 86 LYS cc_start: 0.8881 (tppt) cc_final: 0.8465 (mmpt) REVERT: E 101 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8632 (mtmm) REVERT: E 107 GLU cc_start: 0.8696 (tp30) cc_final: 0.8460 (mm-30) REVERT: E 112 GLN cc_start: 0.9035 (tp40) cc_final: 0.8536 (tp-100) REVERT: E 116 ASP cc_start: 0.8882 (m-30) cc_final: 0.8607 (m-30) REVERT: E 141 GLU cc_start: 0.8658 (tp30) cc_final: 0.8369 (tp30) REVERT: F 17 GLU cc_start: 0.8256 (tt0) cc_final: 0.8028 (tt0) REVERT: F 60 GLU cc_start: 0.8315 (tp30) cc_final: 0.7983 (tp30) REVERT: F 107 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8545 (mm-30) REVERT: F 112 GLN cc_start: 0.9013 (tp40) cc_final: 0.8090 (tp-100) REVERT: F 116 ASP cc_start: 0.8811 (m-30) cc_final: 0.8385 (m-30) REVERT: F 147 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8533 (ttpp) REVERT: G 42 ASP cc_start: 0.8372 (t70) cc_final: 0.8027 (t70) REVERT: G 61 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8151 (mm-30) REVERT: G 84 ASP cc_start: 0.8672 (m-30) cc_final: 0.8162 (m-30) REVERT: G 87 LYS cc_start: 0.8936 (ptmm) cc_final: 0.8708 (ptmm) REVERT: G 144 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9030 (tm) REVERT: H 7 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8827 (pt0) REVERT: H 15 ASP cc_start: 0.8632 (p0) cc_final: 0.8360 (p0) REVERT: H 29 GLN cc_start: 0.8409 (tt0) cc_final: 0.8108 (tt0) REVERT: H 42 ASP cc_start: 0.8413 (t70) cc_final: 0.8132 (t70) REVERT: H 61 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8303 (mm-30) REVERT: H 64 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8302 (mt-10) REVERT: H 86 LYS cc_start: 0.8556 (ptpp) cc_final: 0.8177 (ptmm) REVERT: H 109 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8842 (pttt) REVERT: H 112 GLN cc_start: 0.8965 (tp40) cc_final: 0.8061 (tp-100) REVERT: H 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8258 (m-30) REVERT: H 150 ASP cc_start: 0.8471 (m-30) cc_final: 0.8202 (m-30) REVERT: H 162 GLU cc_start: 0.7641 (pm20) cc_final: 0.7369 (pm20) REVERT: I 60 GLU cc_start: 0.8285 (tp30) cc_final: 0.8044 (tp30) REVERT: I 61 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8193 (mm-30) REVERT: I 64 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7954 (mt-10) REVERT: I 86 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8558 (mmmm) REVERT: I 112 GLN cc_start: 0.9011 (tp40) cc_final: 0.8188 (tp40) REVERT: I 116 ASP cc_start: 0.8784 (m-30) cc_final: 0.8277 (m-30) REVERT: I 140 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8064 (mp0) REVERT: I 147 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8253 (ttpp) REVERT: J 15 ASP cc_start: 0.8514 (p0) cc_final: 0.8304 (p0) REVERT: J 49 GLU cc_start: 0.8242 (tp30) cc_final: 0.7991 (tp30) REVERT: J 61 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8152 (mm-30) REVERT: J 68 ARG cc_start: 0.8667 (ptp90) cc_final: 0.8179 (ptp90) REVERT: J 87 LYS cc_start: 0.8868 (ptmm) cc_final: 0.8559 (ptmm) REVERT: J 112 GLN cc_start: 0.9020 (tp40) cc_final: 0.8156 (tp-100) REVERT: J 116 ASP cc_start: 0.8844 (m-30) cc_final: 0.8339 (m-30) REVERT: J 140 GLU cc_start: 0.8066 (mp0) cc_final: 0.7507 (mp0) REVERT: J 143 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8881 (mtmm) REVERT: J 147 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8364 (ttpp) REVERT: K 42 ASP cc_start: 0.8329 (t70) cc_final: 0.7793 (t70) REVERT: K 45 ASP cc_start: 0.8490 (p0) cc_final: 0.8176 (p0) REVERT: K 61 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8089 (mm-30) REVERT: K 68 ARG cc_start: 0.8597 (ptp-110) cc_final: 0.8308 (ptp90) REVERT: K 79 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7686 (mmt-90) REVERT: K 84 ASP cc_start: 0.8607 (m-30) cc_final: 0.8296 (m-30) REVERT: K 86 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8564 (mmpt) REVERT: K 112 GLN cc_start: 0.9035 (tp40) cc_final: 0.8513 (tp-100) REVERT: K 140 GLU cc_start: 0.8463 (pp20) cc_final: 0.8171 (pp20) REVERT: K 147 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8447 (ttpp) REVERT: L 7 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8967 (pt0) REVERT: L 45 ASP cc_start: 0.8590 (p0) cc_final: 0.8367 (p0) REVERT: L 49 GLU cc_start: 0.8248 (tp30) cc_final: 0.7973 (tp30) REVERT: L 74 ASN cc_start: 0.9099 (m-40) cc_final: 0.8892 (m110) REVERT: L 84 ASP cc_start: 0.8768 (m-30) cc_final: 0.8554 (m-30) REVERT: L 86 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8565 (mmmm) REVERT: L 101 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8366 (mtpt) REVERT: L 112 GLN cc_start: 0.9015 (tp40) cc_final: 0.8197 (tp-100) REVERT: L 116 ASP cc_start: 0.8888 (m-30) cc_final: 0.8375 (m-30) REVERT: L 140 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7976 (mp0) REVERT: M 42 ASP cc_start: 0.8419 (t70) cc_final: 0.7844 (t70) REVERT: M 49 GLU cc_start: 0.8154 (tp30) cc_final: 0.7896 (tp30) REVERT: M 68 ARG cc_start: 0.8673 (ptp90) cc_final: 0.8261 (ptp90) REVERT: M 86 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8594 (mmpt) REVERT: M 98 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8231 (p0) REVERT: M 101 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8266 (mppt) REVERT: M 116 ASP cc_start: 0.8866 (m-30) cc_final: 0.8580 (m-30) REVERT: M 140 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7987 (mp0) REVERT: M 143 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8884 (mtmm) REVERT: M 172 ARG cc_start: 0.9132 (mmm160) cc_final: 0.8792 (mmm160) REVERT: N 45 ASP cc_start: 0.8531 (p0) cc_final: 0.8241 (p0) REVERT: N 49 GLU cc_start: 0.8272 (tp30) cc_final: 0.7989 (tp30) REVERT: N 60 GLU cc_start: 0.8331 (tp30) cc_final: 0.7976 (tp30) REVERT: N 68 ARG cc_start: 0.8663 (ptp90) cc_final: 0.8228 (ptp90) REVERT: N 79 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7549 (mmp80) REVERT: N 84 ASP cc_start: 0.8742 (m-30) cc_final: 0.8351 (m-30) REVERT: N 86 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8546 (mmmm) REVERT: N 112 GLN cc_start: 0.8998 (tp40) cc_final: 0.8107 (tp-100) REVERT: N 116 ASP cc_start: 0.8860 (m-30) cc_final: 0.8292 (m-30) REVERT: N 140 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8066 (mm-30) REVERT: N 150 ASP cc_start: 0.8501 (m-30) cc_final: 0.8232 (m-30) REVERT: O 61 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8106 (mm-30) REVERT: O 79 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7683 (mmp80) REVERT: O 86 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8593 (mmpt) REVERT: O 116 ASP cc_start: 0.8878 (m-30) cc_final: 0.8598 (m-30) REVERT: O 140 GLU cc_start: 0.8273 (mp0) cc_final: 0.7639 (mp0) REVERT: O 144 LEU cc_start: 0.8709 (tp) cc_final: 0.8426 (tm) REVERT: P 22 SER cc_start: 0.9209 (m) cc_final: 0.8943 (p) REVERT: P 42 ASP cc_start: 0.8350 (t70) cc_final: 0.7965 (t70) REVERT: P 61 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8230 (mm-30) REVERT: P 84 ASP cc_start: 0.8661 (m-30) cc_final: 0.8336 (m-30) REVERT: P 112 GLN cc_start: 0.8984 (tp40) cc_final: 0.8071 (tp-100) REVERT: P 116 ASP cc_start: 0.8808 (m-30) cc_final: 0.8402 (m-30) REVERT: P 124 ARG cc_start: 0.8295 (ptp-110) cc_final: 0.8082 (ptp-110) REVERT: P 147 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8367 (ttpp) REVERT: Q 49 GLU cc_start: 0.8203 (tp30) cc_final: 0.7984 (tp30) REVERT: Q 61 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8023 (mm-30) REVERT: Q 74 ASN cc_start: 0.9072 (m-40) cc_final: 0.8470 (m110) REVERT: Q 112 GLN cc_start: 0.9023 (tp40) cc_final: 0.8131 (tp-100) REVERT: Q 116 ASP cc_start: 0.8872 (m-30) cc_final: 0.8306 (m-30) REVERT: Q 162 GLU cc_start: 0.7717 (pm20) cc_final: 0.7434 (pm20) REVERT: R 22 SER cc_start: 0.9239 (m) cc_final: 0.8937 (p) REVERT: R 60 GLU cc_start: 0.8469 (tp30) cc_final: 0.8152 (tp30) REVERT: R 61 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8045 (mm-30) REVERT: R 86 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8536 (mmpt) REVERT: R 116 ASP cc_start: 0.8892 (m-30) cc_final: 0.8592 (m-30) REVERT: R 135 THR cc_start: 0.9317 (m) cc_final: 0.9107 (t) REVERT: R 147 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8530 (ttpp) REVERT: R 162 GLU cc_start: 0.7586 (pm20) cc_final: 0.7345 (pm20) REVERT: S 22 SER cc_start: 0.9226 (m) cc_final: 0.8934 (p) REVERT: S 42 ASP cc_start: 0.8390 (t70) cc_final: 0.7895 (t70) REVERT: S 49 GLU cc_start: 0.8212 (tp30) cc_final: 0.7985 (tp30) REVERT: S 68 ARG cc_start: 0.8711 (ptp90) cc_final: 0.8371 (ptp90) REVERT: S 86 LYS cc_start: 0.8857 (tppt) cc_final: 0.8469 (mmpt) REVERT: S 112 GLN cc_start: 0.9034 (tp40) cc_final: 0.8060 (tp-100) REVERT: S 116 ASP cc_start: 0.8815 (m-30) cc_final: 0.8283 (m-30) REVERT: S 147 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8343 (ttpp) REVERT: S 162 GLU cc_start: 0.7354 (mp0) cc_final: 0.6968 (pm20) REVERT: T 63 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8116 (ttp-110) REVERT: T 68 ARG cc_start: 0.8688 (ptp90) cc_final: 0.8262 (ptp90) REVERT: T 112 GLN cc_start: 0.9066 (tp40) cc_final: 0.8505 (tp-100) REVERT: T 116 ASP cc_start: 0.8866 (m-30) cc_final: 0.8648 (m-30) REVERT: T 140 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8032 (mp0) REVERT: U 10 GLN cc_start: 0.8820 (tt0) cc_final: 0.8603 (tt0) REVERT: U 22 SER cc_start: 0.9225 (m) cc_final: 0.8914 (p) REVERT: U 42 ASP cc_start: 0.8275 (t70) cc_final: 0.7938 (t70) REVERT: U 49 GLU cc_start: 0.8276 (tp30) cc_final: 0.7993 (tp30) REVERT: U 61 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8337 (mm-30) REVERT: U 64 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8057 (mt-10) REVERT: U 112 GLN cc_start: 0.9037 (tp40) cc_final: 0.8127 (tp-100) REVERT: U 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8433 (m-30) REVERT: U 135 THR cc_start: 0.9319 (m) cc_final: 0.9112 (t) REVERT: U 147 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8534 (ttpp) REVERT: V 45 ASP cc_start: 0.8562 (p0) cc_final: 0.8282 (p0) REVERT: V 49 GLU cc_start: 0.8279 (tp30) cc_final: 0.8026 (tp30) REVERT: V 86 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8585 (mmmm) REVERT: V 87 LYS cc_start: 0.8960 (ptmm) cc_final: 0.8685 (ptmm) REVERT: V 108 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8594 (mmmm) REVERT: V 112 GLN cc_start: 0.8965 (tp40) cc_final: 0.8579 (tp-100) REVERT: V 116 ASP cc_start: 0.8686 (m-30) cc_final: 0.8374 (m-30) REVERT: V 147 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8475 (ttpp) REVERT: W 22 SER cc_start: 0.9235 (m) cc_final: 0.8927 (p) REVERT: W 45 ASP cc_start: 0.8730 (p0) cc_final: 0.8501 (p0) REVERT: W 61 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8249 (mm-30) REVERT: W 64 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8190 (mt-10) REVERT: W 79 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7626 (mmp80) REVERT: W 84 ASP cc_start: 0.8696 (m-30) cc_final: 0.8438 (m-30) REVERT: W 104 MET cc_start: 0.8473 (ttp) cc_final: 0.8262 (tpp) REVERT: W 116 ASP cc_start: 0.8876 (m-30) cc_final: 0.8561 (m-30) REVERT: W 140 GLU cc_start: 0.8296 (pp20) cc_final: 0.8046 (pp20) REVERT: W 147 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8537 (ttpp) REVERT: W 162 GLU cc_start: 0.7688 (pm20) cc_final: 0.7466 (pm20) REVERT: X 17 GLU cc_start: 0.7972 (tt0) cc_final: 0.7727 (tt0) REVERT: X 63 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: X 68 ARG cc_start: 0.8688 (ptp90) cc_final: 0.8195 (ptp90) REVERT: X 84 ASP cc_start: 0.8754 (m-30) cc_final: 0.8522 (m-30) REVERT: X 112 GLN cc_start: 0.8940 (tp40) cc_final: 0.8433 (tp-100) REVERT: X 116 ASP cc_start: 0.8895 (m-30) cc_final: 0.8683 (m-30) REVERT: X 147 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8355 (ttpp) REVERT: X 167 GLU cc_start: 0.8501 (tt0) cc_final: 0.8252 (tt0) outliers start: 68 outliers final: 35 residues processed: 1335 average time/residue: 0.9824 time to fit residues: 1499.7956 Evaluate side-chains 1280 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 1234 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain S residue 7 GLN Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 72 MET Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 7 GLN Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 176 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 137 optimal weight: 7.9990 chunk 310 optimal weight: 0.9990 chunk 275 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 303 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 195 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN B 75 GLN D 7 GLN E 7 GLN F 7 GLN F 75 GLN F 111 ASN G 7 GLN H 7 GLN J 7 GLN J 111 ASN K 7 GLN L 7 GLN M 7 GLN N 7 GLN N 111 ASN O 7 GLN O 53 HIS R 7 GLN S 7 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 GLN V 7 GLN W 7 GLN W 75 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084317 restraints weight = 58457.589| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.66 r_work: 0.3067 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33838 Z= 0.144 Angle : 0.683 11.376 45524 Z= 0.349 Chirality : 0.040 0.219 4872 Planarity : 0.005 0.056 5974 Dihedral : 6.189 88.294 4598 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 1.67 % Allowed : 31.67 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.13), residues: 4080 helix: 2.61 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.08 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 63 TYR 0.028 0.002 TYR U 66 PHE 0.016 0.002 PHE T 132 TRP 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00336 (33838) covalent geometry : angle 0.68259 (45524) hydrogen bonds : bond 0.03370 ( 2675) hydrogen bonds : angle 3.82038 ( 8025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20531.08 seconds wall clock time: 348 minutes 54.61 seconds (20934.61 seconds total)