Starting phenix.real_space_refine on Fri Jun 27 16:38:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bq5_44797/06_2025/9bq5_44797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bq5_44797/06_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_44797/06_2025/9bq5_44797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bq5_44797/06_2025/9bq5_44797.map" model { file = "/net/cci-nas-00/data/ceres_data/9bq5_44797/06_2025/9bq5_44797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bq5_44797/06_2025/9bq5_44797.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.03, per 1000 atoms: 0.60 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: 8.47 Conformation dependent library (CDL) restraints added in 4.0 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 78.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 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: 12.03 Time building geometry restraints manager: 10.00 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: 0.01 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.270 Check model and map are aligned: 0.260 Set scattering table: 0.300 Process input model: 73.550 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.160 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.046 0.018 TRP U 93 HIS 0.014 0.003 HIS Q 151 PHE 0.103 0.024 PHE K 41 TYR 0.137 0.027 TYR C 34 ARG 0.016 0.002 ARG E 172 Details of bonding type rmsd hydrogen bonds : bond 0.09853 ( 2675) hydrogen bonds : angle 5.47530 ( 8025) covalent geometry : bond 0.01134 (33838) covalent geometry : angle 1.79098 (45524) *********************** 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 : 3.601 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: 0.6466 (mmm) REVERT: E 136 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7330 (OUTLIER) REVERT: E 176 LYS cc_start: 0.4505 (OUTLIER) cc_final: 0.4177 (tppt) REVERT: P 53 HIS cc_start: 0.6715 (t-90) cc_final: 0.6267 (t-90) REVERT: P 146 LYS cc_start: 0.7734 (tptp) cc_final: 0.7488 (tptp) REVERT: Q 146 LYS cc_start: 0.7776 (tptp) cc_final: 0.7534 (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: 1.9338 time to fit residues: 3813.6297 Evaluate side-chains 1341 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 1298 time to evaluate : 3.616 ------------------------------------------------------------------------------- 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 344 optimal weight: 0.9990 chunk 309 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 319 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 7 GLN E 29 GLN E 53 HIS 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 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: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.080292 restraints weight = 58050.216| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.67 r_work: 0.2930 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3381 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= 0.146 Angle : 0.626 11.384 45524 Z= 0.326 Chirality : 0.037 0.152 4872 Planarity : 0.004 0.038 5974 Dihedral : 7.633 87.668 4658 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.42 % Favored : 98.41 % Rotamer: Outliers : 3.56 % Allowed : 17.87 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.13), residues: 4080 helix: 2.17 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 93 HIS 0.008 0.001 HIS M 128 PHE 0.017 0.003 PHE T 132 TYR 0.031 0.002 TYR L 66 ARG 0.009 0.001 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 2675) hydrogen bonds : angle 3.82537 ( 8025) covalent geometry : bond 0.00323 (33838) covalent geometry : angle 0.62583 (45524) *********************** 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 1582 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1458 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8658 (tt0) cc_final: 0.8282 (tt0) REVERT: A 17 GLU cc_start: 0.8398 (tt0) cc_final: 0.8187 (tt0) REVERT: A 42 ASP cc_start: 0.8452 (t70) cc_final: 0.7899 (t70) REVERT: A 60 GLU cc_start: 0.8459 (tp30) cc_final: 0.8042 (tp30) REVERT: A 61 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 62 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8578 (mmtm) REVERT: A 64 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 86 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8417 (mmmm) REVERT: A 107 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8554 (mm-30) REVERT: A 108 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8318 (mmmm) REVERT: A 116 ASP cc_start: 0.8773 (m-30) cc_final: 0.8572 (m-30) REVERT: A 141 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8164 (tp30) REVERT: A 144 LEU cc_start: 0.9023 (tp) cc_final: 0.8760 (tm) REVERT: A 147 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8181 (ttpp) REVERT: A 150 ASP cc_start: 0.8585 (m-30) cc_final: 0.8136 (m-30) REVERT: B 45 ASP cc_start: 0.8659 (p0) cc_final: 0.8062 (p0) REVERT: B 57 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 61 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8305 (mm-30) REVERT: B 64 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7830 (mt-10) REVERT: B 84 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7717 (t70) REVERT: B 104 MET cc_start: 0.8657 (ttp) cc_final: 0.8314 (ttp) REVERT: B 112 GLN cc_start: 0.8756 (tp40) cc_final: 0.8243 (tp40) REVERT: B 116 ASP cc_start: 0.8711 (m-30) cc_final: 0.8188 (m-30) REVERT: B 147 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8247 (ttpp) REVERT: B 150 ASP cc_start: 0.8554 (m-30) cc_final: 0.8189 (m-30) REVERT: C 7 GLN cc_start: 0.8668 (pt0) cc_final: 0.8448 (pt0) REVERT: C 9 ARG cc_start: 0.8307 (ttt180) cc_final: 0.8102 (ttt90) REVERT: C 42 ASP cc_start: 0.8386 (t70) cc_final: 0.7815 (t70) REVERT: C 57 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8018 (mm-30) REVERT: C 60 GLU cc_start: 0.8228 (tp30) cc_final: 0.7947 (tp30) REVERT: C 61 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8060 (mm-30) REVERT: C 62 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8425 (mmtm) REVERT: C 104 MET cc_start: 0.8572 (ttp) cc_final: 0.8262 (ttp) REVERT: C 107 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8337 (mm-30) REVERT: C 116 ASP cc_start: 0.8798 (m-30) cc_final: 0.8555 (m-30) REVERT: C 131 ASP cc_start: 0.8556 (t70) cc_final: 0.8349 (t70) REVERT: C 135 THR cc_start: 0.9314 (m) cc_final: 0.9108 (p) REVERT: C 141 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8237 (tp30) REVERT: D 15 ASP cc_start: 0.8561 (p0) cc_final: 0.8177 (p0) REVERT: D 53 HIS cc_start: 0.8186 (t-90) cc_final: 0.7689 (t70) REVERT: D 57 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 64 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8177 (mm-30) REVERT: D 68 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7987 (mtm-85) REVERT: D 84 ASP cc_start: 0.8779 (m-30) cc_final: 0.8410 (m-30) REVERT: D 86 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8352 (tppt) REVERT: D 108 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8461 (mmmm) REVERT: D 116 ASP cc_start: 0.8764 (m-30) cc_final: 0.8524 (m-30) REVERT: D 124 ARG cc_start: 0.8944 (mmt-90) cc_final: 0.8651 (mmt-90) REVERT: D 143 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8604 (mtmm) REVERT: D 147 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8173 (ttpp) REVERT: D 162 GLU cc_start: 0.7277 (pm20) cc_final: 0.7042 (pm20) REVERT: E 17 GLU cc_start: 0.8482 (tt0) cc_final: 0.8150 (tt0) REVERT: E 61 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7889 (mm-30) REVERT: E 68 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7953 (ttm110) REVERT: E 71 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8542 (tttm) REVERT: E 92 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7551 (tm-30) REVERT: E 116 ASP cc_start: 0.8735 (m-30) cc_final: 0.8515 (m-30) REVERT: E 136 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.7435 (p-80) REVERT: E 147 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8160 (ttpp) REVERT: E 150 ASP cc_start: 0.8569 (m-30) cc_final: 0.8199 (m-30) REVERT: E 165 LEU cc_start: 0.9240 (tp) cc_final: 0.9004 (tp) REVERT: E 167 GLU cc_start: 0.8349 (tt0) cc_final: 0.8112 (tt0) REVERT: F 17 GLU cc_start: 0.8395 (tt0) cc_final: 0.8117 (tt0) REVERT: F 57 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7778 (mt-10) REVERT: F 60 GLU cc_start: 0.8228 (tp30) cc_final: 0.7741 (tp30) REVERT: F 61 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: F 63 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7394 (ttm-80) REVERT: F 64 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7795 (mt-10) REVERT: F 86 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8346 (mmmm) REVERT: F 87 LYS cc_start: 0.8627 (ptmm) cc_final: 0.8268 (ptpp) REVERT: F 104 MET cc_start: 0.8617 (ttp) cc_final: 0.8267 (ttp) REVERT: F 107 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8515 (mm-30) REVERT: F 112 GLN cc_start: 0.8797 (tp40) cc_final: 0.8273 (tp-100) REVERT: F 116 ASP cc_start: 0.8769 (m-30) cc_final: 0.8235 (m-30) REVERT: F 131 ASP cc_start: 0.8580 (t70) cc_final: 0.8377 (t0) REVERT: F 135 THR cc_start: 0.9318 (m) cc_final: 0.9101 (t) REVERT: F 141 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8057 (mm-30) REVERT: F 147 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8240 (ttpp) REVERT: G 10 GLN cc_start: 0.8616 (tt0) cc_final: 0.8250 (tt0) REVERT: G 17 GLU cc_start: 0.8431 (tt0) cc_final: 0.8147 (tt0) REVERT: G 60 GLU cc_start: 0.8230 (tp30) cc_final: 0.7958 (tp30) REVERT: G 61 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7904 (mm-30) REVERT: G 84 ASP cc_start: 0.8591 (m-30) cc_final: 0.8316 (m-30) REVERT: G 107 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8382 (tp30) REVERT: G 108 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8347 (mtmt) REVERT: G 141 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8675 (tp30) REVERT: G 150 ASP cc_start: 0.8575 (m-30) cc_final: 0.8076 (m-30) REVERT: G 167 GLU cc_start: 0.8469 (tt0) cc_final: 0.8256 (tt0) REVERT: H 57 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8070 (mm-30) REVERT: H 61 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8085 (mm-30) REVERT: H 84 ASP cc_start: 0.8582 (m-30) cc_final: 0.8273 (m-30) REVERT: H 104 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8387 (ttp) REVERT: H 109 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8779 (tttm) REVERT: H 116 ASP cc_start: 0.8731 (m-30) cc_final: 0.8522 (m-30) REVERT: H 147 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8197 (ttpp) REVERT: H 162 GLU cc_start: 0.7524 (pm20) cc_final: 0.7303 (pm20) REVERT: I 22 SER cc_start: 0.9016 (m) cc_final: 0.8693 (p) REVERT: I 57 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8155 (mm-30) REVERT: I 60 GLU cc_start: 0.8369 (tp30) cc_final: 0.8086 (tp30) REVERT: I 61 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8088 (mm-30) REVERT: I 64 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8317 (mm-30) REVERT: I 81 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8451 (mm) REVERT: I 84 ASP cc_start: 0.8679 (m-30) cc_final: 0.8389 (m-30) REVERT: I 86 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8381 (mmmm) REVERT: I 104 MET cc_start: 0.8535 (ttp) cc_final: 0.8300 (ttp) REVERT: I 116 ASP cc_start: 0.8690 (m-30) cc_final: 0.8482 (m-30) REVERT: I 147 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8280 (ttpp) REVERT: I 150 ASP cc_start: 0.8515 (m-30) cc_final: 0.8118 (m-30) REVERT: I 153 THR cc_start: 0.8899 (m) cc_final: 0.8670 (p) REVERT: J 15 ASP cc_start: 0.8610 (p0) cc_final: 0.8157 (p0) REVERT: J 57 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8123 (mm-30) REVERT: J 68 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8181 (ttm110) REVERT: J 87 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8415 (ptmm) REVERT: J 107 GLU cc_start: 0.8844 (tp30) cc_final: 0.8392 (tp30) REVERT: J 116 ASP cc_start: 0.8779 (m-30) cc_final: 0.8520 (m-30) REVERT: J 124 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8653 (mmt-90) REVERT: J 141 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8491 (tp30) REVERT: K 45 ASP cc_start: 0.8662 (p0) cc_final: 0.8384 (p0) REVERT: K 60 GLU cc_start: 0.8288 (tp30) cc_final: 0.8080 (tp30) REVERT: K 61 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7873 (mm-30) REVERT: K 68 ARG cc_start: 0.8430 (ptp-110) cc_final: 0.7986 (ptp90) REVERT: K 84 ASP cc_start: 0.8267 (m-30) cc_final: 0.7814 (m-30) REVERT: K 87 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8473 (ptmm) REVERT: K 92 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7477 (tm-30) REVERT: K 107 GLU cc_start: 0.8983 (tp30) cc_final: 0.8664 (tp30) REVERT: K 116 ASP cc_start: 0.8741 (m-30) cc_final: 0.8514 (m-30) REVERT: K 147 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8081 (ttpp) REVERT: K 150 ASP cc_start: 0.8404 (m-30) cc_final: 0.8113 (m-30) REVERT: K 167 GLU cc_start: 0.8429 (tt0) cc_final: 0.8211 (tt0) REVERT: L 45 ASP cc_start: 0.8828 (p0) cc_final: 0.8407 (p0) REVERT: L 60 GLU cc_start: 0.8339 (tp30) cc_final: 0.7999 (tp30) REVERT: L 61 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: L 64 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7956 (mt-10) REVERT: L 84 ASP cc_start: 0.8751 (m-30) cc_final: 0.8378 (m-30) REVERT: L 86 LYS cc_start: 0.8752 (ptpp) cc_final: 0.8481 (mmmm) REVERT: L 104 MET cc_start: 0.8691 (ttp) cc_final: 0.8373 (ttp) REVERT: L 109 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8777 (tttm) REVERT: L 116 ASP cc_start: 0.8747 (m-30) cc_final: 0.8495 (m-30) REVERT: L 143 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8557 (mtmm) REVERT: L 147 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8201 (ttpp) REVERT: L 150 ASP cc_start: 0.8537 (m-30) cc_final: 0.8144 (m-30) REVERT: L 153 THR cc_start: 0.8886 (m) cc_final: 0.8658 (p) REVERT: M 9 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7566 (ttt180) REVERT: M 56 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8237 (mmm-85) REVERT: M 57 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8213 (mm-30) REVERT: M 60 GLU cc_start: 0.8365 (tp30) cc_final: 0.8131 (tp30) REVERT: M 61 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8050 (mm-30) REVERT: M 84 ASP cc_start: 0.8778 (m-30) cc_final: 0.8465 (m-30) REVERT: M 87 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8290 (ptmm) REVERT: M 104 MET cc_start: 0.8619 (ttp) cc_final: 0.8381 (ttp) REVERT: M 107 GLU cc_start: 0.8932 (tp30) cc_final: 0.8567 (tp30) REVERT: M 116 ASP cc_start: 0.8729 (m-30) cc_final: 0.8507 (m-30) REVERT: M 140 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8241 (mm-30) REVERT: M 147 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8192 (ttpt) REVERT: M 162 GLU cc_start: 0.7540 (pm20) cc_final: 0.7331 (pm20) REVERT: N 31 SER cc_start: 0.9039 (p) cc_final: 0.8829 (t) REVERT: N 43 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7801 (mtm180) REVERT: N 45 ASP cc_start: 0.8719 (p0) cc_final: 0.8405 (p0) REVERT: N 60 GLU cc_start: 0.8403 (tp30) cc_final: 0.8142 (mm-30) REVERT: N 61 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8145 (mm-30) REVERT: N 64 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8213 (mm-30) REVERT: N 79 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7530 (mmp80) REVERT: N 86 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8287 (mmmm) REVERT: N 104 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8365 (ttp) REVERT: N 107 GLU cc_start: 0.8913 (tp30) cc_final: 0.8609 (tp30) REVERT: N 112 GLN cc_start: 0.8718 (tp40) cc_final: 0.8141 (tp40) REVERT: N 140 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8279 (mm-30) REVERT: N 147 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8098 (ttpp) REVERT: O 43 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7667 (mtm180) REVERT: O 45 ASP cc_start: 0.8650 (p0) cc_final: 0.8305 (p0) REVERT: O 49 GLU cc_start: 0.8080 (tp30) cc_final: 0.7795 (tp30) REVERT: O 56 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8172 (mmm-85) REVERT: O 61 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7903 (mm-30) REVERT: O 64 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7872 (mt-10) REVERT: O 79 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7596 (mmt180) REVERT: O 84 ASP cc_start: 0.8741 (m-30) cc_final: 0.8509 (m-30) REVERT: O 86 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8424 (mmmm) REVERT: O 104 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: O 109 LYS cc_start: 0.9102 (tmmt) cc_final: 0.8818 (tttm) REVERT: O 116 ASP cc_start: 0.8779 (m-30) cc_final: 0.8550 (m-30) REVERT: O 147 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8180 (ttpp) REVERT: P 15 ASP cc_start: 0.8579 (p0) cc_final: 0.8297 (p0) REVERT: P 53 HIS cc_start: 0.8380 (t-90) cc_final: 0.8108 (t70) REVERT: P 57 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8104 (mm-30) REVERT: P 61 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8042 (mm-30) REVERT: P 62 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8664 (mmtm) REVERT: P 92 GLU cc_start: 0.7715 (pp20) cc_final: 0.7482 (tm-30) REVERT: P 101 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8493 (mppt) REVERT: P 104 MET cc_start: 0.8653 (ttp) cc_final: 0.8408 (ttp) REVERT: P 112 GLN cc_start: 0.8761 (tp40) cc_final: 0.8225 (tp-100) REVERT: P 116 ASP cc_start: 0.8765 (m-30) cc_final: 0.8253 (m-30) REVERT: P 124 ARG cc_start: 0.8891 (mmt-90) cc_final: 0.8649 (mmt-90) REVERT: P 131 ASP cc_start: 0.8585 (t70) cc_final: 0.8353 (t70) REVERT: P 135 THR cc_start: 0.9273 (m) cc_final: 0.9009 (p) REVERT: P 147 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8169 (ttpp) REVERT: P 167 GLU cc_start: 0.8513 (tt0) cc_final: 0.8250 (tt0) REVERT: Q 34 TYR cc_start: 0.9362 (m-80) cc_final: 0.9133 (m-10) REVERT: Q 61 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8047 (mm-30) REVERT: Q 104 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8246 (ttp) REVERT: Q 107 GLU cc_start: 0.8740 (tp30) cc_final: 0.8286 (tp30) REVERT: Q 116 ASP cc_start: 0.8739 (m-30) cc_final: 0.8515 (m-30) REVERT: Q 140 GLU cc_start: 0.7851 (mp0) cc_final: 0.7614 (mm-30) REVERT: R 10 GLN cc_start: 0.8651 (tt0) cc_final: 0.8246 (tt0) REVERT: R 57 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8155 (mm-30) REVERT: R 60 GLU cc_start: 0.8359 (tp30) cc_final: 0.8025 (tp30) REVERT: R 64 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8021 (mt-10) REVERT: R 84 ASP cc_start: 0.8741 (m-30) cc_final: 0.8526 (m-30) REVERT: R 104 MET cc_start: 0.8630 (ttp) cc_final: 0.8309 (ttp) REVERT: R 107 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: R 116 ASP cc_start: 0.8763 (m-30) cc_final: 0.8555 (m-30) REVERT: R 135 THR cc_start: 0.9206 (m) cc_final: 0.8986 (t) REVERT: S 7 GLN cc_start: 0.8685 (pt0) cc_final: 0.8471 (pt0) REVERT: S 10 GLN cc_start: 0.8658 (tt0) cc_final: 0.8277 (tt0) REVERT: S 17 GLU cc_start: 0.8326 (tt0) cc_final: 0.8038 (tt0) REVERT: S 31 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8916 (t) REVERT: S 45 ASP cc_start: 0.8725 (p0) cc_final: 0.8390 (p0) REVERT: S 60 GLU cc_start: 0.8378 (tp30) cc_final: 0.7935 (tp30) REVERT: S 63 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7299 (ttm-80) REVERT: S 84 ASP cc_start: 0.8283 (m-30) cc_final: 0.8081 (m-30) REVERT: S 90 GLU cc_start: 0.8668 (pm20) cc_final: 0.8350 (pm20) REVERT: S 104 MET cc_start: 0.8655 (ttp) cc_final: 0.8334 (ttp) REVERT: S 107 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8404 (tp30) REVERT: S 116 ASP cc_start: 0.8745 (m-30) cc_final: 0.8518 (m-30) REVERT: S 136 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.7745 (p-80) REVERT: S 147 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8250 (ttpt) REVERT: S 150 ASP cc_start: 0.8548 (m-30) cc_final: 0.8118 (m-30) REVERT: S 167 GLU cc_start: 0.8508 (tt0) cc_final: 0.8282 (tt0) REVERT: T 104 MET cc_start: 0.8707 (ttp) cc_final: 0.8355 (ttp) REVERT: T 112 GLN cc_start: 0.8831 (tp40) cc_final: 0.8196 (tp-100) REVERT: T 116 ASP cc_start: 0.8781 (m-30) cc_final: 0.8227 (m-30) REVERT: T 136 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.8095 (p90) REVERT: T 140 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7957 (mp0) REVERT: T 162 GLU cc_start: 0.7546 (pm20) cc_final: 0.7336 (pm20) REVERT: U 17 GLU cc_start: 0.8324 (tt0) cc_final: 0.8051 (tt0) REVERT: U 44 ASP cc_start: 0.8561 (p0) cc_final: 0.8359 (p0) REVERT: U 57 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8063 (mm-30) REVERT: U 60 GLU cc_start: 0.8188 (tp30) cc_final: 0.7982 (tp30) REVERT: U 61 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8051 (mm-30) REVERT: U 62 LYS cc_start: 0.8813 (mmtm) cc_final: 0.8517 (mmtm) REVERT: U 84 ASP cc_start: 0.8791 (m-30) cc_final: 0.8474 (m-30) REVERT: U 104 MET cc_start: 0.8595 (ttp) cc_final: 0.8272 (ttp) REVERT: U 107 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8434 (tp30) REVERT: U 112 GLN cc_start: 0.8801 (tp40) cc_final: 0.8274 (tp-100) REVERT: U 116 ASP cc_start: 0.8786 (m-30) cc_final: 0.8257 (m-30) REVERT: U 147 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8140 (ttpp) REVERT: U 150 ASP cc_start: 0.8671 (m-30) cc_final: 0.8066 (m-30) REVERT: U 167 GLU cc_start: 0.8483 (tt0) cc_final: 0.8283 (tt0) REVERT: V 43 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7689 (mtm180) REVERT: V 45 ASP cc_start: 0.8713 (p0) cc_final: 0.8264 (p0) REVERT: V 57 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8159 (mm-30) REVERT: V 60 GLU cc_start: 0.8330 (tp30) cc_final: 0.7965 (tp30) REVERT: V 61 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8218 (mm-30) REVERT: V 62 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8358 (mmtm) REVERT: V 63 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: V 64 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7905 (mt-10) REVERT: V 87 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8485 (ptpp) REVERT: V 107 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8351 (tp30) REVERT: V 112 GLN cc_start: 0.8791 (tp40) cc_final: 0.8244 (tp40) REVERT: V 135 THR cc_start: 0.9345 (m) cc_final: 0.9076 (t) REVERT: V 140 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8151 (mm-30) REVERT: V 147 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8258 (ttpp) REVERT: V 153 THR cc_start: 0.8905 (m) cc_final: 0.8675 (p) REVERT: W 45 ASP cc_start: 0.8821 (p0) cc_final: 0.8444 (p0) REVERT: W 57 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8114 (mm-30) REVERT: W 60 GLU cc_start: 0.8359 (tp30) cc_final: 0.8149 (tp30) REVERT: W 61 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8132 (mm-30) REVERT: W 68 ARG cc_start: 0.8318 (mtm110) cc_final: 0.8063 (mtm-85) REVERT: W 79 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7411 (mmt180) REVERT: W 86 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8323 (tppt) REVERT: W 104 MET cc_start: 0.8648 (ttp) cc_final: 0.8292 (ttp) REVERT: W 116 ASP cc_start: 0.8823 (m-30) cc_final: 0.8614 (m-30) REVERT: W 144 LEU cc_start: 0.9171 (tp) cc_final: 0.8893 (tm) REVERT: W 148 MET cc_start: 0.8640 (mtt) cc_final: 0.8439 (mtt) REVERT: X 15 ASP cc_start: 0.8434 (p0) cc_final: 0.8140 (p0) REVERT: X 57 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8062 (mm-30) REVERT: X 84 ASP cc_start: 0.8721 (m-30) cc_final: 0.8361 (m-30) REVERT: X 107 GLU cc_start: 0.8895 (tp30) cc_final: 0.8662 (tp30) REVERT: X 116 ASP cc_start: 0.8771 (m-30) cc_final: 0.8515 (m-30) REVERT: X 124 ARG cc_start: 0.8996 (mmt-90) cc_final: 0.8753 (mmt-90) REVERT: X 135 THR cc_start: 0.9281 (m) cc_final: 0.9077 (t) REVERT: X 150 ASP cc_start: 0.8480 (m-30) cc_final: 0.8149 (m-30) outliers start: 124 outliers final: 28 residues processed: 1498 average time/residue: 1.9169 time to fit residues: 3302.8272 Evaluate side-chains 1303 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 1251 time to evaluate : 3.689 ------------------------------------------------------------------------------- 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 91 ASP Chi-restraints excluded: chain E residue 136 HIS 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 104 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 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 230 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 402 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 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 A 11 ASN A 29 GLN B 11 ASN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 I 7 GLN I 11 ASN I 29 GLN I 136 HIS J 29 GLN J 111 ASN K 29 GLN L 7 GLN L 11 ASN L 111 ASN L 136 HIS M 7 GLN M 11 ASN M 29 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN N 7 GLN N 29 GLN O 7 GLN O 29 GLN ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 136 HIS T 29 GLN T 74 ASN T 136 HIS U 11 ASN U 29 GLN V 7 GLN V 29 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 GLN W 29 GLN W 111 ASN X 7 GLN X 29 GLN X 111 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.088738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.077753 restraints weight = 58571.486| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.73 r_work: 0.2878 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3766 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= 0.182 Angle : 0.605 9.889 45524 Z= 0.312 Chirality : 0.039 0.187 4872 Planarity : 0.004 0.038 5974 Dihedral : 7.164 89.453 4617 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.54 % Favored : 98.31 % Rotamer: Outliers : 3.36 % Allowed : 21.67 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.13), residues: 4080 helix: 2.50 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.36 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.008 0.001 HIS T 136 PHE 0.023 0.002 PHE S 137 TYR 0.024 0.002 TYR B 66 ARG 0.008 0.001 ARG U 56 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 2675) hydrogen bonds : angle 3.71474 ( 8025) covalent geometry : bond 0.00406 (33838) covalent geometry : angle 0.60536 (45524) *********************** 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 1499 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1382 time to evaluate : 3.859 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: A 10 GLN cc_start: 0.8644 (tt0) cc_final: 0.8386 (tt0) REVERT: A 57 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 60 GLU cc_start: 0.8474 (tp30) cc_final: 0.7889 (tp30) REVERT: A 61 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 64 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8215 (mt-10) REVERT: A 86 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8257 (tppt) REVERT: A 87 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8428 (ptpp) REVERT: A 107 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8547 (tp30) REVERT: A 116 ASP cc_start: 0.8728 (m-30) cc_final: 0.8517 (m-30) REVERT: A 147 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8236 (ttpp) REVERT: A 150 ASP cc_start: 0.8474 (m-30) cc_final: 0.8198 (m-30) REVERT: B 17 GLU cc_start: 0.8502 (tt0) cc_final: 0.8179 (tt0) REVERT: B 45 ASP cc_start: 0.8526 (p0) cc_final: 0.8087 (p0) REVERT: B 61 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8424 (mm-30) REVERT: B 64 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 84 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7776 (t70) REVERT: B 86 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8028 (mmmm) REVERT: B 90 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8621 (mm-30) REVERT: B 104 MET cc_start: 0.8584 (ttp) cc_final: 0.8199 (ttp) REVERT: B 107 GLU cc_start: 0.8988 (tp30) cc_final: 0.8770 (mm-30) REVERT: B 116 ASP cc_start: 0.8727 (m-30) cc_final: 0.8441 (m-30) REVERT: B 140 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8198 (mm-30) REVERT: B 147 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8239 (ttpp) REVERT: B 150 ASP cc_start: 0.8375 (m-30) cc_final: 0.8170 (m-30) REVERT: C 10 GLN cc_start: 0.8831 (tt0) cc_final: 0.8627 (tt0) REVERT: C 42 ASP cc_start: 0.8456 (t70) cc_final: 0.7926 (t70) REVERT: C 57 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8081 (mm-30) REVERT: C 60 GLU cc_start: 0.8347 (tp30) cc_final: 0.7976 (tp30) REVERT: C 61 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8083 (mm-30) REVERT: C 64 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8020 (mt-10) REVERT: C 86 LYS cc_start: 0.8854 (tppt) cc_final: 0.8650 (tppt) REVERT: C 91 ASP cc_start: 0.8578 (m-30) cc_final: 0.8348 (p0) REVERT: C 104 MET cc_start: 0.8517 (ttp) cc_final: 0.8133 (ttp) REVERT: C 108 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8280 (mmmm) REVERT: C 116 ASP cc_start: 0.8785 (m-30) cc_final: 0.8530 (m-30) REVERT: C 135 THR cc_start: 0.9300 (m) cc_final: 0.9029 (t) REVERT: C 140 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7789 (mp0) REVERT: C 147 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8260 (ttpp) REVERT: D 15 ASP cc_start: 0.8449 (p0) cc_final: 0.8033 (p0) REVERT: D 17 GLU cc_start: 0.8320 (tt0) cc_final: 0.8088 (tt0) REVERT: D 42 ASP cc_start: 0.8343 (t70) cc_final: 0.7899 (t70) REVERT: D 45 ASP cc_start: 0.8682 (p0) cc_final: 0.8437 (p0) REVERT: D 53 HIS cc_start: 0.8200 (t-90) cc_final: 0.7641 (t70) REVERT: D 57 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8204 (mt-10) REVERT: D 61 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8376 (mm-30) REVERT: D 63 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7465 (ttm-80) REVERT: D 64 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 68 ARG cc_start: 0.8239 (mtm110) cc_final: 0.7984 (mtm-85) REVERT: D 86 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8400 (tppt) REVERT: D 108 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8453 (mmmm) REVERT: D 116 ASP cc_start: 0.8767 (m-30) cc_final: 0.8474 (m-30) REVERT: D 124 ARG cc_start: 0.8915 (mmt-90) cc_final: 0.8614 (mmt-90) REVERT: D 147 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8196 (ttpp) REVERT: D 162 GLU cc_start: 0.7506 (pm20) cc_final: 0.7222 (pm20) REVERT: E 17 GLU cc_start: 0.8473 (tt0) cc_final: 0.8222 (tt0) REVERT: E 61 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7883 (mm-30) REVERT: E 84 ASP cc_start: 0.8630 (m-30) cc_final: 0.8398 (m-30) REVERT: E 92 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7505 (tm-30) REVERT: E 116 ASP cc_start: 0.8748 (m-30) cc_final: 0.8469 (m-30) REVERT: E 147 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8384 (ttpt) REVERT: E 150 ASP cc_start: 0.8465 (m-30) cc_final: 0.8180 (m-30) REVERT: F 10 GLN cc_start: 0.8703 (tt0) cc_final: 0.8431 (tt0) REVERT: F 17 GLU cc_start: 0.8499 (tt0) cc_final: 0.8160 (tt0) REVERT: F 60 GLU cc_start: 0.8227 (tp30) cc_final: 0.7752 (tp30) REVERT: F 61 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8215 (mm-30) REVERT: F 63 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7410 (ttm-80) REVERT: F 86 LYS cc_start: 0.8579 (ptpp) cc_final: 0.8286 (mmmm) REVERT: F 104 MET cc_start: 0.8663 (ttp) cc_final: 0.8289 (ttp) REVERT: F 107 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8258 (mm-30) REVERT: F 116 ASP cc_start: 0.8758 (m-30) cc_final: 0.8455 (m-30) REVERT: F 141 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8095 (mm-30) REVERT: F 147 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8287 (ttpp) REVERT: G 10 GLN cc_start: 0.8637 (tt0) cc_final: 0.8416 (tt0) REVERT: G 49 GLU cc_start: 0.8221 (tp30) cc_final: 0.7974 (tp30) REVERT: G 61 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7910 (mm-30) REVERT: G 84 ASP cc_start: 0.8670 (m-30) cc_final: 0.8428 (m-30) REVERT: G 86 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8260 (mmmm) REVERT: G 150 ASP cc_start: 0.8462 (m-30) cc_final: 0.8167 (m-30) REVERT: H 49 GLU cc_start: 0.8201 (tp30) cc_final: 0.7993 (tp30) REVERT: H 61 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8134 (mm-30) REVERT: H 64 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7955 (mt-10) REVERT: H 84 ASP cc_start: 0.8577 (m-30) cc_final: 0.8351 (m-30) REVERT: H 104 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8280 (ttp) REVERT: H 116 ASP cc_start: 0.8722 (m-30) cc_final: 0.8449 (m-30) REVERT: H 124 ARG cc_start: 0.8943 (mmt-90) cc_final: 0.8711 (mmt-90) REVERT: H 144 LEU cc_start: 0.9096 (tp) cc_final: 0.8895 (tm) REVERT: H 147 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8260 (ttpp) REVERT: H 162 GLU cc_start: 0.7696 (pm20) cc_final: 0.7434 (pm20) REVERT: I 45 ASP cc_start: 0.8528 (p0) cc_final: 0.8272 (p0) REVERT: I 60 GLU cc_start: 0.8386 (tp30) cc_final: 0.8067 (tp30) REVERT: I 61 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8138 (mm-30) REVERT: I 64 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7911 (mt-10) REVERT: I 81 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8405 (mm) REVERT: I 86 LYS cc_start: 0.8580 (ptpp) cc_final: 0.8376 (mmmm) REVERT: I 104 MET cc_start: 0.8564 (ttp) cc_final: 0.8251 (ttp) REVERT: I 116 ASP cc_start: 0.8720 (m-30) cc_final: 0.8442 (m-30) REVERT: I 140 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8214 (mm-30) REVERT: I 147 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8375 (ttpp) REVERT: J 10 GLN cc_start: 0.8832 (tt0) cc_final: 0.8605 (tt0) REVERT: J 15 ASP cc_start: 0.8481 (p0) cc_final: 0.8044 (p0) REVERT: J 57 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8054 (mm-30) REVERT: J 61 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7816 (mm-30) REVERT: J 64 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7940 (mt-10) REVERT: J 87 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8315 (ptmm) REVERT: J 116 ASP cc_start: 0.8770 (m-30) cc_final: 0.8468 (m-30) REVERT: J 124 ARG cc_start: 0.9031 (mmt-90) cc_final: 0.8713 (mmt-90) REVERT: J 140 GLU cc_start: 0.7825 (mp0) cc_final: 0.7536 (mm-30) REVERT: J 147 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8365 (ttpp) REVERT: J 157 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8575 (ptp90) REVERT: K 10 GLN cc_start: 0.8734 (tt0) cc_final: 0.8484 (tt0) REVERT: K 45 ASP cc_start: 0.8493 (p0) cc_final: 0.8055 (p0) REVERT: K 60 GLU cc_start: 0.8258 (tp30) cc_final: 0.8038 (tp30) REVERT: K 61 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7998 (mm-30) REVERT: K 68 ARG cc_start: 0.8450 (ptp-110) cc_final: 0.8021 (ptp90) REVERT: K 84 ASP cc_start: 0.8436 (m-30) cc_final: 0.8055 (m-30) REVERT: K 92 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7565 (tm-30) REVERT: K 107 GLU cc_start: 0.8921 (tp30) cc_final: 0.8711 (tp30) REVERT: K 116 ASP cc_start: 0.8769 (m-30) cc_final: 0.8505 (m-30) REVERT: K 147 LYS cc_start: 0.8395 (ttpp) cc_final: 0.8056 (ttpp) REVERT: K 150 ASP cc_start: 0.8369 (m-30) cc_final: 0.8042 (m-30) REVERT: K 153 THR cc_start: 0.8903 (m) cc_final: 0.8651 (p) REVERT: K 167 GLU cc_start: 0.8459 (tt0) cc_final: 0.8233 (tt0) REVERT: L 10 GLN cc_start: 0.8814 (tt0) cc_final: 0.8600 (tt0) REVERT: L 45 ASP cc_start: 0.8703 (p0) cc_final: 0.8319 (p0) REVERT: L 57 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8190 (mm-30) REVERT: L 60 GLU cc_start: 0.8443 (tp30) cc_final: 0.8102 (tp30) REVERT: L 61 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: L 64 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8227 (mm-30) REVERT: L 90 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8490 (mm-30) REVERT: L 104 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8295 (ttp) REVERT: L 109 LYS cc_start: 0.9060 (tmmt) cc_final: 0.8776 (tttp) REVERT: L 116 ASP cc_start: 0.8722 (m-30) cc_final: 0.8410 (m-30) REVERT: L 150 ASP cc_start: 0.8405 (m-30) cc_final: 0.8140 (m-30) REVERT: L 153 THR cc_start: 0.8960 (m) cc_final: 0.8703 (p) REVERT: L 162 GLU cc_start: 0.7627 (pm20) cc_final: 0.7424 (pm20) REVERT: L 167 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8189 (tt0) REVERT: M 10 GLN cc_start: 0.8694 (tt0) cc_final: 0.8463 (tt0) REVERT: M 49 GLU cc_start: 0.8169 (tp30) cc_final: 0.7816 (tp30) REVERT: M 56 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8179 (mmm-85) REVERT: M 57 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8201 (mm-30) REVERT: M 60 GLU cc_start: 0.8390 (tp30) cc_final: 0.8052 (tp30) REVERT: M 61 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8033 (mm-30) REVERT: M 64 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7944 (mt-10) REVERT: M 71 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8592 (tttm) REVERT: M 101 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8045 (mppt) REVERT: M 104 MET cc_start: 0.8348 (ttp) cc_final: 0.8011 (ttp) REVERT: M 116 ASP cc_start: 0.8764 (m-30) cc_final: 0.8476 (m-30) REVERT: M 140 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8179 (mm-30) REVERT: M 162 GLU cc_start: 0.7571 (pm20) cc_final: 0.7358 (pm20) REVERT: N 31 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8856 (t) REVERT: N 43 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7821 (mtm180) REVERT: N 45 ASP cc_start: 0.8564 (p0) cc_final: 0.8171 (p0) REVERT: N 49 GLU cc_start: 0.8184 (tp30) cc_final: 0.7963 (tp30) REVERT: N 60 GLU cc_start: 0.8405 (tp30) cc_final: 0.8041 (tp30) REVERT: N 61 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8124 (mm-30) REVERT: N 64 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7915 (mt-10) REVERT: N 79 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7453 (mmt-90) REVERT: N 86 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8468 (mmmm) REVERT: N 87 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8398 (ttpp) REVERT: N 104 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7938 (ttp) REVERT: N 107 GLU cc_start: 0.8872 (tp30) cc_final: 0.8671 (tp30) REVERT: N 140 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8116 (mm-30) REVERT: N 147 LYS cc_start: 0.8438 (ttpt) cc_final: 0.8102 (ttpp) REVERT: O 43 ARG cc_start: 0.8020 (mtm180) cc_final: 0.7724 (mtm180) REVERT: O 45 ASP cc_start: 0.8538 (p0) cc_final: 0.8192 (p0) REVERT: O 49 GLU cc_start: 0.8124 (tp30) cc_final: 0.7894 (tp30) REVERT: O 61 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7933 (mm-30) REVERT: O 64 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7922 (mt-10) REVERT: O 79 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7519 (mmt180) REVERT: O 84 ASP cc_start: 0.8713 (m-30) cc_final: 0.8494 (m-30) REVERT: O 104 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8366 (ttp) REVERT: O 109 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8787 (tttp) REVERT: O 116 ASP cc_start: 0.8746 (m-30) cc_final: 0.8504 (m-30) REVERT: O 147 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8215 (ttpp) REVERT: O 148 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8664 (mtm) REVERT: P 10 GLN cc_start: 0.8792 (tt0) cc_final: 0.8591 (tt0) REVERT: P 15 ASP cc_start: 0.8502 (p0) cc_final: 0.8235 (p0) REVERT: P 17 GLU cc_start: 0.8226 (tt0) cc_final: 0.8024 (tt0) REVERT: P 22 SER cc_start: 0.8979 (m) cc_final: 0.8682 (p) REVERT: P 57 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8182 (mm-30) REVERT: P 61 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8170 (mm-30) REVERT: P 64 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8046 (mt-10) REVERT: P 101 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (mppt) REVERT: P 104 MET cc_start: 0.8650 (ttp) cc_final: 0.8264 (ttp) REVERT: P 116 ASP cc_start: 0.8768 (m-30) cc_final: 0.8503 (m-30) REVERT: P 124 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8673 (mmt-90) REVERT: P 147 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8217 (ttpp) REVERT: P 162 GLU cc_start: 0.7649 (pm20) cc_final: 0.7395 (pm20) REVERT: P 167 GLU cc_start: 0.8532 (tt0) cc_final: 0.8258 (tt0) REVERT: Q 34 TYR cc_start: 0.9335 (m-10) cc_final: 0.9058 (m-10) REVERT: Q 61 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7935 (mm-30) REVERT: Q 64 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7947 (mt-10) REVERT: Q 84 ASP cc_start: 0.8737 (m-30) cc_final: 0.8501 (m-30) REVERT: Q 104 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: Q 107 GLU cc_start: 0.8755 (tp30) cc_final: 0.8508 (tp30) REVERT: Q 116 ASP cc_start: 0.8765 (m-30) cc_final: 0.8470 (m-30) REVERT: Q 140 GLU cc_start: 0.7973 (mp0) cc_final: 0.7628 (mm-30) REVERT: R 10 GLN cc_start: 0.8587 (tt0) cc_final: 0.8372 (tt0) REVERT: R 17 GLU cc_start: 0.8503 (tt0) cc_final: 0.8234 (tt0) REVERT: R 60 GLU cc_start: 0.8436 (tp30) cc_final: 0.8072 (tp30) REVERT: R 61 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7996 (mm-30) REVERT: R 64 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8155 (mt-10) REVERT: R 90 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8428 (mm-30) REVERT: R 104 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8392 (ttp) REVERT: R 116 ASP cc_start: 0.8737 (m-30) cc_final: 0.8517 (m-30) REVERT: R 148 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8739 (mtm) REVERT: R 167 GLU cc_start: 0.8537 (tt0) cc_final: 0.8257 (tt0) REVERT: S 10 GLN cc_start: 0.8584 (tt0) cc_final: 0.8375 (tt0) REVERT: S 17 GLU cc_start: 0.8416 (tt0) cc_final: 0.8087 (tt0) REVERT: S 45 ASP cc_start: 0.8567 (p0) cc_final: 0.8291 (OUTLIER) REVERT: S 60 GLU cc_start: 0.8445 (tp30) cc_final: 0.8020 (tp30) REVERT: S 84 ASP cc_start: 0.8420 (m-30) cc_final: 0.7986 (m-30) REVERT: S 90 GLU cc_start: 0.8591 (pm20) cc_final: 0.8322 (pm20) REVERT: S 104 MET cc_start: 0.8608 (ttp) cc_final: 0.8225 (ttp) REVERT: S 116 ASP cc_start: 0.8723 (m-30) cc_final: 0.8496 (m-30) REVERT: S 136 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.8251 (p-80) REVERT: S 141 GLU cc_start: 0.9048 (tp30) cc_final: 0.8847 (tp30) REVERT: S 167 GLU cc_start: 0.8475 (tt0) cc_final: 0.8208 (tt0) REVERT: T 104 MET cc_start: 0.8647 (ttp) cc_final: 0.8291 (ttp) REVERT: T 112 GLN cc_start: 0.8859 (tp40) cc_final: 0.8119 (tp-100) REVERT: T 116 ASP cc_start: 0.8765 (m-30) cc_final: 0.8223 (m-30) REVERT: T 162 GLU cc_start: 0.7638 (pm20) cc_final: 0.7394 (pm20) REVERT: U 17 GLU cc_start: 0.8442 (tt0) cc_final: 0.8104 (tt0) REVERT: U 49 GLU cc_start: 0.8200 (tp30) cc_final: 0.7871 (tp30) REVERT: U 57 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8101 (mm-30) REVERT: U 61 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8122 (mm-30) REVERT: U 84 ASP cc_start: 0.8720 (m-30) cc_final: 0.8489 (m-30) REVERT: U 104 MET cc_start: 0.8577 (ttp) cc_final: 0.8155 (ttp) REVERT: U 116 ASP cc_start: 0.8769 (m-30) cc_final: 0.8492 (m-30) REVERT: U 141 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8136 (tp30) REVERT: U 147 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8235 (ttpp) REVERT: U 150 ASP cc_start: 0.8340 (m-30) cc_final: 0.8105 (m-30) REVERT: U 167 GLU cc_start: 0.8511 (tt0) cc_final: 0.8214 (tt0) REVERT: V 43 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7771 (mtm180) REVERT: V 45 ASP cc_start: 0.8595 (p0) cc_final: 0.8252 (p0) REVERT: V 61 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: V 64 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7855 (mt-10) REVERT: V 84 ASP cc_start: 0.8710 (m-30) cc_final: 0.8396 (m-30) REVERT: V 140 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7888 (mp0) REVERT: V 147 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8265 (ttpp) REVERT: V 153 THR cc_start: 0.8974 (m) cc_final: 0.8652 (p) REVERT: W 10 GLN cc_start: 0.8760 (tt0) cc_final: 0.8551 (tt0) REVERT: W 17 GLU cc_start: 0.8525 (tt0) cc_final: 0.8246 (tt0) REVERT: W 57 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8116 (mm-30) REVERT: W 61 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8095 (mm-30) REVERT: W 64 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8299 (mm-30) REVERT: W 79 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7530 (mmt-90) REVERT: W 86 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8494 (mmmm) REVERT: W 90 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8509 (mm-30) REVERT: W 92 GLU cc_start: 0.7687 (pp20) cc_final: 0.7361 (tm-30) REVERT: W 104 MET cc_start: 0.8636 (ttp) cc_final: 0.8178 (ttp) REVERT: W 107 GLU cc_start: 0.8948 (tp30) cc_final: 0.8681 (mm-30) REVERT: W 116 ASP cc_start: 0.8797 (m-30) cc_final: 0.8572 (m-30) REVERT: W 140 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7839 (mp0) REVERT: W 147 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8233 (ttpp) REVERT: W 162 GLU cc_start: 0.7496 (pm20) cc_final: 0.7287 (pm20) REVERT: W 167 GLU cc_start: 0.8432 (tt0) cc_final: 0.8181 (tt0) REVERT: X 15 ASP cc_start: 0.8280 (p0) cc_final: 0.8073 (p0) REVERT: X 64 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8101 (mt-10) REVERT: X 107 GLU cc_start: 0.8805 (tp30) cc_final: 0.8436 (tp30) REVERT: X 116 ASP cc_start: 0.8772 (m-30) cc_final: 0.8512 (m-30) REVERT: X 124 ARG cc_start: 0.9021 (mmt-90) cc_final: 0.8781 (mmt-90) REVERT: X 135 THR cc_start: 0.9264 (m) cc_final: 0.9046 (t) REVERT: X 148 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8495 (mtm) REVERT: X 150 ASP cc_start: 0.8441 (m-30) cc_final: 0.8147 (m-30) REVERT: X 167 GLU cc_start: 0.8431 (tt0) cc_final: 0.8198 (tt0) outliers start: 117 outliers final: 38 residues processed: 1415 average time/residue: 1.9211 time to fit residues: 3106.8892 Evaluate side-chains 1330 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1270 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 136 HIS 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 104 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 87 LYS 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 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 31 SER 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 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 98 ASP Chi-restraints excluded: chain R residue 104 MET 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 U residue 72 MET Chi-restraints excluded: chain V residue 61 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 101 LYS Chi-restraints excluded: chain X residue 148 MET 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 39 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 311 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 D 7 GLN D 29 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN F 7 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 HIS G 29 GLN G 75 GLN J 29 GLN J 136 HIS K 7 GLN K 11 ASN L 7 GLN L 29 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 HIS N 7 GLN N 29 GLN N 136 HIS O 7 GLN O 29 GLN ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 HIS Q 11 ASN Q 29 GLN R 29 GLN S 29 GLN ** S 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN ** T 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 GLN U 29 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 GLN W 11 ASN W 29 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076235 restraints weight = 58654.522| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.62 r_work: 0.2890 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 33838 Z= 0.254 Angle : 0.636 9.933 45524 Z= 0.323 Chirality : 0.041 0.191 4872 Planarity : 0.005 0.046 5974 Dihedral : 6.930 89.760 4610 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.45 % Favored : 98.41 % Rotamer: Outliers : 3.79 % Allowed : 22.07 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.13), residues: 4080 helix: 2.43 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.31 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.014 0.001 HIS S 136 PHE 0.022 0.003 PHE S 137 TYR 0.023 0.002 TYR F 66 ARG 0.009 0.001 ARG P 56 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 2675) hydrogen bonds : angle 3.82174 ( 8025) covalent geometry : bond 0.00561 (33838) covalent geometry : angle 0.63567 (45524) *********************** 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 1434 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1302 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8728 (t70) cc_final: 0.8404 (t70) REVERT: A 60 GLU cc_start: 0.8858 (tp30) cc_final: 0.8305 (tp30) REVERT: A 61 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8334 (mm-30) REVERT: A 64 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8589 (mt-10) REVERT: A 86 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8557 (tppt) REVERT: A 104 MET cc_start: 0.9141 (tpp) cc_final: 0.8924 (ttp) REVERT: A 116 ASP cc_start: 0.8942 (m-30) cc_final: 0.8733 (m-30) REVERT: A 147 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8680 (ttpp) REVERT: A 150 ASP cc_start: 0.8790 (m-30) cc_final: 0.8569 (m-30) REVERT: B 45 ASP cc_start: 0.8822 (p0) cc_final: 0.8495 (p0) REVERT: B 64 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8277 (mt-10) REVERT: B 84 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7911 (t70) REVERT: B 104 MET cc_start: 0.8973 (ttp) cc_final: 0.8627 (ttp) REVERT: B 116 ASP cc_start: 0.8959 (m-30) cc_final: 0.8737 (m-30) REVERT: C 17 GLU cc_start: 0.8537 (tt0) cc_final: 0.8314 (tt0) REVERT: C 42 ASP cc_start: 0.8786 (t70) cc_final: 0.8228 (t70) REVERT: C 49 GLU cc_start: 0.8458 (tp30) cc_final: 0.8170 (tp30) REVERT: C 57 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8475 (mm-30) REVERT: C 60 GLU cc_start: 0.8770 (tp30) cc_final: 0.8540 (tp30) REVERT: C 61 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8609 (mm-30) REVERT: C 64 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8503 (mm-30) REVERT: C 104 MET cc_start: 0.8965 (ttp) cc_final: 0.8588 (ttp) REVERT: C 116 ASP cc_start: 0.8961 (m-30) cc_final: 0.8734 (m-30) REVERT: C 140 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8220 (mp0) REVERT: C 143 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8980 (mtmm) REVERT: C 147 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8756 (ttpp) REVERT: D 42 ASP cc_start: 0.8661 (t70) cc_final: 0.8270 (t70) REVERT: D 53 HIS cc_start: 0.8591 (t-90) cc_final: 0.8079 (t70) REVERT: D 57 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8420 (mt-10) REVERT: D 64 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 68 ARG cc_start: 0.8724 (mtm110) cc_final: 0.8472 (mtm-85) REVERT: D 86 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8618 (tppt) REVERT: D 108 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8814 (mmmm) REVERT: D 116 ASP cc_start: 0.9017 (m-30) cc_final: 0.8787 (m-30) REVERT: D 147 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8688 (ttpp) REVERT: D 162 GLU cc_start: 0.7721 (pm20) cc_final: 0.7387 (pm20) REVERT: E 61 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8390 (mm-30) REVERT: E 92 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7777 (tm-30) REVERT: E 116 ASP cc_start: 0.8979 (m-30) cc_final: 0.8752 (m-30) REVERT: E 147 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8796 (ttpp) REVERT: E 157 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8991 (ptp90) REVERT: F 104 MET cc_start: 0.9048 (ttp) cc_final: 0.8686 (ttp) REVERT: F 107 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8799 (tp30) REVERT: F 116 ASP cc_start: 0.9000 (m-30) cc_final: 0.8782 (m-30) REVERT: F 141 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8804 (tp30) REVERT: F 147 LYS cc_start: 0.9005 (ttpp) cc_final: 0.8743 (ttpp) REVERT: G 61 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8408 (mm-30) REVERT: G 84 ASP cc_start: 0.8903 (m-30) cc_final: 0.8672 (m-30) REVERT: G 86 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8568 (mmmm) REVERT: G 150 ASP cc_start: 0.8739 (m-30) cc_final: 0.8515 (m-30) REVERT: H 42 ASP cc_start: 0.8721 (t70) cc_final: 0.8259 (t70) REVERT: H 49 GLU cc_start: 0.8497 (tp30) cc_final: 0.8275 (tp30) REVERT: H 61 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8655 (mm-30) REVERT: H 84 ASP cc_start: 0.8864 (m-30) cc_final: 0.8619 (m-30) REVERT: H 90 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8616 (mm-30) REVERT: H 104 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8680 (ttp) REVERT: H 107 GLU cc_start: 0.8978 (tp30) cc_final: 0.8767 (tp30) REVERT: H 109 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9058 (ttmt) REVERT: H 116 ASP cc_start: 0.8957 (m-30) cc_final: 0.8736 (m-30) REVERT: H 124 ARG cc_start: 0.9192 (mmt-90) cc_final: 0.8928 (mmt-90) REVERT: H 147 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8673 (ttpp) REVERT: H 162 GLU cc_start: 0.7835 (pm20) cc_final: 0.7552 (pm20) REVERT: I 60 GLU cc_start: 0.8738 (tp30) cc_final: 0.8365 (tp30) REVERT: I 61 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8559 (mm-30) REVERT: I 64 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8246 (mt-10) REVERT: I 104 MET cc_start: 0.8926 (ttp) cc_final: 0.8669 (ttp) REVERT: I 116 ASP cc_start: 0.8993 (m-30) cc_final: 0.8781 (m-30) REVERT: I 147 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8800 (ttpp) REVERT: J 61 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8323 (mm-30) REVERT: J 64 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8316 (mt-10) REVERT: J 116 ASP cc_start: 0.8948 (m-30) cc_final: 0.8718 (m-30) REVERT: J 140 GLU cc_start: 0.8143 (mp0) cc_final: 0.7824 (mm-30) REVERT: J 143 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8862 (mtmm) REVERT: J 147 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8732 (ttpp) REVERT: J 157 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8952 (ptp90) REVERT: K 45 ASP cc_start: 0.8787 (p0) cc_final: 0.8321 (p0) REVERT: K 49 GLU cc_start: 0.8498 (tp30) cc_final: 0.8218 (tp30) REVERT: K 60 GLU cc_start: 0.8631 (tp30) cc_final: 0.8374 (tp30) REVERT: K 61 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8413 (mm-30) REVERT: K 68 ARG cc_start: 0.8841 (ptp-110) cc_final: 0.8487 (ptp90) REVERT: K 84 ASP cc_start: 0.8747 (m-30) cc_final: 0.8399 (m-30) REVERT: K 107 GLU cc_start: 0.9137 (tp30) cc_final: 0.8667 (tp30) REVERT: K 116 ASP cc_start: 0.8947 (m-30) cc_final: 0.8724 (m-30) REVERT: K 141 GLU cc_start: 0.8686 (tp30) cc_final: 0.8349 (tp30) REVERT: K 147 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8680 (ttpp) REVERT: L 45 ASP cc_start: 0.8873 (p0) cc_final: 0.8476 (p0) REVERT: L 60 GLU cc_start: 0.8818 (tp30) cc_final: 0.8483 (tp30) REVERT: L 61 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8598 (mm-30) REVERT: L 64 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8346 (mt-10) REVERT: L 104 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8631 (ttp) REVERT: L 116 ASP cc_start: 0.8987 (m-30) cc_final: 0.8757 (m-30) REVERT: L 140 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8141 (mp0) REVERT: L 147 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8628 (ttpp) REVERT: M 49 GLU cc_start: 0.8465 (tp30) cc_final: 0.8090 (tp30) REVERT: M 56 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8644 (mmm-85) REVERT: M 60 GLU cc_start: 0.8772 (tp30) cc_final: 0.8469 (tp30) REVERT: M 61 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8579 (mm-30) REVERT: M 64 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8299 (mt-10) REVERT: M 104 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8598 (ttp) REVERT: M 116 ASP cc_start: 0.8946 (m-30) cc_final: 0.8725 (m-30) REVERT: M 140 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8418 (mm-30) REVERT: M 147 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8642 (ttpp) REVERT: M 162 GLU cc_start: 0.7670 (pm20) cc_final: 0.7439 (pm20) REVERT: N 31 SER cc_start: 0.9395 (OUTLIER) cc_final: 0.9190 (t) REVERT: N 60 GLU cc_start: 0.8760 (tp30) cc_final: 0.8404 (tp30) REVERT: N 61 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8602 (mm-30) REVERT: N 64 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8380 (mt-10) REVERT: N 79 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7810 (mmt-90) REVERT: N 104 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8520 (ttp) REVERT: N 107 GLU cc_start: 0.9042 (tp30) cc_final: 0.8790 (tp30) REVERT: N 140 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8404 (mm-30) REVERT: N 147 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8638 (ttpp) REVERT: N 172 ARG cc_start: 0.9359 (mmm160) cc_final: 0.9146 (mmm160) REVERT: O 49 GLU cc_start: 0.8524 (tp30) cc_final: 0.8310 (tp30) REVERT: O 56 ARG cc_start: 0.9017 (mmm160) cc_final: 0.8805 (mmm-85) REVERT: O 64 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8320 (mt-10) REVERT: O 79 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7999 (mmt-90) REVERT: O 84 ASP cc_start: 0.8952 (m-30) cc_final: 0.8736 (m-30) REVERT: O 104 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8686 (ttp) REVERT: O 116 ASP cc_start: 0.8954 (m-30) cc_final: 0.8732 (m-30) REVERT: O 147 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8731 (ttpp) REVERT: P 22 SER cc_start: 0.9329 (m) cc_final: 0.9043 (p) REVERT: P 61 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8542 (mm-30) REVERT: P 64 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8324 (mt-10) REVERT: P 86 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8620 (tppt) REVERT: P 104 MET cc_start: 0.8952 (ttp) cc_final: 0.8735 (ttp) REVERT: P 116 ASP cc_start: 0.9009 (m-30) cc_final: 0.8786 (m-30) REVERT: P 147 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8743 (ttpp) REVERT: Q 61 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8422 (mm-30) REVERT: Q 64 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8283 (mt-10) REVERT: Q 104 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8670 (ttp) REVERT: Q 116 ASP cc_start: 0.8937 (m-30) cc_final: 0.8720 (m-30) REVERT: Q 140 GLU cc_start: 0.8320 (mp0) cc_final: 0.8098 (mm-30) REVERT: Q 162 GLU cc_start: 0.7840 (pm20) cc_final: 0.7604 (pm20) REVERT: R 42 ASP cc_start: 0.8788 (t70) cc_final: 0.8435 (t70) REVERT: R 45 ASP cc_start: 0.8991 (p0) cc_final: 0.8783 (p0) REVERT: R 60 GLU cc_start: 0.8808 (tp30) cc_final: 0.8423 (tp30) REVERT: R 61 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8306 (mm-30) REVERT: R 64 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8461 (mt-10) REVERT: R 104 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8630 (ttp) REVERT: R 116 ASP cc_start: 0.8976 (m-30) cc_final: 0.8753 (m-30) REVERT: R 147 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8767 (ttpp) REVERT: R 148 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9080 (mtm) REVERT: S 49 GLU cc_start: 0.8930 (tt0) cc_final: 0.8696 (tp30) REVERT: S 57 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7772 (mm-30) REVERT: S 60 GLU cc_start: 0.8793 (tp30) cc_final: 0.7987 (pt0) REVERT: S 61 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8055 (mm-30) REVERT: S 84 ASP cc_start: 0.8806 (m-30) cc_final: 0.8550 (m-30) REVERT: S 104 MET cc_start: 0.9035 (ttp) cc_final: 0.8617 (ttp) REVERT: S 116 ASP cc_start: 0.8975 (m-30) cc_final: 0.8762 (m-30) REVERT: S 147 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8718 (ttpp) REVERT: S 167 GLU cc_start: 0.8780 (tt0) cc_final: 0.8573 (tt0) REVERT: T 104 MET cc_start: 0.9058 (ttp) cc_final: 0.8706 (ttp) REVERT: T 116 ASP cc_start: 0.8986 (m-30) cc_final: 0.8758 (m-30) REVERT: T 136 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.7736 (p90) REVERT: T 162 GLU cc_start: 0.7762 (pm20) cc_final: 0.7448 (pm20) REVERT: U 45 ASP cc_start: 0.8842 (p0) cc_final: 0.8606 (p0) REVERT: U 49 GLU cc_start: 0.8546 (tp30) cc_final: 0.8167 (tp30) REVERT: U 61 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8568 (mm-30) REVERT: U 64 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8323 (mt-10) REVERT: U 104 MET cc_start: 0.9016 (ttp) cc_final: 0.8615 (ttp) REVERT: U 116 ASP cc_start: 0.8950 (m-30) cc_final: 0.8720 (m-30) REVERT: U 147 LYS cc_start: 0.9008 (ttpp) cc_final: 0.8727 (ttpp) REVERT: U 162 GLU cc_start: 0.7668 (pm20) cc_final: 0.7374 (pm20) REVERT: V 10 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8842 (tt0) REVERT: V 64 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8234 (mt-10) REVERT: V 140 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8150 (mp0) REVERT: V 144 LEU cc_start: 0.9531 (tp) cc_final: 0.9324 (tp) REVERT: W 61 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8559 (mm-30) REVERT: W 79 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7835 (mmt180) REVERT: W 84 ASP cc_start: 0.8958 (m-30) cc_final: 0.8679 (m-30) REVERT: W 86 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8616 (tppt) REVERT: W 104 MET cc_start: 0.8969 (ttp) cc_final: 0.8532 (ttp) REVERT: W 116 ASP cc_start: 0.9004 (m-30) cc_final: 0.8794 (m-30) REVERT: W 140 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8143 (mp0) REVERT: W 141 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8669 (tp30) REVERT: W 147 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8688 (ttpp) REVERT: W 162 GLU cc_start: 0.7779 (pm20) cc_final: 0.7539 (pm20) REVERT: W 167 GLU cc_start: 0.8665 (tt0) cc_final: 0.8428 (tt0) REVERT: X 64 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8650 (mm-30) REVERT: X 107 GLU cc_start: 0.9097 (tp30) cc_final: 0.8627 (tp30) REVERT: X 116 ASP cc_start: 0.9017 (m-30) cc_final: 0.8790 (m-30) REVERT: X 135 THR cc_start: 0.9438 (m) cc_final: 0.9214 (t) REVERT: X 140 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8146 (mp0) REVERT: X 141 GLU cc_start: 0.8751 (tp30) cc_final: 0.8403 (tp30) REVERT: X 148 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9088 (mtm) REVERT: X 167 GLU cc_start: 0.8711 (tt0) cc_final: 0.8490 (tt0) outliers start: 132 outliers final: 55 residues processed: 1333 average time/residue: 2.2212 time to fit residues: 3393.4143 Evaluate side-chains 1298 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 1223 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG 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 C residue 165 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 49 GLU 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 157 ARG 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 104 MET Chi-restraints excluded: chain H residue 109 LYS 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 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 176 LYS Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain N residue 31 SER 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 104 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 104 MET 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 10 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 98 ASP Chi-restraints excluded: chain X residue 101 LYS Chi-restraints excluded: chain X residue 148 MET 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 347 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 374 optimal weight: 0.4980 chunk 407 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 C 7 GLN D 7 GLN E 7 GLN G 29 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN K 7 GLN L 7 GLN L 10 GLN M 7 GLN N 7 GLN O 7 GLN O 29 GLN ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 HIS Q 29 GLN S 136 HIS T 29 GLN ** T 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 GLN W 7 GLN W 29 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081291 restraints weight = 58282.295| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.60 r_work: 0.2999 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33838 Z= 0.136 Angle : 0.597 10.512 45524 Z= 0.306 Chirality : 0.037 0.150 4872 Planarity : 0.004 0.042 5974 Dihedral : 6.704 88.483 4604 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.57 % Favored : 98.28 % Rotamer: Outliers : 2.84 % Allowed : 25.46 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.13), residues: 4080 helix: 2.63 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.29 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 93 HIS 0.007 0.001 HIS T 136 PHE 0.016 0.002 PHE T 132 TYR 0.025 0.002 TYR H 66 ARG 0.009 0.001 ARG X 56 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 2675) hydrogen bonds : angle 3.68046 ( 8025) covalent geometry : bond 0.00305 (33838) covalent geometry : angle 0.59669 (45524) *********************** 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 1507 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1408 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8526 (t70) cc_final: 0.8037 (t70) REVERT: A 49 GLU cc_start: 0.8240 (tp30) cc_final: 0.7924 (tp30) REVERT: A 60 GLU cc_start: 0.8642 (tp30) cc_final: 0.8265 (tp30) REVERT: A 61 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 64 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8279 (mm-30) REVERT: A 86 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8565 (tppt) REVERT: A 104 MET cc_start: 0.8986 (tpp) cc_final: 0.8710 (tpp) REVERT: A 116 ASP cc_start: 0.8830 (m-30) cc_final: 0.8586 (m-30) REVERT: A 141 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8213 (tp30) REVERT: A 147 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8551 (ttpp) REVERT: A 150 ASP cc_start: 0.8504 (m-30) cc_final: 0.8274 (m-30) REVERT: B 7 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8942 (pt0) REVERT: B 45 ASP cc_start: 0.8621 (p0) cc_final: 0.8309 (p0) REVERT: B 61 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8153 (mm-30) REVERT: B 64 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8191 (mt-10) REVERT: B 84 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7767 (t70) REVERT: B 104 MET cc_start: 0.8803 (ttp) cc_final: 0.8415 (ttp) REVERT: B 116 ASP cc_start: 0.8810 (m-30) cc_final: 0.8562 (m-30) REVERT: B 143 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8891 (mtmm) REVERT: C 17 GLU cc_start: 0.8195 (tt0) cc_final: 0.7917 (tt0) REVERT: C 42 ASP cc_start: 0.8562 (t70) cc_final: 0.7968 (t70) REVERT: C 49 GLU cc_start: 0.8085 (tp30) cc_final: 0.7784 (tp30) REVERT: C 57 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8279 (mm-30) REVERT: C 60 GLU cc_start: 0.8512 (tp30) cc_final: 0.8245 (tp30) REVERT: C 61 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8441 (mm-30) REVERT: C 68 ARG cc_start: 0.8749 (ptp90) cc_final: 0.8306 (ptp90) REVERT: C 86 LYS cc_start: 0.8902 (tppt) cc_final: 0.8559 (tppt) REVERT: C 104 MET cc_start: 0.8786 (ttp) cc_final: 0.8357 (ttp) REVERT: C 112 GLN cc_start: 0.9087 (tp40) cc_final: 0.8251 (tp-100) REVERT: C 116 ASP cc_start: 0.8872 (m-30) cc_final: 0.8288 (m-30) REVERT: C 140 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8013 (mp0) REVERT: C 141 GLU cc_start: 0.8790 (tp30) cc_final: 0.8589 (tp30) REVERT: C 147 LYS cc_start: 0.8885 (ttpp) cc_final: 0.8548 (ttpp) REVERT: D 22 SER cc_start: 0.9301 (m) cc_final: 0.9001 (p) REVERT: D 42 ASP cc_start: 0.8442 (t70) cc_final: 0.8107 (t70) REVERT: D 45 ASP cc_start: 0.8527 (p0) cc_final: 0.8300 (p0) REVERT: D 53 HIS cc_start: 0.8457 (t-90) cc_final: 0.7799 (t70) REVERT: D 57 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8141 (mt-10) REVERT: D 61 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8458 (mm-30) REVERT: D 63 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7863 (ttm-80) REVERT: D 64 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8211 (mm-30) REVERT: D 74 ASN cc_start: 0.9179 (m-40) cc_final: 0.8701 (m110) REVERT: D 107 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 108 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8632 (mmmm) REVERT: D 116 ASP cc_start: 0.8876 (m-30) cc_final: 0.8567 (m-30) REVERT: D 147 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8581 (ttpp) REVERT: D 150 ASP cc_start: 0.8494 (m-30) cc_final: 0.8266 (m-30) REVERT: D 162 GLU cc_start: 0.7613 (pm20) cc_final: 0.7346 (pm20) REVERT: E 42 ASP cc_start: 0.8325 (t70) cc_final: 0.7675 (t70) REVERT: E 61 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8108 (mm-30) REVERT: E 84 ASP cc_start: 0.8761 (m-30) cc_final: 0.8527 (m-30) REVERT: E 116 ASP cc_start: 0.8856 (m-30) cc_final: 0.8574 (m-30) REVERT: F 17 GLU cc_start: 0.8536 (tt0) cc_final: 0.8272 (tt0) REVERT: F 104 MET cc_start: 0.8719 (ttp) cc_final: 0.8355 (ttp) REVERT: F 107 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8462 (mm-30) REVERT: F 116 ASP cc_start: 0.8829 (m-30) cc_final: 0.8550 (m-30) REVERT: F 147 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8649 (ttpp) REVERT: G 61 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8183 (mm-30) REVERT: G 84 ASP cc_start: 0.8739 (m-30) cc_final: 0.8475 (m-30) REVERT: G 86 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8484 (tppt) REVERT: G 150 ASP cc_start: 0.8555 (m-30) cc_final: 0.8315 (m-30) REVERT: H 42 ASP cc_start: 0.8556 (t70) cc_final: 0.8119 (t70) REVERT: H 49 GLU cc_start: 0.8244 (tp30) cc_final: 0.8014 (tp30) REVERT: H 61 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8435 (mm-30) REVERT: H 64 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8152 (mt-10) REVERT: H 104 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8245 (ttp) REVERT: H 112 GLN cc_start: 0.9051 (tp40) cc_final: 0.8211 (tp-100) REVERT: H 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8224 (m-30) REVERT: H 140 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7998 (mp0) REVERT: H 147 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8517 (ttpp) REVERT: H 162 GLU cc_start: 0.7733 (pm20) cc_final: 0.7501 (pm20) REVERT: I 57 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8316 (mm-30) REVERT: I 60 GLU cc_start: 0.8497 (tp30) cc_final: 0.8189 (tp30) REVERT: I 61 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8246 (mm-30) REVERT: I 64 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8201 (mt-10) REVERT: I 104 MET cc_start: 0.8790 (ttp) cc_final: 0.8510 (ttp) REVERT: I 108 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8688 (mmmm) REVERT: I 112 GLN cc_start: 0.9040 (tp40) cc_final: 0.8279 (tp-100) REVERT: I 116 ASP cc_start: 0.8814 (m-30) cc_final: 0.8265 (m-30) REVERT: I 143 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8913 (mtmm) REVERT: I 147 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8617 (ttpp) REVERT: J 42 ASP cc_start: 0.8489 (t70) cc_final: 0.7956 (t70) REVERT: J 61 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8140 (mm-30) REVERT: J 64 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8228 (mt-10) REVERT: J 74 ASN cc_start: 0.9162 (m-40) cc_final: 0.8576 (m110) REVERT: J 84 ASP cc_start: 0.8614 (m-30) cc_final: 0.8317 (m-30) REVERT: J 116 ASP cc_start: 0.8842 (m-30) cc_final: 0.8540 (m-30) REVERT: J 140 GLU cc_start: 0.8068 (mp0) cc_final: 0.7541 (mp0) REVERT: J 143 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8915 (mtmm) REVERT: J 147 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8504 (ttpp) REVERT: J 150 ASP cc_start: 0.8532 (m-30) cc_final: 0.8291 (m-30) REVERT: K 34 TYR cc_start: 0.9381 (m-10) cc_final: 0.9073 (m-10) REVERT: K 45 ASP cc_start: 0.8627 (p0) cc_final: 0.8303 (p0) REVERT: K 61 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8149 (mm-30) REVERT: K 64 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8026 (mt-10) REVERT: K 68 ARG cc_start: 0.8681 (ptp-110) cc_final: 0.8378 (ptp90) REVERT: K 79 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7861 (mmt-90) REVERT: K 84 ASP cc_start: 0.8556 (m-30) cc_final: 0.8211 (m-30) REVERT: K 86 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8586 (mmmm) REVERT: K 107 GLU cc_start: 0.8885 (tp30) cc_final: 0.8277 (tp30) REVERT: K 112 GLN cc_start: 0.9058 (tp40) cc_final: 0.8292 (tp-100) REVERT: K 116 ASP cc_start: 0.8859 (m-30) cc_final: 0.8318 (m-30) REVERT: K 135 THR cc_start: 0.9332 (m) cc_final: 0.9129 (t) REVERT: K 147 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8533 (ttpp) REVERT: L 45 ASP cc_start: 0.8720 (p0) cc_final: 0.8376 (p0) REVERT: L 60 GLU cc_start: 0.8590 (tp30) cc_final: 0.8318 (tp30) REVERT: L 87 LYS cc_start: 0.9092 (ptmm) cc_final: 0.8749 (ptmm) REVERT: L 90 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8526 (mm-30) REVERT: L 104 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8246 (ttp) REVERT: L 107 GLU cc_start: 0.8674 (tp30) cc_final: 0.8404 (tp30) REVERT: L 112 GLN cc_start: 0.9075 (tp40) cc_final: 0.8278 (tp-100) REVERT: L 116 ASP cc_start: 0.8885 (m-30) cc_final: 0.8281 (m-30) REVERT: L 140 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8023 (mp0) REVERT: L 144 LEU cc_start: 0.9225 (tm) cc_final: 0.9019 (tm) REVERT: L 147 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8506 (ttpp) REVERT: L 167 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8065 (tt0) REVERT: M 42 ASP cc_start: 0.8454 (t70) cc_final: 0.7904 (t70) REVERT: M 49 GLU cc_start: 0.8241 (tp30) cc_final: 0.7915 (tp30) REVERT: M 60 GLU cc_start: 0.8580 (tp30) cc_final: 0.8274 (tp30) REVERT: M 61 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8375 (mm-30) REVERT: M 68 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8302 (ttm110) REVERT: M 104 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8311 (ttp) REVERT: M 116 ASP cc_start: 0.8859 (m-30) cc_final: 0.8567 (m-30) REVERT: M 140 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8190 (mm-30) REVERT: M 147 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8473 (ttpp) REVERT: N 17 GLU cc_start: 0.8576 (tt0) cc_final: 0.8348 (tt0) REVERT: N 34 TYR cc_start: 0.9356 (m-10) cc_final: 0.9095 (m-10) REVERT: N 43 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8101 (mtm180) REVERT: N 60 GLU cc_start: 0.8574 (tp30) cc_final: 0.8259 (tp30) REVERT: N 61 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8428 (mm-30) REVERT: N 79 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7708 (mmp80) REVERT: N 84 ASP cc_start: 0.8831 (m-30) cc_final: 0.8526 (m-30) REVERT: N 86 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8669 (mmmm) REVERT: N 101 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8794 (ttmm) REVERT: N 104 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: N 107 GLU cc_start: 0.8846 (tp30) cc_final: 0.8479 (tp30) REVERT: N 112 GLN cc_start: 0.8944 (tp40) cc_final: 0.8495 (tp-100) REVERT: N 116 ASP cc_start: 0.8764 (m-30) cc_final: 0.8401 (m-30) REVERT: N 140 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8058 (mp0) REVERT: N 147 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8513 (ttpp) REVERT: O 34 TYR cc_start: 0.9435 (m-10) cc_final: 0.9159 (m-10) REVERT: O 45 ASP cc_start: 0.8634 (p0) cc_final: 0.8330 (p0) REVERT: O 61 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8204 (mm-30) REVERT: O 64 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8294 (mt-10) REVERT: O 79 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7709 (mmt180) REVERT: O 101 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8773 (ttmm) REVERT: O 104 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8400 (ttp) REVERT: O 109 LYS cc_start: 0.9180 (tmmt) cc_final: 0.8891 (tttm) REVERT: O 116 ASP cc_start: 0.8876 (m-30) cc_final: 0.8594 (m-30) REVERT: O 140 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7923 (mp0) REVERT: O 147 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8570 (ttpp) REVERT: P 22 SER cc_start: 0.9267 (m) cc_final: 0.8999 (p) REVERT: P 42 ASP cc_start: 0.8427 (t70) cc_final: 0.8096 (t70) REVERT: P 61 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8345 (mm-30) REVERT: P 64 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8326 (mt-10) REVERT: P 104 MET cc_start: 0.8812 (ttp) cc_final: 0.8528 (ttp) REVERT: P 107 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8303 (tp30) REVERT: P 112 GLN cc_start: 0.9079 (tp40) cc_final: 0.8303 (tp-100) REVERT: P 116 ASP cc_start: 0.8858 (m-30) cc_final: 0.8353 (m-30) REVERT: P 141 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8525 (tp30) REVERT: P 147 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8536 (ttpp) REVERT: P 162 GLU cc_start: 0.7650 (pm20) cc_final: 0.7407 (pm20) REVERT: P 167 GLU cc_start: 0.8535 (tt0) cc_final: 0.8296 (tt0) REVERT: Q 61 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8268 (mm-30) REVERT: Q 64 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8255 (mt-10) REVERT: Q 84 ASP cc_start: 0.8763 (m-30) cc_final: 0.8550 (m-30) REVERT: Q 86 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8673 (mmmm) REVERT: Q 104 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8289 (ttp) REVERT: Q 107 GLU cc_start: 0.8731 (tp30) cc_final: 0.8369 (tp30) REVERT: Q 116 ASP cc_start: 0.8871 (m-30) cc_final: 0.8588 (m-30) REVERT: Q 140 GLU cc_start: 0.8086 (mp0) cc_final: 0.7518 (mp0) REVERT: Q 141 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8455 (tp30) REVERT: Q 147 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8486 (ttpp) REVERT: Q 162 GLU cc_start: 0.7749 (pm20) cc_final: 0.7539 (pm20) REVERT: R 42 ASP cc_start: 0.8508 (t70) cc_final: 0.7977 (t70) REVERT: R 45 ASP cc_start: 0.8812 (p0) cc_final: 0.8508 (p0) REVERT: R 60 GLU cc_start: 0.8596 (tp30) cc_final: 0.8168 (tp30) REVERT: R 61 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8110 (mm-30) REVERT: R 104 MET cc_start: 0.8681 (ttp) cc_final: 0.8303 (ttp) REVERT: R 108 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8704 (mmmm) REVERT: R 116 ASP cc_start: 0.8865 (m-30) cc_final: 0.8626 (m-30) REVERT: R 147 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8598 (ttpp) REVERT: S 17 GLU cc_start: 0.8455 (tt0) cc_final: 0.8197 (tt0) REVERT: S 42 ASP cc_start: 0.8410 (t70) cc_final: 0.7947 (t70) REVERT: S 57 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7535 (mm-30) REVERT: S 60 GLU cc_start: 0.8530 (tp30) cc_final: 0.7920 (pt0) REVERT: S 61 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7704 (mm-30) REVERT: S 84 ASP cc_start: 0.8687 (m-30) cc_final: 0.8231 (m-30) REVERT: S 86 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8679 (tppt) REVERT: S 104 MET cc_start: 0.8721 (ttp) cc_final: 0.8299 (ttp) REVERT: S 107 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8770 (mm-30) REVERT: S 112 GLN cc_start: 0.9092 (tp40) cc_final: 0.8327 (tp-100) REVERT: S 116 ASP cc_start: 0.8830 (m-30) cc_final: 0.8277 (m-30) REVERT: S 147 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8584 (ttpp) REVERT: S 162 GLU cc_start: 0.7530 (mp0) cc_final: 0.7211 (pm20) REVERT: S 167 GLU cc_start: 0.8554 (tt0) cc_final: 0.8314 (tt0) REVERT: T 45 ASP cc_start: 0.8593 (p0) cc_final: 0.8208 (p0) REVERT: T 104 MET cc_start: 0.8766 (ttp) cc_final: 0.8366 (ttp) REVERT: T 112 GLN cc_start: 0.9117 (tp40) cc_final: 0.8365 (tp-100) REVERT: T 116 ASP cc_start: 0.8808 (m-30) cc_final: 0.8246 (m-30) REVERT: T 136 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8508 (p-80) REVERT: T 140 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7899 (mp0) REVERT: T 162 GLU cc_start: 0.7602 (pm20) cc_final: 0.7378 (pm20) REVERT: U 42 ASP cc_start: 0.8379 (t70) cc_final: 0.7947 (t70) REVERT: U 45 ASP cc_start: 0.8670 (p0) cc_final: 0.8447 (p0) REVERT: U 49 GLU cc_start: 0.8312 (tp30) cc_final: 0.7997 (tp30) REVERT: U 61 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8343 (mm-30) REVERT: U 64 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8191 (mt-10) REVERT: U 104 MET cc_start: 0.8631 (ttp) cc_final: 0.8258 (ttp) REVERT: U 112 GLN cc_start: 0.9066 (tp40) cc_final: 0.8241 (tp-100) REVERT: U 116 ASP cc_start: 0.8810 (m-30) cc_final: 0.8221 (m-30) REVERT: U 147 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8625 (ttpp) REVERT: V 43 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8209 (mtm180) REVERT: V 45 ASP cc_start: 0.8687 (p0) cc_final: 0.8438 (p0) REVERT: V 60 GLU cc_start: 0.8619 (tp30) cc_final: 0.8055 (tp30) REVERT: V 61 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7887 (mm-30) REVERT: V 64 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8297 (mt-10) REVERT: V 84 ASP cc_start: 0.8785 (m-30) cc_final: 0.8524 (m-30) REVERT: V 87 LYS cc_start: 0.9035 (ptpp) cc_final: 0.8751 (ptmm) REVERT: V 108 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8766 (mmmm) REVERT: V 112 GLN cc_start: 0.9021 (tp40) cc_final: 0.8634 (tp-100) REVERT: V 116 ASP cc_start: 0.8712 (m-30) cc_final: 0.8421 (m-30) REVERT: V 140 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8052 (mp0) REVERT: V 144 LEU cc_start: 0.9386 (tp) cc_final: 0.9043 (tm) REVERT: V 147 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8538 (ttpp) REVERT: V 150 ASP cc_start: 0.8489 (m-30) cc_final: 0.8160 (m-30) REVERT: W 22 SER cc_start: 0.9295 (m) cc_final: 0.9026 (p) REVERT: W 61 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8256 (mm-30) REVERT: W 64 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8171 (mt-10) REVERT: W 79 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7820 (mmp80) REVERT: W 84 ASP cc_start: 0.8674 (m-30) cc_final: 0.8436 (m-30) REVERT: W 86 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8632 (tppt) REVERT: W 104 MET cc_start: 0.8668 (ttp) cc_final: 0.8331 (ttp) REVERT: W 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8602 (m-30) REVERT: W 140 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7968 (mp0) REVERT: W 147 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8609 (ttpp) REVERT: W 162 GLU cc_start: 0.7595 (pm20) cc_final: 0.7378 (pm20) REVERT: X 15 ASP cc_start: 0.8410 (p0) cc_final: 0.7968 (p0) REVERT: X 45 ASP cc_start: 0.8819 (p0) cc_final: 0.8580 (p0) REVERT: X 60 GLU cc_start: 0.8615 (tp30) cc_final: 0.8221 (tp30) REVERT: X 63 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8012 (ttm-80) REVERT: X 64 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8331 (mt-10) REVERT: X 84 ASP cc_start: 0.8837 (m-30) cc_final: 0.8513 (m-30) REVERT: X 107 GLU cc_start: 0.8857 (tp30) cc_final: 0.8041 (tp30) REVERT: X 112 GLN cc_start: 0.9093 (tp40) cc_final: 0.8311 (tp-100) REVERT: X 116 ASP cc_start: 0.8881 (m-30) cc_final: 0.8311 (m-30) REVERT: X 140 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8003 (mp0) REVERT: X 141 GLU cc_start: 0.8541 (tp30) cc_final: 0.8229 (tp30) outliers start: 99 outliers final: 43 residues processed: 1438 average time/residue: 2.0470 time to fit residues: 3365.2890 Evaluate side-chains 1321 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 1265 time to evaluate : 4.066 ------------------------------------------------------------------------------- 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 7 GLN Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 141 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 104 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 72 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP 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 M residue 104 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 104 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 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 V residue 147 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 390 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 312 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 136 HIS D 7 GLN E 7 GLN E 136 HIS F 7 GLN F 136 HIS G 7 GLN H 7 GLN H 136 HIS I 7 GLN K 7 GLN M 10 GLN N 7 GLN O 7 GLN ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN P 53 HIS P 136 HIS Q 29 GLN R 136 HIS S 7 GLN S 136 HIS T 74 ASN T 83 GLN T 136 HIS U 7 GLN U 83 GLN U 136 HIS V 10 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 136 HIS W 7 GLN W 29 GLN W 136 HIS X 136 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078475 restraints weight = 58546.774| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.59 r_work: 0.2943 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 33838 Z= 0.200 Angle : 0.639 11.241 45524 Z= 0.325 Chirality : 0.040 0.171 4872 Planarity : 0.004 0.042 5974 Dihedral : 6.671 89.536 4602 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.40 % Favored : 98.46 % Rotamer: Outliers : 3.07 % Allowed : 25.09 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.13), residues: 4080 helix: 2.51 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.00 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.008 0.001 HIS S 136 PHE 0.021 0.002 PHE T 137 TYR 0.025 0.002 TYR E 66 ARG 0.010 0.001 ARG P 56 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 2675) hydrogen bonds : angle 3.77586 ( 8025) covalent geometry : bond 0.00451 (33838) covalent geometry : angle 0.63882 (45524) *********************** 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 1409 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1302 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8289 (tp30) cc_final: 0.7957 (tp30) REVERT: A 60 GLU cc_start: 0.8664 (tp30) cc_final: 0.8349 (tp30) REVERT: A 61 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 75 GLN cc_start: 0.8987 (mt0) cc_final: 0.8769 (mt0) REVERT: A 86 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8685 (tppt) REVERT: A 116 ASP cc_start: 0.8811 (m-30) cc_final: 0.8560 (m-30) REVERT: A 147 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8639 (ttpp) REVERT: A 150 ASP cc_start: 0.8504 (m-30) cc_final: 0.8291 (m-30) REVERT: B 45 ASP cc_start: 0.8642 (p0) cc_final: 0.8394 (p0) REVERT: B 49 GLU cc_start: 0.8299 (tp30) cc_final: 0.8039 (tp30) REVERT: B 61 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 64 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8197 (mt-10) REVERT: B 84 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7812 (t70) REVERT: B 104 MET cc_start: 0.8587 (ttp) cc_final: 0.8311 (ttp) REVERT: B 116 ASP cc_start: 0.8825 (m-30) cc_final: 0.8538 (m-30) REVERT: C 17 GLU cc_start: 0.8328 (tt0) cc_final: 0.8028 (tt0) REVERT: C 42 ASP cc_start: 0.8655 (t70) cc_final: 0.8068 (t70) REVERT: C 49 GLU cc_start: 0.8142 (tp30) cc_final: 0.7913 (tp30) REVERT: C 60 GLU cc_start: 0.8476 (tp30) cc_final: 0.8253 (tp30) REVERT: C 104 MET cc_start: 0.8876 (ttp) cc_final: 0.8479 (ttp) REVERT: C 107 GLU cc_start: 0.8934 (tp30) cc_final: 0.8619 (mm-30) REVERT: C 116 ASP cc_start: 0.8861 (m-30) cc_final: 0.8627 (m-30) REVERT: C 140 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8030 (mp0) REVERT: C 147 LYS cc_start: 0.8964 (ttpp) cc_final: 0.8707 (ttpp) REVERT: D 42 ASP cc_start: 0.8498 (t70) cc_final: 0.8168 (t70) REVERT: D 53 HIS cc_start: 0.8464 (t-90) cc_final: 0.7856 (t70) REVERT: D 57 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8162 (mt-10) REVERT: D 61 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8489 (mm-30) REVERT: D 63 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: D 64 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8138 (mm-30) REVERT: D 74 ASN cc_start: 0.9231 (m-40) cc_final: 0.8770 (m110) REVERT: D 107 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8467 (mm-30) REVERT: D 116 ASP cc_start: 0.8842 (m-30) cc_final: 0.8606 (m-30) REVERT: D 147 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8620 (ttpp) REVERT: D 150 ASP cc_start: 0.8536 (m-30) cc_final: 0.8295 (m-30) REVERT: D 162 GLU cc_start: 0.7638 (pm20) cc_final: 0.7367 (pm20) REVERT: E 7 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8817 (pt0) REVERT: E 17 GLU cc_start: 0.8545 (tt0) cc_final: 0.8284 (tt0) REVERT: E 84 ASP cc_start: 0.8752 (m-30) cc_final: 0.8548 (m-30) REVERT: E 86 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8571 (mmmm) REVERT: E 116 ASP cc_start: 0.8835 (m-30) cc_final: 0.8612 (m-30) REVERT: E 147 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8619 (ttpp) REVERT: F 49 GLU cc_start: 0.8256 (tp30) cc_final: 0.7914 (tp30) REVERT: F 60 GLU cc_start: 0.8488 (tp30) cc_final: 0.8236 (mm-30) REVERT: F 61 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8115 (mm-30) REVERT: F 63 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7961 (ttm-80) REVERT: F 104 MET cc_start: 0.8746 (ttp) cc_final: 0.8374 (ttp) REVERT: F 107 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8564 (mm-30) REVERT: F 116 ASP cc_start: 0.8845 (m-30) cc_final: 0.8610 (m-30) REVERT: F 147 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8673 (ttpp) REVERT: G 49 GLU cc_start: 0.8227 (tp30) cc_final: 0.7928 (tp30) REVERT: G 61 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8232 (mm-30) REVERT: G 84 ASP cc_start: 0.8749 (m-30) cc_final: 0.8509 (m-30) REVERT: G 86 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8586 (mmmm) REVERT: G 150 ASP cc_start: 0.8579 (m-30) cc_final: 0.8311 (m-30) REVERT: G 162 GLU cc_start: 0.7537 (pm20) cc_final: 0.7332 (pm20) REVERT: H 42 ASP cc_start: 0.8507 (t70) cc_final: 0.8254 (t70) REVERT: H 49 GLU cc_start: 0.8276 (tp30) cc_final: 0.7980 (tp30) REVERT: H 61 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8439 (mm-30) REVERT: H 64 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8162 (mt-10) REVERT: H 104 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8432 (ttp) REVERT: H 116 ASP cc_start: 0.8842 (m-30) cc_final: 0.8551 (m-30) REVERT: H 140 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7996 (mp0) REVERT: H 144 LEU cc_start: 0.9328 (tm) cc_final: 0.9038 (tm) REVERT: H 147 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8590 (ttpp) REVERT: H 162 GLU cc_start: 0.7722 (pm20) cc_final: 0.7512 (pm20) REVERT: I 45 ASP cc_start: 0.8743 (p0) cc_final: 0.8513 (p0) REVERT: I 60 GLU cc_start: 0.8519 (tp30) cc_final: 0.8257 (tp30) REVERT: I 61 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8318 (mm-30) REVERT: I 64 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8292 (mt-10) REVERT: I 104 MET cc_start: 0.8904 (ttp) cc_final: 0.8606 (ttp) REVERT: I 108 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8787 (mmmm) REVERT: I 116 ASP cc_start: 0.8815 (m-30) cc_final: 0.8515 (m-30) REVERT: I 140 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8017 (mp0) REVERT: I 143 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8934 (mtmm) REVERT: I 147 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8645 (ttpp) REVERT: J 61 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8154 (mm-30) REVERT: J 64 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8325 (mt-10) REVERT: J 84 ASP cc_start: 0.8657 (m-30) cc_final: 0.8259 (m-30) REVERT: J 116 ASP cc_start: 0.8857 (m-30) cc_final: 0.8541 (m-30) REVERT: J 140 GLU cc_start: 0.7986 (mp0) cc_final: 0.7481 (mp0) REVERT: J 143 LYS cc_start: 0.9160 (mtmm) cc_final: 0.8910 (mtmm) REVERT: J 147 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8559 (ttpp) REVERT: K 45 ASP cc_start: 0.8620 (p0) cc_final: 0.8307 (p0) REVERT: K 61 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8243 (mm-30) REVERT: K 68 ARG cc_start: 0.8746 (ptp-110) cc_final: 0.8423 (ptp90) REVERT: K 84 ASP cc_start: 0.8594 (m-30) cc_final: 0.8269 (m-30) REVERT: K 86 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8595 (mmmm) REVERT: K 107 GLU cc_start: 0.8775 (tp30) cc_final: 0.8269 (tp30) REVERT: K 116 ASP cc_start: 0.8855 (m-30) cc_final: 0.8567 (m-30) REVERT: K 141 GLU cc_start: 0.8448 (tp30) cc_final: 0.8204 (tp30) REVERT: K 147 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8625 (ttpp) REVERT: L 45 ASP cc_start: 0.8765 (p0) cc_final: 0.8382 (p0) REVERT: L 49 GLU cc_start: 0.8288 (tp30) cc_final: 0.8001 (tp30) REVERT: L 60 GLU cc_start: 0.8498 (tp30) cc_final: 0.8237 (tp30) REVERT: L 61 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8210 (mm-30) REVERT: L 84 ASP cc_start: 0.8751 (m-30) cc_final: 0.8459 (m-30) REVERT: L 104 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8441 (ttp) REVERT: L 116 ASP cc_start: 0.8863 (m-30) cc_final: 0.8617 (m-30) REVERT: L 140 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8074 (mp0) REVERT: L 147 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8577 (ttpp) REVERT: M 34 TYR cc_start: 0.9373 (m-10) cc_final: 0.8885 (m-10) REVERT: M 49 GLU cc_start: 0.8242 (tp30) cc_final: 0.7924 (tp30) REVERT: M 60 GLU cc_start: 0.8505 (tp30) cc_final: 0.8276 (tp30) REVERT: M 61 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8343 (mm-30) REVERT: M 86 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8767 (mmpt) REVERT: M 104 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8477 (ttp) REVERT: M 107 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8421 (tp30) REVERT: M 116 ASP cc_start: 0.8867 (m-30) cc_final: 0.8618 (m-30) REVERT: M 140 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8271 (mm-30) REVERT: M 147 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8539 (ttpp) REVERT: N 45 ASP cc_start: 0.8743 (p0) cc_final: 0.8508 (p0) REVERT: N 60 GLU cc_start: 0.8497 (tp30) cc_final: 0.8209 (tp30) REVERT: N 61 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8448 (mm-30) REVERT: N 79 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7823 (mmp80) REVERT: N 86 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8706 (mmmm) REVERT: N 104 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8462 (ttp) REVERT: N 116 ASP cc_start: 0.8784 (m-30) cc_final: 0.8581 (m-30) REVERT: N 140 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8113 (mp0) REVERT: N 141 GLU cc_start: 0.8846 (tp30) cc_final: 0.8352 (tp30) REVERT: N 147 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8587 (ttpp) REVERT: O 34 TYR cc_start: 0.9464 (m-10) cc_final: 0.9206 (m-10) REVERT: O 49 GLU cc_start: 0.8384 (tp30) cc_final: 0.8131 (tp30) REVERT: O 61 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8263 (mm-30) REVERT: O 64 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8317 (mt-10) REVERT: O 79 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7996 (mmt-90) REVERT: O 86 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8679 (mmpt) REVERT: O 104 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8454 (ttp) REVERT: O 109 LYS cc_start: 0.9215 (tmmt) cc_final: 0.8934 (tttp) REVERT: O 116 ASP cc_start: 0.8860 (m-30) cc_final: 0.8632 (m-30) REVERT: O 140 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7948 (mp0) REVERT: O 147 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8563 (ttpp) REVERT: P 15 ASP cc_start: 0.8705 (p0) cc_final: 0.8409 (p0) REVERT: P 22 SER cc_start: 0.9304 (m) cc_final: 0.9031 (p) REVERT: P 63 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8240 (ttm-80) REVERT: P 104 MET cc_start: 0.8897 (ttp) cc_final: 0.8587 (ttp) REVERT: P 107 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8155 (mm-30) REVERT: P 116 ASP cc_start: 0.8851 (m-30) cc_final: 0.8553 (m-30) REVERT: P 124 ARG cc_start: 0.8792 (mmt-90) cc_final: 0.8582 (mmt-90) REVERT: P 141 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8749 (tp30) REVERT: P 147 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8601 (ttpp) REVERT: P 162 GLU cc_start: 0.7685 (pm20) cc_final: 0.7429 (pm20) REVERT: P 167 GLU cc_start: 0.8590 (tt0) cc_final: 0.8255 (tt0) REVERT: Q 45 ASP cc_start: 0.8847 (p0) cc_final: 0.8591 (p0) REVERT: Q 61 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8195 (mm-30) REVERT: Q 64 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8185 (mt-10) REVERT: Q 86 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8648 (mmmm) REVERT: Q 104 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8435 (ttp) REVERT: Q 116 ASP cc_start: 0.8829 (m-30) cc_final: 0.8591 (m-30) REVERT: Q 140 GLU cc_start: 0.8160 (mp0) cc_final: 0.7586 (mp0) REVERT: Q 147 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8546 (ttpp) REVERT: R 42 ASP cc_start: 0.8566 (t70) cc_final: 0.8077 (t70) REVERT: R 45 ASP cc_start: 0.8732 (p0) cc_final: 0.8518 (p0) REVERT: R 60 GLU cc_start: 0.8494 (tp30) cc_final: 0.8120 (tp30) REVERT: R 61 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8254 (mm-30) REVERT: R 104 MET cc_start: 0.8805 (ttp) cc_final: 0.8546 (ttp) REVERT: R 107 GLU cc_start: 0.8991 (tp30) cc_final: 0.8769 (tp30) REVERT: R 116 ASP cc_start: 0.8869 (m-30) cc_final: 0.8615 (m-30) REVERT: R 140 GLU cc_start: 0.8361 (pp20) cc_final: 0.8135 (pp20) REVERT: R 147 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8671 (ttpp) REVERT: R 148 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.9056 (mtm) REVERT: S 17 GLU cc_start: 0.8525 (tt0) cc_final: 0.8301 (tt0) REVERT: S 42 ASP cc_start: 0.8504 (t70) cc_final: 0.7971 (t70) REVERT: S 57 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7570 (mm-30) REVERT: S 60 GLU cc_start: 0.8489 (tp30) cc_final: 0.7947 (pt0) REVERT: S 61 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7737 (mm-30) REVERT: S 84 ASP cc_start: 0.8634 (m-30) cc_final: 0.8409 (m-30) REVERT: S 86 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8570 (tppt) REVERT: S 104 MET cc_start: 0.8752 (ttp) cc_final: 0.8382 (ttp) REVERT: S 116 ASP cc_start: 0.8826 (m-30) cc_final: 0.8571 (m-30) REVERT: S 147 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8671 (ttpp) REVERT: S 162 GLU cc_start: 0.7516 (mp0) cc_final: 0.7177 (pm20) REVERT: S 167 GLU cc_start: 0.8579 (tt0) cc_final: 0.8323 (tt0) REVERT: T 49 GLU cc_start: 0.8305 (tp30) cc_final: 0.8013 (tp30) REVERT: T 104 MET cc_start: 0.8841 (ttp) cc_final: 0.8478 (ttp) REVERT: T 116 ASP cc_start: 0.8819 (m-30) cc_final: 0.8573 (m-30) REVERT: T 136 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8610 (p-80) REVERT: T 140 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7911 (mp0) REVERT: T 162 GLU cc_start: 0.7673 (pm20) cc_final: 0.7376 (pm20) REVERT: U 42 ASP cc_start: 0.8428 (t70) cc_final: 0.8013 (t70) REVERT: U 45 ASP cc_start: 0.8710 (p0) cc_final: 0.8484 (p0) REVERT: U 49 GLU cc_start: 0.8309 (tp30) cc_final: 0.8005 (tp30) REVERT: U 61 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8379 (mm-30) REVERT: U 64 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8238 (mt-10) REVERT: U 104 MET cc_start: 0.8673 (ttp) cc_final: 0.8319 (ttp) REVERT: U 116 ASP cc_start: 0.8831 (m-30) cc_final: 0.8528 (m-30) REVERT: U 147 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8704 (ttpp) REVERT: V 43 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8277 (mtm180) REVERT: V 45 ASP cc_start: 0.8685 (p0) cc_final: 0.8405 (p0) REVERT: V 49 GLU cc_start: 0.8228 (tp30) cc_final: 0.7925 (tp30) REVERT: V 60 GLU cc_start: 0.8637 (tp30) cc_final: 0.8090 (tp30) REVERT: V 61 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7898 (mm-30) REVERT: V 64 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8288 (mt-10) REVERT: V 87 LYS cc_start: 0.9041 (ptpp) cc_final: 0.8776 (ptmm) REVERT: V 108 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8799 (mmmm) REVERT: V 140 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8019 (mp0) REVERT: V 143 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8901 (mtmm) REVERT: V 144 LEU cc_start: 0.9403 (tp) cc_final: 0.9160 (tm) REVERT: V 147 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8586 (ttpp) REVERT: W 7 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8792 (pt0) REVERT: W 22 SER cc_start: 0.9319 (m) cc_final: 0.9047 (p) REVERT: W 61 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8309 (mm-30) REVERT: W 64 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8165 (mt-10) REVERT: W 79 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7861 (mmt-90) REVERT: W 84 ASP cc_start: 0.8713 (m-30) cc_final: 0.8469 (m-30) REVERT: W 86 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8601 (tppt) REVERT: W 104 MET cc_start: 0.8699 (ttp) cc_final: 0.8323 (ttp) REVERT: W 116 ASP cc_start: 0.8826 (m-30) cc_final: 0.8589 (m-30) REVERT: W 140 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8004 (mp0) REVERT: W 162 GLU cc_start: 0.7571 (pm20) cc_final: 0.7363 (pm20) REVERT: X 116 ASP cc_start: 0.8868 (m-30) cc_final: 0.8643 (m-30) REVERT: X 140 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8031 (mp0) outliers start: 107 outliers final: 43 residues processed: 1332 average time/residue: 1.9249 time to fit residues: 2937.1857 Evaluate side-chains 1299 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1242 time to evaluate : 3.792 ------------------------------------------------------------------------------- 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 84 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 141 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 91 ASP Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 104 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 98 ASP Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain M residue 104 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 104 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 98 ASP Chi-restraints excluded: chain R residue 148 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 136 HIS 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 7 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 218 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 351 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 chunk 328 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN B 7 GLN B 74 ASN C 7 GLN D 7 GLN E 7 GLN F 111 ASN G 7 GLN I 7 GLN J 74 ASN L 7 GLN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 ASN P 7 GLN P 53 HIS Q 29 GLN Q 156 HIS S 136 HIS T 10 GLN T 136 HIS U 83 GLN W 7 GLN ** W 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 11 ASN W 29 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081936 restraints weight = 58166.556| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.63 r_work: 0.2999 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33838 Z= 0.145 Angle : 0.623 10.649 45524 Z= 0.319 Chirality : 0.039 0.164 4872 Planarity : 0.004 0.050 5974 Dihedral : 6.452 86.541 4600 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.84 % Favored : 98.11 % Rotamer: Outliers : 2.59 % Allowed : 27.50 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.13), residues: 4080 helix: 2.65 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.26 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 93 HIS 0.014 0.001 HIS T 136 PHE 0.020 0.002 PHE T 137 TYR 0.026 0.002 TYR H 66 ARG 0.011 0.001 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 2675) hydrogen bonds : angle 3.73940 ( 8025) covalent geometry : bond 0.00329 (33838) covalent geometry : angle 0.62300 (45524) *********************** 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 1445 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1355 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.9286 (m) cc_final: 0.8962 (p) REVERT: A 49 GLU cc_start: 0.8244 (tp30) cc_final: 0.8015 (tp30) REVERT: A 60 GLU cc_start: 0.8492 (tp30) cc_final: 0.8260 (tp30) REVERT: A 61 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8225 (mm-30) REVERT: A 104 MET cc_start: 0.8935 (tpp) cc_final: 0.8619 (tpp) REVERT: A 107 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8548 (mm-30) REVERT: A 116 ASP cc_start: 0.8827 (m-30) cc_final: 0.8542 (m-30) REVERT: A 141 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8549 (tp30) REVERT: A 147 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8589 (ttpp) REVERT: A 150 ASP cc_start: 0.8534 (m-30) cc_final: 0.8267 (m-30) REVERT: B 45 ASP cc_start: 0.8580 (p0) cc_final: 0.8320 (p0) REVERT: B 61 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8159 (mm-30) REVERT: B 64 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8313 (mt-10) REVERT: B 104 MET cc_start: 0.8604 (ttp) cc_final: 0.8261 (ttp) REVERT: B 116 ASP cc_start: 0.8826 (m-30) cc_final: 0.8560 (m-30) REVERT: B 143 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8943 (mtmm) REVERT: C 42 ASP cc_start: 0.8611 (t70) cc_final: 0.8083 (t70) REVERT: C 60 GLU cc_start: 0.8483 (tp30) cc_final: 0.8236 (tp30) REVERT: C 68 ARG cc_start: 0.8689 (ptp90) cc_final: 0.8322 (ptp90) REVERT: C 104 MET cc_start: 0.8697 (ttp) cc_final: 0.8425 (tpp) REVERT: C 112 GLN cc_start: 0.9080 (tp40) cc_final: 0.8266 (tp-100) REVERT: C 116 ASP cc_start: 0.8877 (m-30) cc_final: 0.8366 (m-30) REVERT: C 140 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8015 (mp0) REVERT: C 147 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8660 (ttpp) REVERT: D 15 ASP cc_start: 0.8691 (p0) cc_final: 0.7832 (p0) REVERT: D 17 GLU cc_start: 0.8079 (tt0) cc_final: 0.7849 (tt0) REVERT: D 42 ASP cc_start: 0.8431 (t70) cc_final: 0.8090 (t70) REVERT: D 53 HIS cc_start: 0.8475 (t-90) cc_final: 0.7804 (t70) REVERT: D 57 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8136 (mt-10) REVERT: D 61 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 64 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8050 (mm-30) REVERT: D 74 ASN cc_start: 0.9164 (m-40) cc_final: 0.8684 (m110) REVERT: D 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8612 (m-30) REVERT: D 147 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8621 (ttpp) REVERT: D 162 GLU cc_start: 0.7603 (pm20) cc_final: 0.7337 (pm20) REVERT: E 17 GLU cc_start: 0.8364 (tt0) cc_final: 0.8080 (tt0) REVERT: E 42 ASP cc_start: 0.8340 (t70) cc_final: 0.7654 (t70) REVERT: E 57 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7984 (mt-10) REVERT: E 84 ASP cc_start: 0.8717 (m-30) cc_final: 0.8515 (m-30) REVERT: E 86 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8591 (tppt) REVERT: E 116 ASP cc_start: 0.8841 (m-30) cc_final: 0.8533 (m-30) REVERT: E 147 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8602 (ttpp) REVERT: F 49 GLU cc_start: 0.8251 (tp30) cc_final: 0.7899 (tp30) REVERT: F 104 MET cc_start: 0.8575 (ttp) cc_final: 0.8250 (ttp) REVERT: F 116 ASP cc_start: 0.8834 (m-30) cc_final: 0.8551 (m-30) REVERT: G 49 GLU cc_start: 0.8234 (tp30) cc_final: 0.7964 (tp30) REVERT: G 61 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8235 (mm-30) REVERT: G 84 ASP cc_start: 0.8695 (m-30) cc_final: 0.8166 (m-30) REVERT: G 86 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8557 (tppt) REVERT: H 15 ASP cc_start: 0.8714 (p0) cc_final: 0.8311 (p0) REVERT: H 42 ASP cc_start: 0.8558 (t70) cc_final: 0.8244 (t70) REVERT: H 49 GLU cc_start: 0.8235 (tp30) cc_final: 0.7944 (tp30) REVERT: H 57 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8363 (mm-30) REVERT: H 61 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8395 (mm-30) REVERT: H 64 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8291 (mt-10) REVERT: H 84 ASP cc_start: 0.8589 (m-30) cc_final: 0.8375 (m-30) REVERT: H 104 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8371 (ttp) REVERT: H 112 GLN cc_start: 0.9046 (tp40) cc_final: 0.8258 (tp-100) REVERT: H 116 ASP cc_start: 0.8863 (m-30) cc_final: 0.8329 (m-30) REVERT: H 140 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8023 (mp0) REVERT: H 144 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8993 (tm) REVERT: H 147 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8517 (ttpp) REVERT: H 172 ARG cc_start: 0.9258 (mmm160) cc_final: 0.9018 (mmm160) REVERT: I 60 GLU cc_start: 0.8497 (tp30) cc_final: 0.8209 (tp30) REVERT: I 61 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8335 (mm-30) REVERT: I 104 MET cc_start: 0.8562 (ttp) cc_final: 0.8246 (ttp) REVERT: I 107 GLU cc_start: 0.8918 (tp30) cc_final: 0.8482 (mm-30) REVERT: I 112 GLN cc_start: 0.9051 (tp40) cc_final: 0.8250 (tp40) REVERT: I 116 ASP cc_start: 0.8800 (m-30) cc_final: 0.8278 (m-30) REVERT: I 140 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7941 (mp0) REVERT: J 15 ASP cc_start: 0.8752 (p0) cc_final: 0.8232 (p0) REVERT: J 61 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8025 (mm-30) REVERT: J 68 ARG cc_start: 0.8742 (ptp90) cc_final: 0.8357 (ptp90) REVERT: J 84 ASP cc_start: 0.8636 (m-30) cc_final: 0.8221 (m-30) REVERT: J 116 ASP cc_start: 0.8887 (m-30) cc_final: 0.8584 (m-30) REVERT: J 140 GLU cc_start: 0.7981 (mp0) cc_final: 0.7446 (mp0) REVERT: J 143 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8884 (mtmm) REVERT: J 147 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8508 (ttpp) REVERT: K 22 SER cc_start: 0.9287 (m) cc_final: 0.8985 (p) REVERT: K 34 TYR cc_start: 0.9413 (m-10) cc_final: 0.9173 (m-10) REVERT: K 42 ASP cc_start: 0.8418 (t70) cc_final: 0.7855 (t70) REVERT: K 45 ASP cc_start: 0.8583 (p0) cc_final: 0.8341 (p0) REVERT: K 61 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8199 (mm-30) REVERT: K 68 ARG cc_start: 0.8670 (ptp-110) cc_final: 0.8375 (ptp90) REVERT: K 84 ASP cc_start: 0.8597 (m-30) cc_final: 0.8325 (m-30) REVERT: K 86 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8566 (tppt) REVERT: K 107 GLU cc_start: 0.8786 (tp30) cc_final: 0.8034 (tp30) REVERT: K 112 GLN cc_start: 0.9064 (tp40) cc_final: 0.8170 (tp-100) REVERT: K 116 ASP cc_start: 0.8861 (m-30) cc_final: 0.8359 (m-30) REVERT: K 141 GLU cc_start: 0.8728 (tp30) cc_final: 0.8305 (tp30) REVERT: K 147 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8542 (ttpp) REVERT: L 45 ASP cc_start: 0.8686 (p0) cc_final: 0.8243 (p0) REVERT: L 49 GLU cc_start: 0.8256 (tp30) cc_final: 0.7967 (tp30) REVERT: L 84 ASP cc_start: 0.8764 (m-30) cc_final: 0.8424 (m-30) REVERT: L 112 GLN cc_start: 0.9081 (tp40) cc_final: 0.8321 (tp-100) REVERT: L 116 ASP cc_start: 0.8880 (m-30) cc_final: 0.8292 (m-30) REVERT: L 140 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8072 (mp0) REVERT: L 147 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8367 (ttpp) REVERT: M 9 ARG cc_start: 0.8533 (ttt180) cc_final: 0.7900 (ttt180) REVERT: M 49 GLU cc_start: 0.8266 (tp30) cc_final: 0.7975 (tp30) REVERT: M 60 GLU cc_start: 0.8403 (tp30) cc_final: 0.8181 (tp30) REVERT: M 61 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8259 (mm-30) REVERT: M 64 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8026 (mt-10) REVERT: M 68 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8317 (ttm110) REVERT: M 86 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8756 (mmpt) REVERT: M 87 LYS cc_start: 0.9120 (ptmm) cc_final: 0.8823 (ptmm) REVERT: M 116 ASP cc_start: 0.8876 (m-30) cc_final: 0.8566 (m-30) REVERT: M 140 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8129 (mm-30) REVERT: M 143 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8927 (mtmm) REVERT: M 172 ARG cc_start: 0.9178 (mmm160) cc_final: 0.8877 (mmm160) REVERT: N 43 ARG cc_start: 0.8456 (mtm180) cc_final: 0.8095 (mtm180) REVERT: N 49 GLU cc_start: 0.8218 (tp30) cc_final: 0.7949 (tp30) REVERT: N 60 GLU cc_start: 0.8460 (tp30) cc_final: 0.8159 (tp30) REVERT: N 61 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8441 (mm-30) REVERT: N 68 ARG cc_start: 0.8759 (ptp90) cc_final: 0.8407 (ptp90) REVERT: N 79 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7792 (mmp80) REVERT: N 84 ASP cc_start: 0.8768 (m-30) cc_final: 0.8550 (m-30) REVERT: N 101 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8778 (ttmm) REVERT: N 104 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8324 (ttp) REVERT: N 112 GLN cc_start: 0.8993 (tp40) cc_final: 0.8293 (tp-100) REVERT: N 116 ASP cc_start: 0.8846 (m-30) cc_final: 0.8338 (m-30) REVERT: N 140 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8038 (mp0) REVERT: N 147 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8540 (ttpp) REVERT: O 34 TYR cc_start: 0.9433 (m-10) cc_final: 0.9197 (m-10) REVERT: O 45 ASP cc_start: 0.8735 (p0) cc_final: 0.8484 (p0) REVERT: O 61 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8234 (mm-30) REVERT: O 64 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8331 (mt-10) REVERT: O 79 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7749 (mmt-90) REVERT: O 86 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8663 (mmpt) REVERT: O 90 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8500 (mm-30) REVERT: O 104 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8231 (ttp) REVERT: O 107 GLU cc_start: 0.8640 (tp30) cc_final: 0.8228 (tp30) REVERT: O 109 LYS cc_start: 0.9168 (tmmt) cc_final: 0.8942 (tttt) REVERT: O 116 ASP cc_start: 0.8888 (m-30) cc_final: 0.8570 (m-30) REVERT: O 140 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7994 (mp0) REVERT: O 147 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8464 (ttpp) REVERT: O 167 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8068 (tt0) REVERT: O 172 ARG cc_start: 0.9251 (mmm160) cc_final: 0.9036 (mmm160) REVERT: P 22 SER cc_start: 0.9262 (m) cc_final: 0.8993 (p) REVERT: P 42 ASP cc_start: 0.8437 (t70) cc_final: 0.8058 (t70) REVERT: P 86 LYS cc_start: 0.8963 (tppt) cc_final: 0.8622 (mmpt) REVERT: P 112 GLN cc_start: 0.9057 (tp40) cc_final: 0.8177 (tp-100) REVERT: P 116 ASP cc_start: 0.8841 (m-30) cc_final: 0.8342 (m-30) REVERT: P 147 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8514 (ttpp) REVERT: P 162 GLU cc_start: 0.7656 (pm20) cc_final: 0.7394 (pm20) REVERT: P 167 GLU cc_start: 0.8564 (tt0) cc_final: 0.8295 (tt0) REVERT: Q 61 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8283 (mm-30) REVERT: Q 74 ASN cc_start: 0.9122 (m-40) cc_final: 0.8454 (m110) REVERT: Q 84 ASP cc_start: 0.8725 (m-30) cc_final: 0.8494 (m-30) REVERT: Q 86 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8692 (mmmm) REVERT: Q 104 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8407 (ttp) REVERT: Q 107 GLU cc_start: 0.8834 (tp30) cc_final: 0.8476 (tp30) REVERT: Q 116 ASP cc_start: 0.8861 (m-30) cc_final: 0.8550 (m-30) REVERT: Q 140 GLU cc_start: 0.8115 (mp0) cc_final: 0.7564 (mp0) REVERT: Q 147 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8528 (ttpp) REVERT: Q 162 GLU cc_start: 0.7648 (pm20) cc_final: 0.7390 (pm20) REVERT: R 42 ASP cc_start: 0.8502 (t70) cc_final: 0.8021 (t70) REVERT: R 45 ASP cc_start: 0.8666 (p0) cc_final: 0.8396 (p0) REVERT: R 60 GLU cc_start: 0.8476 (tp30) cc_final: 0.8213 (tp30) REVERT: R 61 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8213 (mm-30) REVERT: R 86 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8618 (mmpt) REVERT: R 104 MET cc_start: 0.8648 (ttp) cc_final: 0.8353 (ttp) REVERT: R 112 GLN cc_start: 0.9114 (tp40) cc_final: 0.8278 (tp-100) REVERT: R 116 ASP cc_start: 0.8872 (m-30) cc_final: 0.8241 (m-30) REVERT: R 148 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.9047 (mtm) REVERT: S 17 GLU cc_start: 0.8501 (tt0) cc_final: 0.8269 (tt0) REVERT: S 42 ASP cc_start: 0.8432 (t70) cc_final: 0.7877 (t70) REVERT: S 57 GLU cc_start: 0.8641 (mm-30) cc_final: 0.7541 (mm-30) REVERT: S 60 GLU cc_start: 0.8432 (tp30) cc_final: 0.7887 (pt0) REVERT: S 61 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7683 (mm-30) REVERT: S 104 MET cc_start: 0.8599 (ttp) cc_final: 0.8188 (ttp) REVERT: S 108 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8690 (mmmm) REVERT: S 112 GLN cc_start: 0.9072 (tp40) cc_final: 0.8316 (tp-100) REVERT: S 116 ASP cc_start: 0.8829 (m-30) cc_final: 0.8331 (m-30) REVERT: S 147 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8612 (ttpp) REVERT: S 162 GLU cc_start: 0.7435 (mp0) cc_final: 0.7106 (pm20) REVERT: S 167 GLU cc_start: 0.8535 (tt0) cc_final: 0.8295 (tt0) REVERT: T 45 ASP cc_start: 0.8655 (p0) cc_final: 0.8410 (p0) REVERT: T 49 GLU cc_start: 0.8263 (tp30) cc_final: 0.8007 (tp30) REVERT: T 63 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8219 (ttm-80) REVERT: T 104 MET cc_start: 0.8787 (ttp) cc_final: 0.8356 (ttp) REVERT: T 112 GLN cc_start: 0.9137 (tp40) cc_final: 0.8356 (tp-100) REVERT: T 116 ASP cc_start: 0.8831 (m-30) cc_final: 0.8329 (m-30) REVERT: T 140 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7962 (mp0) REVERT: T 162 GLU cc_start: 0.7701 (pm20) cc_final: 0.7451 (pm20) REVERT: U 42 ASP cc_start: 0.8358 (t70) cc_final: 0.7940 (t70) REVERT: U 45 ASP cc_start: 0.8678 (p0) cc_final: 0.8415 (p0) REVERT: U 49 GLU cc_start: 0.8303 (tp30) cc_final: 0.7995 (tp30) REVERT: U 61 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8377 (mm-30) REVERT: U 64 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8329 (mt-10) REVERT: U 104 MET cc_start: 0.8553 (ttp) cc_final: 0.8154 (ttp) REVERT: U 107 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8379 (tp30) REVERT: U 109 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8974 (ttmt) REVERT: U 116 ASP cc_start: 0.8841 (m-30) cc_final: 0.8560 (m-30) REVERT: U 147 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8645 (ttpp) REVERT: U 162 GLU cc_start: 0.7561 (pm20) cc_final: 0.7237 (pm20) REVERT: U 167 GLU cc_start: 0.8562 (tt0) cc_final: 0.8263 (tt0) REVERT: V 45 ASP cc_start: 0.8645 (p0) cc_final: 0.8312 (p0) REVERT: V 49 GLU cc_start: 0.8233 (tp30) cc_final: 0.7978 (tp30) REVERT: V 60 GLU cc_start: 0.8608 (tp30) cc_final: 0.8213 (tp30) REVERT: V 61 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7873 (mm-30) REVERT: V 84 ASP cc_start: 0.8777 (m-30) cc_final: 0.8552 (m-30) REVERT: V 86 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8625 (mmmm) REVERT: V 87 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8722 (ptmm) REVERT: V 112 GLN cc_start: 0.8994 (tp40) cc_final: 0.8627 (tp-100) REVERT: V 116 ASP cc_start: 0.8696 (m-30) cc_final: 0.8393 (m-30) REVERT: V 140 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8006 (mp0) REVERT: V 143 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8886 (mtmm) REVERT: V 147 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8488 (ttpp) REVERT: W 22 SER cc_start: 0.9291 (m) cc_final: 0.9027 (p) REVERT: W 57 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8451 (mm-30) REVERT: W 60 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8366 (mm-30) REVERT: W 61 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8254 (mm-30) REVERT: W 63 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8129 (ttm-80) REVERT: W 64 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8284 (mt-10) REVERT: W 79 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7810 (mmp80) REVERT: W 84 ASP cc_start: 0.8634 (m-30) cc_final: 0.8400 (m-30) REVERT: W 86 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8612 (tppt) REVERT: W 104 MET cc_start: 0.8651 (ttp) cc_final: 0.8283 (ttp) REVERT: W 116 ASP cc_start: 0.8875 (m-30) cc_final: 0.8579 (m-30) REVERT: W 140 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7997 (mp0) REVERT: W 162 GLU cc_start: 0.7593 (pm20) cc_final: 0.7379 (pm20) REVERT: W 167 GLU cc_start: 0.8401 (tt0) cc_final: 0.8174 (tt0) REVERT: X 60 GLU cc_start: 0.8604 (tp30) cc_final: 0.8221 (mm-30) REVERT: X 68 ARG cc_start: 0.8724 (ptp90) cc_final: 0.8297 (ptp90) REVERT: X 84 ASP cc_start: 0.8760 (m-30) cc_final: 0.8534 (m-30) REVERT: X 112 GLN cc_start: 0.9094 (tp40) cc_final: 0.8320 (tp-100) REVERT: X 116 ASP cc_start: 0.8867 (m-30) cc_final: 0.8314 (m-30) REVERT: X 140 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8050 (mp0) REVERT: X 141 GLU cc_start: 0.8765 (tp30) cc_final: 0.8219 (tp30) outliers start: 90 outliers final: 47 residues processed: 1388 average time/residue: 1.9600 time to fit residues: 3103.0363 Evaluate side-chains 1341 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1284 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D 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 141 GLU Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 72 MET 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 104 MET Chi-restraints excluded: chain H residue 144 LEU 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 72 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 72 MET 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 79 ARG Chi-restraints excluded: chain O residue 104 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 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 72 MET Chi-restraints excluded: chain U residue 109 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 108 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 305 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN B 75 GLN C 7 GLN D 7 GLN E 7 GLN F 7 GLN F 10 GLN F 75 GLN F 111 ASN G 7 GLN H 7 GLN J 111 ASN K 7 GLN K 136 HIS M 7 GLN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN O 7 GLN ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 ASN P 7 GLN R 7 GLN S 7 GLN S 136 HIS T 10 GLN T 136 HIS U 7 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 GLN W 10 GLN ** W 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081811 restraints weight = 58072.483| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.63 r_work: 0.3011 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33838 Z= 0.154 Angle : 0.643 10.233 45524 Z= 0.330 Chirality : 0.039 0.195 4872 Planarity : 0.004 0.047 5974 Dihedral : 6.406 85.210 4598 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 2.59 % Allowed : 28.51 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.13), residues: 4080 helix: 2.66 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.35 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.007 0.001 HIS T 136 PHE 0.016 0.002 PHE T 132 TYR 0.025 0.002 TYR Q 66 ARG 0.012 0.001 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 2675) hydrogen bonds : angle 3.77464 ( 8025) covalent geometry : bond 0.00353 (33838) covalent geometry : angle 0.64334 (45524) *********************** 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 1433 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1343 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.9304 (m) cc_final: 0.8991 (p) REVERT: A 49 GLU cc_start: 0.8299 (tp30) cc_final: 0.8096 (tp30) REVERT: A 60 GLU cc_start: 0.8538 (tp30) cc_final: 0.8274 (tp30) REVERT: A 61 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 86 LYS cc_start: 0.8922 (tppt) cc_final: 0.8596 (mmpt) REVERT: A 104 MET cc_start: 0.8930 (tpp) cc_final: 0.8719 (tpp) REVERT: A 112 GLN cc_start: 0.9102 (tp40) cc_final: 0.8215 (tp-100) REVERT: A 116 ASP cc_start: 0.8843 (m-30) cc_final: 0.8290 (m-30) REVERT: A 147 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8552 (ttpp) REVERT: A 150 ASP cc_start: 0.8547 (m-30) cc_final: 0.8271 (m-30) REVERT: B 7 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8933 (pt0) REVERT: B 45 ASP cc_start: 0.8577 (p0) cc_final: 0.8338 (p0) REVERT: B 60 GLU cc_start: 0.8644 (tp30) cc_final: 0.8183 (mm-30) REVERT: B 61 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 63 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8045 (ttm-80) REVERT: B 64 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8362 (mt-10) REVERT: B 92 GLU cc_start: 0.8010 (pp20) cc_final: 0.7809 (pm20) REVERT: B 104 MET cc_start: 0.8649 (ttp) cc_final: 0.8309 (ttp) REVERT: B 107 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8465 (mm-30) REVERT: B 116 ASP cc_start: 0.8817 (m-30) cc_final: 0.8552 (m-30) REVERT: B 140 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7987 (mp0) REVERT: B 143 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8939 (mtmm) REVERT: B 167 GLU cc_start: 0.8560 (tt0) cc_final: 0.8360 (tt0) REVERT: C 42 ASP cc_start: 0.8608 (t70) cc_final: 0.8102 (t70) REVERT: C 60 GLU cc_start: 0.8456 (tp30) cc_final: 0.8220 (tp30) REVERT: C 68 ARG cc_start: 0.8694 (ptp90) cc_final: 0.8323 (ptp90) REVERT: C 104 MET cc_start: 0.8710 (ttp) cc_final: 0.8433 (tpp) REVERT: C 107 GLU cc_start: 0.8902 (tp30) cc_final: 0.8663 (tp30) REVERT: C 112 GLN cc_start: 0.9087 (tp40) cc_final: 0.8280 (tp-100) REVERT: C 116 ASP cc_start: 0.8870 (m-30) cc_final: 0.8372 (m-30) REVERT: C 140 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8017 (mp0) REVERT: C 147 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8506 (ttpp) REVERT: D 7 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: D 15 ASP cc_start: 0.8549 (p0) cc_final: 0.8176 (p0) REVERT: D 17 GLU cc_start: 0.8041 (tt0) cc_final: 0.7817 (tt0) REVERT: D 22 SER cc_start: 0.9308 (m) cc_final: 0.9019 (p) REVERT: D 42 ASP cc_start: 0.8481 (t70) cc_final: 0.8138 (t70) REVERT: D 53 HIS cc_start: 0.8472 (t-90) cc_final: 0.7776 (t70) REVERT: D 57 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8116 (mt-10) REVERT: D 61 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8302 (mm-30) REVERT: D 63 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: D 64 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7955 (mm-30) REVERT: D 116 ASP cc_start: 0.8876 (m-30) cc_final: 0.8565 (m-30) REVERT: D 147 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8582 (ttpp) REVERT: D 162 GLU cc_start: 0.7646 (pm20) cc_final: 0.7354 (pm20) REVERT: E 7 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8938 (pt0) REVERT: E 17 GLU cc_start: 0.8381 (tt0) cc_final: 0.8116 (tt0) REVERT: E 45 ASP cc_start: 0.8700 (p0) cc_final: 0.8406 (p0) REVERT: E 57 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7707 (mt-10) REVERT: E 61 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7998 (mm-30) REVERT: E 86 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8569 (tppt) REVERT: E 107 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8553 (mm-30) REVERT: E 112 GLN cc_start: 0.9090 (tp40) cc_final: 0.8221 (tp-100) REVERT: E 116 ASP cc_start: 0.8836 (m-30) cc_final: 0.8258 (m-30) REVERT: E 147 LYS cc_start: 0.8830 (ttpp) cc_final: 0.8561 (ttpp) REVERT: F 49 GLU cc_start: 0.8272 (tp30) cc_final: 0.7954 (tp30) REVERT: F 63 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: F 68 ARG cc_start: 0.8645 (ptp90) cc_final: 0.8307 (ptp90) REVERT: F 101 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8690 (mtmm) REVERT: F 104 MET cc_start: 0.8576 (ttp) cc_final: 0.8220 (ttp) REVERT: F 116 ASP cc_start: 0.8843 (m-30) cc_final: 0.8567 (m-30) REVERT: G 60 GLU cc_start: 0.8601 (tp30) cc_final: 0.8136 (mm-30) REVERT: G 61 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8218 (mm-30) REVERT: G 63 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8048 (ttm-80) REVERT: G 84 ASP cc_start: 0.8734 (m-30) cc_final: 0.8220 (m-30) REVERT: G 86 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8562 (tppt) REVERT: G 143 LYS cc_start: 0.9099 (mtmm) cc_final: 0.8881 (mtmm) REVERT: G 150 ASP cc_start: 0.8551 (m-30) cc_final: 0.8285 (m-30) REVERT: G 162 GLU cc_start: 0.7454 (pm20) cc_final: 0.7217 (pm20) REVERT: G 167 GLU cc_start: 0.8488 (tt0) cc_final: 0.8288 (tt0) REVERT: H 15 ASP cc_start: 0.8630 (p0) cc_final: 0.8361 (p0) REVERT: H 42 ASP cc_start: 0.8576 (t70) cc_final: 0.8136 (t70) REVERT: H 57 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8322 (mm-30) REVERT: H 61 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8430 (mm-30) REVERT: H 68 ARG cc_start: 0.8694 (ptp90) cc_final: 0.8369 (ptp90) REVERT: H 84 ASP cc_start: 0.8673 (m-30) cc_final: 0.8461 (m-30) REVERT: H 104 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8445 (ttp) REVERT: H 112 GLN cc_start: 0.9026 (tp40) cc_final: 0.8173 (tp-100) REVERT: H 116 ASP cc_start: 0.8852 (m-30) cc_final: 0.8291 (m-30) REVERT: H 140 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8023 (mp0) REVERT: H 147 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8485 (ttpp) REVERT: I 60 GLU cc_start: 0.8376 (tp30) cc_final: 0.8161 (tp30) REVERT: I 61 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8322 (mm-30) REVERT: I 101 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8785 (ttmm) REVERT: I 104 MET cc_start: 0.8751 (ttp) cc_final: 0.8368 (ttp) REVERT: I 108 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8729 (mmmm) REVERT: I 112 GLN cc_start: 0.9048 (tp40) cc_final: 0.8165 (tp40) REVERT: I 116 ASP cc_start: 0.8765 (m-30) cc_final: 0.8233 (m-30) REVERT: I 140 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8041 (mp0) REVERT: I 147 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8552 (ttpp) REVERT: J 15 ASP cc_start: 0.8601 (p0) cc_final: 0.8401 (p0) REVERT: J 68 ARG cc_start: 0.8736 (ptp90) cc_final: 0.8422 (ptp90) REVERT: J 116 ASP cc_start: 0.8869 (m-30) cc_final: 0.8561 (m-30) REVERT: J 140 GLU cc_start: 0.8073 (mp0) cc_final: 0.7534 (mp0) REVERT: J 143 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8869 (mtmm) REVERT: J 147 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8537 (ttpp) REVERT: J 172 ARG cc_start: 0.9273 (mmm160) cc_final: 0.9007 (mmm160) REVERT: K 17 GLU cc_start: 0.8298 (tt0) cc_final: 0.8064 (tt0) REVERT: K 22 SER cc_start: 0.9296 (m) cc_final: 0.8990 (p) REVERT: K 42 ASP cc_start: 0.8428 (t70) cc_final: 0.7897 (t70) REVERT: K 61 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8225 (mm-30) REVERT: K 68 ARG cc_start: 0.8693 (ptp-110) cc_final: 0.8406 (ptp90) REVERT: K 79 ARG cc_start: 0.7915 (mmp80) cc_final: 0.7699 (mmp80) REVERT: K 84 ASP cc_start: 0.8614 (m-30) cc_final: 0.8334 (m-30) REVERT: K 86 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8570 (tppt) REVERT: K 107 GLU cc_start: 0.8779 (tp30) cc_final: 0.8128 (tp30) REVERT: K 116 ASP cc_start: 0.8851 (m-30) cc_final: 0.8599 (m-30) REVERT: K 141 GLU cc_start: 0.8698 (tp30) cc_final: 0.8496 (tp30) REVERT: K 147 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8527 (ttpp) REVERT: K 167 GLU cc_start: 0.8484 (tt0) cc_final: 0.8280 (tt0) REVERT: L 49 GLU cc_start: 0.8295 (tp30) cc_final: 0.8021 (tp30) REVERT: L 86 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8645 (mmmm) REVERT: L 112 GLN cc_start: 0.9091 (tp40) cc_final: 0.8309 (tp-100) REVERT: L 116 ASP cc_start: 0.8887 (m-30) cc_final: 0.8306 (m-30) REVERT: L 140 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8063 (mp0) REVERT: L 143 LYS cc_start: 0.8985 (mtmm) cc_final: 0.8779 (mtmm) REVERT: L 147 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8429 (ttpp) REVERT: M 9 ARG cc_start: 0.8479 (ttt180) cc_final: 0.7837 (ttt180) REVERT: M 49 GLU cc_start: 0.8210 (tp30) cc_final: 0.7942 (tp30) REVERT: M 61 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8271 (mm-30) REVERT: M 68 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8308 (ttm110) REVERT: M 86 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8741 (mmpt) REVERT: M 116 ASP cc_start: 0.8872 (m-30) cc_final: 0.8558 (m-30) REVERT: M 140 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8090 (mp0) REVERT: M 143 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8943 (mtmm) REVERT: M 172 ARG cc_start: 0.9152 (mmm160) cc_final: 0.8856 (mmm160) REVERT: N 43 ARG cc_start: 0.8410 (mtm180) cc_final: 0.8113 (mtm180) REVERT: N 45 ASP cc_start: 0.8598 (p0) cc_final: 0.8355 (p0) REVERT: N 49 GLU cc_start: 0.8207 (tp30) cc_final: 0.7969 (tp30) REVERT: N 60 GLU cc_start: 0.8451 (tp30) cc_final: 0.8138 (tp30) REVERT: N 61 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8434 (mm-30) REVERT: N 68 ARG cc_start: 0.8745 (ptp90) cc_final: 0.8446 (ptp90) REVERT: N 79 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7838 (mmp80) REVERT: N 101 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8793 (ttmm) REVERT: N 104 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: N 112 GLN cc_start: 0.9012 (tp40) cc_final: 0.8281 (tp-100) REVERT: N 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8337 (m-30) REVERT: N 147 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8523 (ttpp) REVERT: O 17 GLU cc_start: 0.8542 (tt0) cc_final: 0.8335 (tt0) REVERT: O 61 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8279 (mm-30) REVERT: O 64 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8301 (mt-10) REVERT: O 79 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7666 (mmp80) REVERT: O 86 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8709 (mmpt) REVERT: O 90 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8508 (mm-30) REVERT: O 104 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8295 (ttp) REVERT: O 107 GLU cc_start: 0.8582 (tp30) cc_final: 0.8366 (tp30) REVERT: O 109 LYS cc_start: 0.9154 (tmmt) cc_final: 0.8931 (tttt) REVERT: O 116 ASP cc_start: 0.8895 (m-30) cc_final: 0.8573 (m-30) REVERT: O 140 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8053 (mp0) REVERT: O 147 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8549 (ttpp) REVERT: O 167 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8110 (tt0) REVERT: P 15 ASP cc_start: 0.8638 (p0) cc_final: 0.8119 (p0) REVERT: P 22 SER cc_start: 0.9267 (m) cc_final: 0.8998 (p) REVERT: P 112 GLN cc_start: 0.9038 (tp40) cc_final: 0.8145 (tp-100) REVERT: P 116 ASP cc_start: 0.8814 (m-30) cc_final: 0.8316 (m-30) REVERT: P 147 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8458 (ttpp) REVERT: P 162 GLU cc_start: 0.7636 (pm20) cc_final: 0.7370 (pm20) REVERT: Q 61 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8144 (mm-30) REVERT: Q 86 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8753 (mmmm) REVERT: Q 104 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8421 (ttp) REVERT: Q 112 GLN cc_start: 0.9056 (tp40) cc_final: 0.8137 (tp-100) REVERT: Q 116 ASP cc_start: 0.8849 (m-30) cc_final: 0.8293 (m-30) REVERT: Q 140 GLU cc_start: 0.8263 (mp0) cc_final: 0.7642 (mp0) REVERT: Q 141 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: Q 143 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8923 (mtmm) REVERT: Q 147 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8537 (ttpp) REVERT: Q 162 GLU cc_start: 0.7639 (pm20) cc_final: 0.7374 (pm20) REVERT: R 45 ASP cc_start: 0.8611 (p0) cc_final: 0.8314 (p0) REVERT: R 61 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8215 (mm-30) REVERT: R 86 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8616 (mmpt) REVERT: R 104 MET cc_start: 0.8632 (ttp) cc_final: 0.8370 (ttp) REVERT: R 112 GLN cc_start: 0.9117 (tp40) cc_final: 0.8229 (tp-100) REVERT: R 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8309 (m-30) REVERT: R 147 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8598 (ttpp) REVERT: R 167 GLU cc_start: 0.8483 (tt0) cc_final: 0.8229 (tt0) REVERT: S 17 GLU cc_start: 0.8412 (tt0) cc_final: 0.8169 (tt0) REVERT: S 42 ASP cc_start: 0.8475 (t70) cc_final: 0.7892 (t70) REVERT: S 57 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7460 (mm-30) REVERT: S 60 GLU cc_start: 0.8425 (tp30) cc_final: 0.7829 (pt0) REVERT: S 61 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7682 (mm-30) REVERT: S 63 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7911 (ttm-80) REVERT: S 86 LYS cc_start: 0.8905 (tppt) cc_final: 0.8477 (mmpt) REVERT: S 104 MET cc_start: 0.8606 (ttp) cc_final: 0.8210 (ttp) REVERT: S 112 GLN cc_start: 0.9091 (tp40) cc_final: 0.8328 (tp40) REVERT: S 116 ASP cc_start: 0.8832 (m-30) cc_final: 0.8350 (m-30) REVERT: S 147 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8593 (ttpp) REVERT: S 162 GLU cc_start: 0.7370 (mp0) cc_final: 0.7050 (pm20) REVERT: S 167 GLU cc_start: 0.8566 (tt0) cc_final: 0.8321 (tt0) REVERT: T 49 GLU cc_start: 0.8269 (tp30) cc_final: 0.8039 (tp30) REVERT: T 68 ARG cc_start: 0.8712 (ptp90) cc_final: 0.8314 (ptp90) REVERT: T 104 MET cc_start: 0.8778 (ttp) cc_final: 0.8385 (ttp) REVERT: T 112 GLN cc_start: 0.9139 (tp40) cc_final: 0.8382 (tp-100) REVERT: T 116 ASP cc_start: 0.8828 (m-30) cc_final: 0.8344 (m-30) REVERT: T 140 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7996 (mp0) REVERT: T 162 GLU cc_start: 0.7742 (pm20) cc_final: 0.7402 (pm20) REVERT: U 42 ASP cc_start: 0.8344 (t70) cc_final: 0.7941 (t70) REVERT: U 45 ASP cc_start: 0.8593 (p0) cc_final: 0.8384 (p0) REVERT: U 49 GLU cc_start: 0.8298 (tp30) cc_final: 0.8022 (tp30) REVERT: U 60 GLU cc_start: 0.8659 (tp30) cc_final: 0.8457 (mm-30) REVERT: U 61 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8390 (mm-30) REVERT: U 64 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8297 (mt-10) REVERT: U 104 MET cc_start: 0.8549 (ttp) cc_final: 0.8148 (ttp) REVERT: U 112 GLN cc_start: 0.9067 (tp40) cc_final: 0.8245 (tp-100) REVERT: U 116 ASP cc_start: 0.8845 (m-30) cc_final: 0.8384 (m-30) REVERT: U 143 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8899 (mtmm) REVERT: U 147 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8655 (ttpp) REVERT: U 162 GLU cc_start: 0.7527 (pm20) cc_final: 0.7236 (pm20) REVERT: V 45 ASP cc_start: 0.8723 (p0) cc_final: 0.8459 (p0) REVERT: V 49 GLU cc_start: 0.8214 (tp30) cc_final: 0.7971 (tp30) REVERT: V 60 GLU cc_start: 0.8371 (tp30) cc_final: 0.8169 (tp30) REVERT: V 84 ASP cc_start: 0.8759 (m-30) cc_final: 0.8549 (m-30) REVERT: V 86 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8635 (mmmm) REVERT: V 87 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8715 (ptmm) REVERT: V 112 GLN cc_start: 0.8970 (tp40) cc_final: 0.8509 (tp-100) REVERT: V 116 ASP cc_start: 0.8708 (m-30) cc_final: 0.8374 (m-30) REVERT: V 140 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8011 (mp0) REVERT: V 143 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8866 (mtpt) REVERT: V 147 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8440 (ttpp) REVERT: W 22 SER cc_start: 0.9305 (m) cc_final: 0.9048 (p) REVERT: W 45 ASP cc_start: 0.8874 (p0) cc_final: 0.8651 (p0) REVERT: W 60 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8323 (mm-30) REVERT: W 61 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8304 (mm-30) REVERT: W 63 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: W 64 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8235 (mt-10) REVERT: W 79 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7856 (mmp80) REVERT: W 86 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8608 (tppt) REVERT: W 104 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8430 (tpp) REVERT: W 107 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8375 (tp30) REVERT: W 116 ASP cc_start: 0.8861 (m-30) cc_final: 0.8569 (m-30) REVERT: W 140 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7995 (mp0) REVERT: W 162 GLU cc_start: 0.7623 (pm20) cc_final: 0.7411 (pm20) REVERT: W 167 GLU cc_start: 0.8382 (tt0) cc_final: 0.8121 (tt0) REVERT: X 15 ASP cc_start: 0.8516 (p0) cc_final: 0.8283 (p0) REVERT: X 45 ASP cc_start: 0.8729 (p0) cc_final: 0.8513 (p0) REVERT: X 60 GLU cc_start: 0.8613 (tp30) cc_final: 0.8354 (mm-30) REVERT: X 63 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8251 (ttm-80) REVERT: X 68 ARG cc_start: 0.8721 (ptp90) cc_final: 0.8342 (ptp90) REVERT: X 112 GLN cc_start: 0.9083 (tp40) cc_final: 0.8284 (tp-100) REVERT: X 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8274 (m-30) REVERT: X 140 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8015 (mp0) REVERT: X 141 GLU cc_start: 0.8714 (tp30) cc_final: 0.8276 (tp30) outliers start: 90 outliers final: 48 residues processed: 1372 average time/residue: 2.0166 time to fit residues: 3165.1430 Evaluate side-chains 1331 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 1269 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 101 LYS 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 91 ASP Chi-restraints excluded: chain H residue 104 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 7 GLN Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 72 MET 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 104 MET 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 104 MET Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 72 MET 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 141 GLU Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain S residue 7 GLN 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 7 GLN Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 104 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 267 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 391 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 397 optimal weight: 9.9990 chunk 325 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN D 7 GLN E 7 GLN F 111 ASN G 7 GLN H 7 GLN I 7 GLN J 7 GLN J 111 ASN K 7 GLN L 7 GLN M 7 GLN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN O 7 GLN O 53 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN Q 74 ASN S 7 GLN S 136 HIS T 10 GLN U 7 GLN V 10 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080056 restraints weight = 58059.050| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.67 r_work: 0.2968 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4433 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= 0.193 Angle : 0.684 9.988 45524 Z= 0.351 Chirality : 0.041 0.224 4872 Planarity : 0.005 0.047 5974 Dihedral : 6.443 83.046 4598 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 2.39 % Allowed : 29.66 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.13), residues: 4080 helix: 2.48 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.09 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.008 0.001 HIS T 136 PHE 0.017 0.002 PHE T 137 TYR 0.025 0.002 TYR T 66 ARG 0.011 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 2675) hydrogen bonds : angle 3.86511 ( 8025) covalent geometry : bond 0.00441 (33838) covalent geometry : angle 0.68360 (45524) *********************** 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 1385 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1302 time to evaluate : 4.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.9273 (m) cc_final: 0.8943 (p) REVERT: A 49 GLU cc_start: 0.8307 (tp30) cc_final: 0.8001 (tp30) REVERT: A 60 GLU cc_start: 0.8495 (tp30) cc_final: 0.8183 (tp30) REVERT: A 61 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 84 ASP cc_start: 0.8699 (m-30) cc_final: 0.8487 (m-30) REVERT: A 104 MET cc_start: 0.8937 (tpp) cc_final: 0.8635 (tpp) REVERT: A 116 ASP cc_start: 0.8858 (m-30) cc_final: 0.8542 (m-30) REVERT: A 147 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8541 (ttpp) REVERT: A 150 ASP cc_start: 0.8550 (m-30) cc_final: 0.8278 (m-30) REVERT: B 17 GLU cc_start: 0.8502 (tt0) cc_final: 0.8260 (tt0) REVERT: B 45 ASP cc_start: 0.8574 (p0) cc_final: 0.8285 (p0) REVERT: B 60 GLU cc_start: 0.8610 (tp30) cc_final: 0.8254 (tp30) REVERT: B 61 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8222 (mm-30) REVERT: B 63 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7738 (ttp-110) REVERT: B 64 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8353 (mt-10) REVERT: B 92 GLU cc_start: 0.8016 (pp20) cc_final: 0.7671 (pm20) REVERT: B 104 MET cc_start: 0.8689 (ttp) cc_final: 0.8435 (ttp) REVERT: B 116 ASP cc_start: 0.8830 (m-30) cc_final: 0.8544 (m-30) REVERT: B 140 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7982 (mp0) REVERT: B 143 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8927 (mtmm) REVERT: B 167 GLU cc_start: 0.8605 (tt0) cc_final: 0.8367 (tt0) REVERT: C 60 GLU cc_start: 0.8472 (tp30) cc_final: 0.8175 (tp30) REVERT: C 68 ARG cc_start: 0.8701 (ptp90) cc_final: 0.8327 (ptp90) REVERT: C 101 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8440 (mppt) REVERT: C 104 MET cc_start: 0.8737 (ttp) cc_final: 0.8459 (tpp) REVERT: C 116 ASP cc_start: 0.8877 (m-30) cc_final: 0.8627 (m-30) REVERT: C 140 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8022 (mp0) REVERT: C 147 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8566 (ttpp) REVERT: D 7 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: D 22 SER cc_start: 0.9291 (m) cc_final: 0.8999 (p) REVERT: D 42 ASP cc_start: 0.8529 (t70) cc_final: 0.8167 (t70) REVERT: D 53 HIS cc_start: 0.8479 (t-90) cc_final: 0.7816 (t70) REVERT: D 57 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8062 (mt-10) REVERT: D 63 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: D 64 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7865 (mm-30) REVERT: D 107 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8487 (mm-30) REVERT: D 116 ASP cc_start: 0.8882 (m-30) cc_final: 0.8625 (m-30) REVERT: D 147 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8568 (ttpp) REVERT: D 162 GLU cc_start: 0.7725 (pm20) cc_final: 0.7410 (pm20) REVERT: E 17 GLU cc_start: 0.8454 (tt0) cc_final: 0.8243 (tt0) REVERT: E 57 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7773 (mt-10) REVERT: E 61 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8005 (mm-30) REVERT: E 84 ASP cc_start: 0.8785 (m-30) cc_final: 0.8338 (m-30) REVERT: E 86 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8653 (tppt) REVERT: E 87 LYS cc_start: 0.9027 (ptmm) cc_final: 0.8720 (ptmm) REVERT: E 116 ASP cc_start: 0.8859 (m-30) cc_final: 0.8535 (m-30) REVERT: E 147 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8577 (ttpp) REVERT: F 49 GLU cc_start: 0.8281 (tp30) cc_final: 0.7965 (tp30) REVERT: F 63 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: F 68 ARG cc_start: 0.8673 (ptp90) cc_final: 0.8330 (ptp90) REVERT: F 104 MET cc_start: 0.8597 (ttp) cc_final: 0.8179 (ttp) REVERT: F 116 ASP cc_start: 0.8848 (m-30) cc_final: 0.8534 (m-30) REVERT: F 147 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8476 (ttpp) REVERT: G 60 GLU cc_start: 0.8630 (tp30) cc_final: 0.8419 (tp30) REVERT: G 61 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8218 (mm-30) REVERT: G 63 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.7951 (ttp-110) REVERT: G 84 ASP cc_start: 0.8778 (m-30) cc_final: 0.8244 (m-30) REVERT: G 86 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8549 (tppt) REVERT: G 143 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8837 (mtmm) REVERT: G 150 ASP cc_start: 0.8498 (m-30) cc_final: 0.8195 (m-30) REVERT: G 162 GLU cc_start: 0.7480 (pm20) cc_final: 0.7236 (pm20) REVERT: G 167 GLU cc_start: 0.8541 (tt0) cc_final: 0.8316 (tt0) REVERT: H 17 GLU cc_start: 0.8589 (tt0) cc_final: 0.8309 (tt0) REVERT: H 42 ASP cc_start: 0.8578 (t70) cc_final: 0.8161 (t70) REVERT: H 61 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8413 (mm-30) REVERT: H 68 ARG cc_start: 0.8698 (ptp90) cc_final: 0.8388 (ptp90) REVERT: H 84 ASP cc_start: 0.8720 (m-30) cc_final: 0.8406 (m-30) REVERT: H 104 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8211 (ttp) REVERT: H 107 GLU cc_start: 0.8576 (tp30) cc_final: 0.8329 (tp30) REVERT: H 116 ASP cc_start: 0.8837 (m-30) cc_final: 0.8500 (m-30) REVERT: H 140 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7948 (mp0) REVERT: H 141 GLU cc_start: 0.8745 (tp30) cc_final: 0.8378 (tp30) REVERT: H 147 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8338 (ttpp) REVERT: I 17 GLU cc_start: 0.8620 (tt0) cc_final: 0.8417 (tt0) REVERT: I 60 GLU cc_start: 0.8409 (tp30) cc_final: 0.8129 (tp30) REVERT: I 61 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8322 (mm-30) REVERT: I 63 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7710 (ttp-110) REVERT: I 104 MET cc_start: 0.8811 (ttp) cc_final: 0.8443 (ttp) REVERT: I 108 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8735 (mmmm) REVERT: I 116 ASP cc_start: 0.8814 (m-30) cc_final: 0.8527 (m-30) REVERT: I 140 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8079 (mp0) REVERT: I 147 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8519 (ttpp) REVERT: J 15 ASP cc_start: 0.8515 (p0) cc_final: 0.8309 (p0) REVERT: J 68 ARG cc_start: 0.8738 (ptp90) cc_final: 0.8432 (ptp90) REVERT: J 109 LYS cc_start: 0.9153 (ptmm) cc_final: 0.8926 (pttt) REVERT: J 116 ASP cc_start: 0.8861 (m-30) cc_final: 0.8539 (m-30) REVERT: J 124 ARG cc_start: 0.8466 (ptp-110) cc_final: 0.8261 (ptp-110) REVERT: J 140 GLU cc_start: 0.8115 (mp0) cc_final: 0.7568 (mp0) REVERT: J 143 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8876 (mtmm) REVERT: J 147 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8578 (ttpp) REVERT: J 172 ARG cc_start: 0.9199 (mmm160) cc_final: 0.8902 (mmm160) REVERT: K 45 ASP cc_start: 0.8639 (p0) cc_final: 0.8302 (p0) REVERT: K 49 GLU cc_start: 0.8232 (tp30) cc_final: 0.7989 (tp30) REVERT: K 61 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8183 (mm-30) REVERT: K 68 ARG cc_start: 0.8690 (ptp-110) cc_final: 0.8370 (ptp90) REVERT: K 84 ASP cc_start: 0.8576 (m-30) cc_final: 0.8290 (m-30) REVERT: K 86 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8599 (mmpt) REVERT: K 107 GLU cc_start: 0.8818 (tp30) cc_final: 0.8114 (tp30) REVERT: K 116 ASP cc_start: 0.8878 (m-30) cc_final: 0.8584 (m-30) REVERT: K 147 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8542 (ttpp) REVERT: K 172 ARG cc_start: 0.9193 (mmm160) cc_final: 0.8974 (mmm160) REVERT: L 49 GLU cc_start: 0.8321 (tp30) cc_final: 0.8052 (tp30) REVERT: L 86 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8677 (mmmm) REVERT: L 116 ASP cc_start: 0.8905 (m-30) cc_final: 0.8564 (m-30) REVERT: L 140 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8131 (mp0) REVERT: L 143 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8644 (mtmm) REVERT: L 147 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8379 (ttpp) REVERT: M 9 ARG cc_start: 0.8478 (ttt180) cc_final: 0.7753 (ttt180) REVERT: M 49 GLU cc_start: 0.8228 (tp30) cc_final: 0.7972 (tp30) REVERT: M 61 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8204 (mm-30) REVERT: M 86 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8755 (mmpt) REVERT: M 107 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8032 (mm-30) REVERT: M 116 ASP cc_start: 0.8846 (m-30) cc_final: 0.8523 (m-30) REVERT: M 140 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8101 (mp0) REVERT: M 143 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8940 (mtmm) REVERT: N 7 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8859 (pt0) REVERT: N 43 ARG cc_start: 0.8392 (mtm180) cc_final: 0.8128 (mtm180) REVERT: N 49 GLU cc_start: 0.8191 (tp30) cc_final: 0.7959 (tp30) REVERT: N 60 GLU cc_start: 0.8463 (tp30) cc_final: 0.8238 (tp30) REVERT: N 61 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8421 (mm-30) REVERT: N 68 ARG cc_start: 0.8762 (ptp90) cc_final: 0.8470 (ptp90) REVERT: N 101 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8781 (ttmm) REVERT: N 104 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8409 (ttp) REVERT: N 116 ASP cc_start: 0.8860 (m-30) cc_final: 0.8586 (m-30) REVERT: N 147 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8533 (ttpp) REVERT: O 10 GLN cc_start: 0.8925 (tt0) cc_final: 0.8722 (tt0) REVERT: O 49 GLU cc_start: 0.8279 (tp30) cc_final: 0.8051 (tp30) REVERT: O 60 GLU cc_start: 0.8667 (tp30) cc_final: 0.8458 (mm-30) REVERT: O 61 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8230 (mm-30) REVERT: O 64 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8285 (mt-10) REVERT: O 79 ARG cc_start: 0.8037 (mmp80) cc_final: 0.7791 (mmp80) REVERT: O 86 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8692 (mmpt) REVERT: O 109 LYS cc_start: 0.9146 (tmmt) cc_final: 0.8932 (tttt) REVERT: O 116 ASP cc_start: 0.8877 (m-30) cc_final: 0.8548 (m-30) REVERT: O 147 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8510 (ttpp) REVERT: P 15 ASP cc_start: 0.8543 (p0) cc_final: 0.8227 (p0) REVERT: P 22 SER cc_start: 0.9266 (m) cc_final: 0.8983 (p) REVERT: P 60 GLU cc_start: 0.8606 (tp30) cc_final: 0.8001 (tm-30) REVERT: P 63 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8013 (ttp80) REVERT: P 112 GLN cc_start: 0.9044 (tp40) cc_final: 0.8247 (tp-100) REVERT: P 116 ASP cc_start: 0.8828 (m-30) cc_final: 0.8332 (m-30) REVERT: P 147 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8572 (ttpp) REVERT: P 162 GLU cc_start: 0.7751 (pm20) cc_final: 0.7495 (pm20) REVERT: Q 49 GLU cc_start: 0.8170 (tp30) cc_final: 0.7923 (tp30) REVERT: Q 61 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8188 (mm-30) REVERT: Q 84 ASP cc_start: 0.8743 (m-30) cc_final: 0.8525 (m-30) REVERT: Q 86 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8603 (mmmm) REVERT: Q 104 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8411 (ttp) REVERT: Q 116 ASP cc_start: 0.8873 (m-30) cc_final: 0.8550 (m-30) REVERT: Q 140 GLU cc_start: 0.8294 (mp0) cc_final: 0.7632 (mp0) REVERT: Q 141 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: Q 143 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8888 (mtmm) REVERT: Q 162 GLU cc_start: 0.7717 (pm20) cc_final: 0.7428 (pm20) REVERT: R 45 ASP cc_start: 0.8612 (p0) cc_final: 0.8337 (p0) REVERT: R 61 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8220 (mm-30) REVERT: R 86 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8558 (mmpt) REVERT: R 104 MET cc_start: 0.8545 (ttp) cc_final: 0.8220 (ttp) REVERT: R 116 ASP cc_start: 0.8869 (m-30) cc_final: 0.8599 (m-30) REVERT: R 147 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8566 (ttpp) REVERT: S 17 GLU cc_start: 0.8515 (tt0) cc_final: 0.8259 (tt0) REVERT: S 42 ASP cc_start: 0.8553 (t70) cc_final: 0.7966 (t70) REVERT: S 57 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8361 (mm-30) REVERT: S 61 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7984 (mm-30) REVERT: S 86 LYS cc_start: 0.8889 (tppt) cc_final: 0.8428 (mmpt) REVERT: S 104 MET cc_start: 0.8595 (ttp) cc_final: 0.8230 (ttp) REVERT: S 116 ASP cc_start: 0.8852 (m-30) cc_final: 0.8601 (m-30) REVERT: S 147 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8565 (ttpp) REVERT: S 162 GLU cc_start: 0.7482 (mp0) cc_final: 0.7126 (pm20) REVERT: S 167 GLU cc_start: 0.8549 (tt0) cc_final: 0.8313 (tt0) REVERT: T 49 GLU cc_start: 0.8308 (tp30) cc_final: 0.8074 (tp30) REVERT: T 63 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8137 (ttp-110) REVERT: T 104 MET cc_start: 0.8794 (ttp) cc_final: 0.8399 (ttp) REVERT: T 116 ASP cc_start: 0.8854 (m-30) cc_final: 0.8605 (m-30) REVERT: T 140 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8016 (mp0) REVERT: T 162 GLU cc_start: 0.7796 (pm20) cc_final: 0.7443 (pm20) REVERT: U 17 GLU cc_start: 0.8452 (tt0) cc_final: 0.8215 (tt0) REVERT: U 42 ASP cc_start: 0.8352 (t70) cc_final: 0.8033 (t70) REVERT: U 49 GLU cc_start: 0.8340 (tp30) cc_final: 0.8056 (tp30) REVERT: U 61 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8434 (mm-30) REVERT: U 64 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8342 (mt-10) REVERT: U 104 MET cc_start: 0.8564 (ttp) cc_final: 0.8229 (ttp) REVERT: U 112 GLN cc_start: 0.9057 (tp40) cc_final: 0.8193 (tp-100) REVERT: U 116 ASP cc_start: 0.8856 (m-30) cc_final: 0.8308 (m-30) REVERT: U 147 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8633 (ttpp) REVERT: U 162 GLU cc_start: 0.7589 (pm20) cc_final: 0.7260 (pm20) REVERT: U 167 GLU cc_start: 0.8592 (tt0) cc_final: 0.8293 (tt0) REVERT: V 45 ASP cc_start: 0.8778 (p0) cc_final: 0.8523 (p0) REVERT: V 49 GLU cc_start: 0.8242 (tp30) cc_final: 0.7990 (tp30) REVERT: V 60 GLU cc_start: 0.8426 (tp30) cc_final: 0.8213 (tp30) REVERT: V 84 ASP cc_start: 0.8753 (m-30) cc_final: 0.8536 (m-30) REVERT: V 86 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8621 (mmmm) REVERT: V 87 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8702 (ptmm) REVERT: V 112 GLN cc_start: 0.8983 (tp40) cc_final: 0.8366 (tp-100) REVERT: V 116 ASP cc_start: 0.8723 (m-30) cc_final: 0.8332 (m-30) REVERT: V 140 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8055 (mp0) REVERT: V 147 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8444 (ttpp) REVERT: W 22 SER cc_start: 0.9286 (m) cc_final: 0.8993 (p) REVERT: W 57 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8430 (mm-30) REVERT: W 60 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8353 (mm-30) REVERT: W 61 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8244 (mm-30) REVERT: W 63 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.8038 (ttm-80) REVERT: W 64 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8308 (mt-10) REVERT: W 75 GLN cc_start: 0.8841 (mt0) cc_final: 0.8553 (mt0) REVERT: W 79 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7843 (mmt-90) REVERT: W 86 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8570 (tppt) REVERT: W 101 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8454 (mppt) REVERT: W 104 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8298 (ttp) REVERT: W 107 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8379 (tp30) REVERT: W 116 ASP cc_start: 0.8880 (m-30) cc_final: 0.8580 (m-30) REVERT: W 140 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7950 (mp0) REVERT: W 162 GLU cc_start: 0.7731 (pm20) cc_final: 0.7499 (pm20) REVERT: W 167 GLU cc_start: 0.8394 (tt0) cc_final: 0.8145 (tt0) REVERT: X 60 GLU cc_start: 0.8584 (tp30) cc_final: 0.8366 (mm-30) REVERT: X 68 ARG cc_start: 0.8732 (ptp90) cc_final: 0.8363 (ptp90) REVERT: X 116 ASP cc_start: 0.8861 (m-30) cc_final: 0.8626 (m-30) REVERT: X 124 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8217 (ptp-110) REVERT: X 140 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8004 (mp0) REVERT: X 141 GLU cc_start: 0.8754 (tp30) cc_final: 0.8232 (tp30) outliers start: 83 outliers final: 49 residues processed: 1330 average time/residue: 2.2918 time to fit residues: 3490.7448 Evaluate side-chains 1306 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 1245 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP 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 91 ASP Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain I residue 7 GLN Chi-restraints excluded: chain I residue 45 ASP 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 K residue 174 THR Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain N residue 7 GLN 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 7 GLN 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 141 GLU 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 S residue 7 GLN Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 72 MET Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 176 LYS Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 101 LYS Chi-restraints excluded: chain W residue 104 MET 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 124 ARG 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 361 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN D 7 GLN E 7 GLN F 7 GLN F 75 GLN G 7 GLN G 156 HIS I 7 GLN K 7 GLN L 7 GLN M 7 GLN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN O 7 GLN O 53 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN R 7 GLN S 7 GLN S 136 HIS T 10 GLN U 7 GLN V 10 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 156 HIS W 7 GLN ** W 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.081190 restraints weight = 58035.489| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.63 r_work: 0.2995 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33838 Z= 0.174 Angle : 0.686 9.718 45524 Z= 0.353 Chirality : 0.041 0.213 4872 Planarity : 0.005 0.057 5974 Dihedral : 6.407 83.253 4598 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 2.18 % Allowed : 30.55 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.13), residues: 4080 helix: 2.39 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 93 HIS 0.007 0.001 HIS T 136 PHE 0.016 0.002 PHE T 132 TYR 0.026 0.002 TYR K 66 ARG 0.014 0.001 ARG J 63 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 2675) hydrogen bonds : angle 3.88457 ( 8025) covalent geometry : bond 0.00402 (33838) covalent geometry : angle 0.68621 (45524) ********************** 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 1362 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1286 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.9284 (m) cc_final: 0.8964 (p) REVERT: A 49 GLU cc_start: 0.8271 (tp30) cc_final: 0.8066 (tp30) REVERT: A 60 GLU cc_start: 0.8461 (tp30) cc_final: 0.8260 (tp30) REVERT: A 84 ASP cc_start: 0.8710 (m-30) cc_final: 0.8493 (m-30) REVERT: A 86 LYS cc_start: 0.8787 (tppt) cc_final: 0.8435 (mmpt) REVERT: A 104 MET cc_start: 0.8967 (tpp) cc_final: 0.8602 (tpp) REVERT: A 116 ASP cc_start: 0.8843 (m-30) cc_final: 0.8533 (m-30) REVERT: A 147 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8623 (ttmm) REVERT: A 150 ASP cc_start: 0.8614 (m-30) cc_final: 0.8292 (m-30) REVERT: B 45 ASP cc_start: 0.8566 (p0) cc_final: 0.8288 (p0) REVERT: B 49 GLU cc_start: 0.8181 (tp30) cc_final: 0.7973 (tp30) REVERT: B 61 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 64 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8286 (mt-10) REVERT: B 104 MET cc_start: 0.8378 (ttp) cc_final: 0.8144 (ttp) REVERT: B 116 ASP cc_start: 0.8838 (m-30) cc_final: 0.8541 (m-30) REVERT: B 140 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8067 (mp0) REVERT: B 143 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8953 (mtmm) REVERT: C 42 ASP cc_start: 0.8608 (t70) cc_final: 0.8112 (t70) REVERT: C 60 GLU cc_start: 0.8428 (tp30) cc_final: 0.8206 (tp30) REVERT: C 68 ARG cc_start: 0.8689 (ptp90) cc_final: 0.8324 (ptp90) REVERT: C 101 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8469 (mppt) REVERT: C 104 MET cc_start: 0.8677 (ttp) cc_final: 0.8414 (tpp) REVERT: C 112 GLN cc_start: 0.9075 (tp40) cc_final: 0.8250 (tp-100) REVERT: C 116 ASP cc_start: 0.8875 (m-30) cc_final: 0.8363 (m-30) REVERT: C 140 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8069 (mp0) REVERT: C 147 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8661 (ttpp) REVERT: D 7 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: D 22 SER cc_start: 0.9313 (m) cc_final: 0.9030 (p) REVERT: D 42 ASP cc_start: 0.8497 (t70) cc_final: 0.8136 (t70) REVERT: D 53 HIS cc_start: 0.8475 (t-90) cc_final: 0.7836 (t70) REVERT: D 57 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 64 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7906 (mm-30) REVERT: D 116 ASP cc_start: 0.8877 (m-30) cc_final: 0.8566 (m-30) REVERT: D 124 ARG cc_start: 0.8428 (ptp-110) cc_final: 0.8103 (ptp-110) REVERT: D 147 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8573 (ttpp) REVERT: D 162 GLU cc_start: 0.7706 (pm20) cc_final: 0.7396 (pm20) REVERT: E 17 GLU cc_start: 0.8421 (tt0) cc_final: 0.8216 (tt0) REVERT: E 42 ASP cc_start: 0.8391 (t70) cc_final: 0.7801 (t70) REVERT: E 57 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7771 (mt-10) REVERT: E 61 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8010 (mm-30) REVERT: E 75 GLN cc_start: 0.8869 (mt0) cc_final: 0.8656 (mt0) REVERT: E 86 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8639 (mmpt) REVERT: E 107 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8569 (mm-30) REVERT: E 116 ASP cc_start: 0.8856 (m-30) cc_final: 0.8537 (m-30) REVERT: E 147 LYS cc_start: 0.8871 (ttpp) cc_final: 0.8598 (ttpp) REVERT: F 49 GLU cc_start: 0.8278 (tp30) cc_final: 0.7969 (tp30) REVERT: F 68 ARG cc_start: 0.8691 (ptp90) cc_final: 0.8358 (ptp90) REVERT: F 104 MET cc_start: 0.8573 (ttp) cc_final: 0.8186 (ttp) REVERT: F 116 ASP cc_start: 0.8830 (m-30) cc_final: 0.8523 (m-30) REVERT: F 147 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8487 (ttpp) REVERT: G 49 GLU cc_start: 0.8221 (tp30) cc_final: 0.8001 (tp30) REVERT: G 61 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8241 (mm-30) REVERT: G 84 ASP cc_start: 0.8755 (m-30) cc_final: 0.8270 (m-30) REVERT: G 86 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8552 (tppt) REVERT: G 143 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8774 (mtmm) REVERT: G 162 GLU cc_start: 0.7431 (pm20) cc_final: 0.7172 (pm20) REVERT: H 15 ASP cc_start: 0.8474 (p0) cc_final: 0.8253 (p0) REVERT: H 17 GLU cc_start: 0.8601 (tt0) cc_final: 0.8326 (tt0) REVERT: H 42 ASP cc_start: 0.8580 (t70) cc_final: 0.8182 (t70) REVERT: H 57 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8320 (mm-30) REVERT: H 61 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8365 (mm-30) REVERT: H 68 ARG cc_start: 0.8696 (ptp90) cc_final: 0.8382 (ptp90) REVERT: H 84 ASP cc_start: 0.8692 (m-30) cc_final: 0.8262 (m-30) REVERT: H 107 GLU cc_start: 0.8610 (tp30) cc_final: 0.8377 (tp30) REVERT: H 112 GLN cc_start: 0.9031 (tp40) cc_final: 0.8215 (tp-100) REVERT: H 116 ASP cc_start: 0.8835 (m-30) cc_final: 0.8254 (m-30) REVERT: H 124 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.8236 (ptp-110) REVERT: H 141 GLU cc_start: 0.8654 (tp30) cc_final: 0.8391 (tp30) REVERT: H 147 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8382 (ttpp) REVERT: I 60 GLU cc_start: 0.8386 (tp30) cc_final: 0.8163 (tp30) REVERT: I 61 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8342 (mm-30) REVERT: I 64 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8032 (mt-10) REVERT: I 101 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8819 (ttmm) REVERT: I 104 MET cc_start: 0.8819 (ttp) cc_final: 0.8452 (ttp) REVERT: I 108 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8766 (mmmm) REVERT: I 112 GLN cc_start: 0.9061 (tp40) cc_final: 0.8233 (tp-100) REVERT: I 116 ASP cc_start: 0.8793 (m-30) cc_final: 0.8237 (m-30) REVERT: I 140 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8052 (mp0) REVERT: I 147 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8526 (ttpp) REVERT: J 63 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8064 (ttp-110) REVERT: J 68 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8256 (ptp90) REVERT: J 109 LYS cc_start: 0.9144 (ptmm) cc_final: 0.8920 (pttt) REVERT: J 116 ASP cc_start: 0.8863 (m-30) cc_final: 0.8546 (m-30) REVERT: J 124 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8156 (ptp-110) REVERT: J 140 GLU cc_start: 0.8081 (mp0) cc_final: 0.7572 (mp0) REVERT: J 143 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8970 (mtmm) REVERT: J 147 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8541 (ttpp) REVERT: J 172 ARG cc_start: 0.9227 (mmm160) cc_final: 0.8949 (mmm160) REVERT: K 34 TYR cc_start: 0.9427 (m-10) cc_final: 0.9188 (m-10) REVERT: K 49 GLU cc_start: 0.8166 (tp30) cc_final: 0.7930 (tp30) REVERT: K 61 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8181 (mm-30) REVERT: K 68 ARG cc_start: 0.8701 (ptp-110) cc_final: 0.8384 (ptp90) REVERT: K 84 ASP cc_start: 0.8551 (m-30) cc_final: 0.8250 (m-30) REVERT: K 86 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8642 (mmpt) REVERT: K 116 ASP cc_start: 0.8865 (m-30) cc_final: 0.8569 (m-30) REVERT: K 143 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8823 (mtmm) REVERT: K 147 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8566 (ttpp) REVERT: L 7 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8752 (pt0) REVERT: L 45 ASP cc_start: 0.8647 (p0) cc_final: 0.8135 (p0) REVERT: L 49 GLU cc_start: 0.8304 (tp30) cc_final: 0.8023 (tp30) REVERT: L 86 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8531 (tppt) REVERT: L 101 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8337 (mppt) REVERT: L 112 GLN cc_start: 0.9071 (tp40) cc_final: 0.8289 (tp-100) REVERT: L 116 ASP cc_start: 0.8902 (m-30) cc_final: 0.8333 (m-30) REVERT: L 140 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8113 (mp0) REVERT: L 147 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8410 (ttpp) REVERT: M 9 ARG cc_start: 0.8482 (ttt180) cc_final: 0.7775 (ttt180) REVERT: M 49 GLU cc_start: 0.8181 (tp30) cc_final: 0.7931 (tp30) REVERT: M 57 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8312 (mm-30) REVERT: M 61 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8141 (mm-30) REVERT: M 116 ASP cc_start: 0.8857 (m-30) cc_final: 0.8535 (m-30) REVERT: M 140 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8057 (mp0) REVERT: M 143 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8949 (mtmm) REVERT: N 7 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8916 (pt0) REVERT: N 43 ARG cc_start: 0.8419 (mtm180) cc_final: 0.8198 (mtm180) REVERT: N 49 GLU cc_start: 0.8141 (tp30) cc_final: 0.7927 (tp30) REVERT: N 60 GLU cc_start: 0.8441 (tp30) cc_final: 0.8222 (tp30) REVERT: N 61 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8446 (mm-30) REVERT: N 64 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8060 (mt-10) REVERT: N 68 ARG cc_start: 0.8754 (ptp90) cc_final: 0.8268 (ptp90) REVERT: N 84 ASP cc_start: 0.8782 (m-30) cc_final: 0.8570 (m-30) REVERT: N 86 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8707 (mmmm) REVERT: N 101 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8791 (ttmm) REVERT: N 104 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8334 (ttp) REVERT: N 116 ASP cc_start: 0.8849 (m-30) cc_final: 0.8572 (m-30) REVERT: N 147 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8566 (ttpp) REVERT: O 49 GLU cc_start: 0.8258 (tp30) cc_final: 0.8012 (tp30) REVERT: O 61 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8184 (mm-30) REVERT: O 64 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8285 (mt-10) REVERT: O 79 ARG cc_start: 0.8232 (mmp80) cc_final: 0.7977 (mmt180) REVERT: O 84 ASP cc_start: 0.8727 (m-30) cc_final: 0.8481 (m-30) REVERT: O 86 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8702 (mmpt) REVERT: O 109 LYS cc_start: 0.9104 (tmmt) cc_final: 0.8895 (tttt) REVERT: O 116 ASP cc_start: 0.8865 (m-30) cc_final: 0.8543 (m-30) REVERT: O 140 GLU cc_start: 0.8370 (pp20) cc_final: 0.8097 (pp20) REVERT: O 147 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8412 (ttpp) REVERT: P 22 SER cc_start: 0.9272 (m) cc_final: 0.8996 (p) REVERT: P 60 GLU cc_start: 0.8569 (tp30) cc_final: 0.7959 (tm-30) REVERT: P 112 GLN cc_start: 0.9042 (tp40) cc_final: 0.8263 (tp-100) REVERT: P 116 ASP cc_start: 0.8836 (m-30) cc_final: 0.8391 (m-30) REVERT: P 124 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.8135 (ptp-110) REVERT: P 147 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8585 (ttpp) REVERT: P 162 GLU cc_start: 0.7763 (pm20) cc_final: 0.7544 (pm20) REVERT: Q 49 GLU cc_start: 0.8158 (tp30) cc_final: 0.7928 (tp30) REVERT: Q 61 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8247 (mm-30) REVERT: Q 86 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8662 (mmmm) REVERT: Q 104 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8409 (ttp) REVERT: Q 112 GLN cc_start: 0.9049 (tp40) cc_final: 0.8135 (tp-100) REVERT: Q 116 ASP cc_start: 0.8868 (m-30) cc_final: 0.8254 (m-30) REVERT: Q 140 GLU cc_start: 0.8243 (mp0) cc_final: 0.7620 (mp0) REVERT: Q 141 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8372 (tp30) REVERT: Q 143 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8907 (mtmm) REVERT: Q 162 GLU cc_start: 0.7744 (pm20) cc_final: 0.7463 (pm20) REVERT: R 45 ASP cc_start: 0.8603 (p0) cc_final: 0.8321 (p0) REVERT: R 61 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8090 (mm-30) REVERT: R 86 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8584 (mmpt) REVERT: R 101 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8521 (mtmm) REVERT: R 104 MET cc_start: 0.8671 (ttp) cc_final: 0.8333 (ttp) REVERT: R 116 ASP cc_start: 0.8869 (m-30) cc_final: 0.8531 (m-30) REVERT: R 144 LEU cc_start: 0.9004 (tp) cc_final: 0.8369 (tm) REVERT: R 147 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8447 (ttpp) REVERT: S 42 ASP cc_start: 0.8534 (t70) cc_final: 0.7910 (t70) REVERT: S 57 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7543 (mm-30) REVERT: S 60 GLU cc_start: 0.8374 (tp30) cc_final: 0.7832 (pt0) REVERT: S 61 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7652 (mm-30) REVERT: S 86 LYS cc_start: 0.8933 (tppt) cc_final: 0.8588 (mmpt) REVERT: S 104 MET cc_start: 0.8588 (ttp) cc_final: 0.8245 (ttp) REVERT: S 116 ASP cc_start: 0.8850 (m-30) cc_final: 0.8534 (m-30) REVERT: S 147 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8604 (ttpp) REVERT: S 162 GLU cc_start: 0.7499 (mp0) cc_final: 0.7149 (pm20) REVERT: S 167 GLU cc_start: 0.8516 (tt0) cc_final: 0.8285 (tt0) REVERT: T 49 GLU cc_start: 0.8243 (tp30) cc_final: 0.7999 (tp30) REVERT: T 104 MET cc_start: 0.8790 (ttp) cc_final: 0.8408 (ttp) REVERT: T 116 ASP cc_start: 0.8852 (m-30) cc_final: 0.8517 (m-30) REVERT: T 140 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8012 (mp0) REVERT: T 162 GLU cc_start: 0.7736 (pm20) cc_final: 0.7388 (pm20) REVERT: U 17 GLU cc_start: 0.8401 (tt0) cc_final: 0.8186 (tt0) REVERT: U 42 ASP cc_start: 0.8302 (t70) cc_final: 0.7976 (t70) REVERT: U 49 GLU cc_start: 0.8267 (tp30) cc_final: 0.7981 (tp30) REVERT: U 57 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8269 (mm-30) REVERT: U 60 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8385 (mm-30) REVERT: U 61 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8395 (mm-30) REVERT: U 63 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8256 (ttm-80) REVERT: U 104 MET cc_start: 0.8628 (ttp) cc_final: 0.8390 (ttp) REVERT: U 107 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8778 (mm-30) REVERT: U 112 GLN cc_start: 0.9064 (tp40) cc_final: 0.8224 (tp-100) REVERT: U 116 ASP cc_start: 0.8847 (m-30) cc_final: 0.8350 (m-30) REVERT: U 147 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8651 (ttpp) REVERT: U 162 GLU cc_start: 0.7514 (pm20) cc_final: 0.7197 (pm20) REVERT: U 167 GLU cc_start: 0.8569 (tt0) cc_final: 0.8265 (tt0) REVERT: V 49 GLU cc_start: 0.8252 (tp30) cc_final: 0.8002 (tp30) REVERT: V 60 GLU cc_start: 0.8464 (tp30) cc_final: 0.8192 (tp30) REVERT: V 86 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8626 (mmmm) REVERT: V 112 GLN cc_start: 0.8983 (tp40) cc_final: 0.8353 (tp-100) REVERT: V 116 ASP cc_start: 0.8713 (m-30) cc_final: 0.8289 (m-30) REVERT: V 140 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8027 (mp0) REVERT: V 147 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8453 (ttpp) REVERT: W 22 SER cc_start: 0.9299 (m) cc_final: 0.9003 (p) REVERT: W 63 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: W 75 GLN cc_start: 0.8803 (mt0) cc_final: 0.8553 (mt0) REVERT: W 79 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7800 (mmp80) REVERT: W 101 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8457 (mppt) REVERT: W 104 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8322 (ttp) REVERT: W 116 ASP cc_start: 0.8879 (m-30) cc_final: 0.8568 (m-30) REVERT: W 140 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8004 (mm-30) REVERT: W 162 GLU cc_start: 0.7730 (pm20) cc_final: 0.7513 (pm20) REVERT: X 57 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8053 (mm-30) REVERT: X 60 GLU cc_start: 0.8619 (tp30) cc_final: 0.8151 (mt-10) REVERT: X 63 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8143 (ttp80) REVERT: X 112 GLN cc_start: 0.9084 (tp40) cc_final: 0.8304 (tp-100) REVERT: X 116 ASP cc_start: 0.8853 (m-30) cc_final: 0.8283 (m-30) REVERT: X 124 ARG cc_start: 0.8494 (ptp-110) cc_final: 0.8152 (ptp-110) REVERT: X 140 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8012 (mp0) REVERT: X 141 GLU cc_start: 0.8716 (tp30) cc_final: 0.8277 (tp30) outliers start: 76 outliers final: 52 residues processed: 1311 average time/residue: 1.9497 time to fit residues: 2916.2793 Evaluate side-chains 1303 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1239 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 91 ASP 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 98 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 7 GLN 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 124 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 K residue 174 THR 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 101 LYS Chi-restraints excluded: chain N residue 7 GLN Chi-restraints excluded: chain N residue 72 MET 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 7 GLN Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 45 ASP 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 141 GLU Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 7 GLN Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 176 LYS Chi-restraints excluded: chain T residue 72 MET 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 72 MET Chi-restraints excluded: chain W residue 79 ARG Chi-restraints excluded: chain W residue 98 ASP Chi-restraints excluded: chain W residue 101 LYS Chi-restraints excluded: chain W residue 104 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 251 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 269 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 181 optimal weight: 0.6980 chunk 322 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 384 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN C 7 GLN D 7 GLN D 75 GLN F 10 GLN F 75 GLN F 156 HIS G 7 GLN H 7 GLN I 7 GLN J 7 GLN K 7 GLN L 7 GLN M 7 GLN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN O 7 GLN O 53 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN R 7 GLN S 7 GLN S 136 HIS T 10 GLN U 7 GLN ** V 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083289 restraints weight = 58277.930| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.62 r_work: 0.3045 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4678 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= 0.148 Angle : 0.682 9.594 45524 Z= 0.352 Chirality : 0.040 0.193 4872 Planarity : 0.005 0.052 5974 Dihedral : 6.430 89.112 4598 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 2.18 % Allowed : 31.06 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.13), residues: 4080 helix: 2.48 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.14 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 93 HIS 0.008 0.001 HIS O 128 PHE 0.016 0.002 PHE T 132 TYR 0.028 0.002 TYR K 66 ARG 0.014 0.001 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 2675) hydrogen bonds : angle 3.86585 ( 8025) covalent geometry : bond 0.00343 (33838) covalent geometry : angle 0.68221 (45524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46959.31 seconds wall clock time: 810 minutes 7.56 seconds (48607.56 seconds total)