Starting phenix.real_space_refine on Wed Feb 4 21:17:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvq_61843/02_2026/9jvq_61843.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvq_61843/02_2026/9jvq_61843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvq_61843/02_2026/9jvq_61843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvq_61843/02_2026/9jvq_61843.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvq_61843/02_2026/9jvq_61843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvq_61843/02_2026/9jvq_61843.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 30 5.16 5 C 8166 2.51 5 N 2130 2.21 5 O 2501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12827 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2137 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "B" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2138 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "C" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2138 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2138 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "E" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2138 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "F" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2138 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 268} Time building chain proxies: 2.93, per 1000 atoms: 0.23 Number of scatterers: 12827 At special positions: 0 Unit cell: (130.725, 173.055, 59.76, 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 30 16.00 O 2501 8.00 N 2130 7.00 C 8166 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: 1.00 Conformation dependent library (CDL) restraints added in 622.0 milliseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3132 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 6 sheets defined 4.3% alpha, 51.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.669A pdb=" N LEU B 16 " --> pdb=" O ASN B 12 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 removed outlier: 3.504A pdb=" N LEU C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 10 through 18 removed outlier: 3.524A pdb=" N ASN D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 16 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 17 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 10 through 15 removed outlier: 3.667A pdb=" N ASN E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.930A pdb=" N ASN F 14 " --> pdb=" O SER F 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 164 removed outlier: 7.023A pdb=" N GLY A 154 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 166 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 171 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 28 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 281 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP A 30 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 27 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 47 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 55 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 82 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 110 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 139 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP A 128 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 135 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 136 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 34 removed outlier: 3.558A pdb=" N GLU B 59 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 71 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 135 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 148 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 179 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 235 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 30 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 34 removed outlier: 5.357A pdb=" N ASN C 89 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LEU C 94 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 124 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 164 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP C 156 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE C 162 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY C 179 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 196 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN C 218 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 235 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 28 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE C 281 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP C 30 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 34 removed outlier: 3.847A pdb=" N LEU D 71 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN D 82 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 85 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR D 135 " --> pdb=" O ASP D 128 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG D 164 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASP D 156 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 162 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 179 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR D 207 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 218 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 235 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 27 through 33 removed outlier: 4.498A pdb=" N ALA E 27 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 102 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 83 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 100 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 115 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 123 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 142 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG E 164 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP E 156 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE E 162 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 178 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 196 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU E 200 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 243 " --> pdb=" O PHE E 263 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 28 through 33 removed outlier: 3.675A pdb=" N GLU F 86 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 72 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 83 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR F 114 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA F 123 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 139 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 126 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 137 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP F 128 " --> pdb=" O THR F 135 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR F 135 " --> pdb=" O ASP F 128 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG F 164 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP F 156 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE F 162 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY F 179 " --> pdb=" O ASP F 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 196 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 235 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS F 274 " --> pdb=" O SER F 262 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 1983 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: 1.76 Time building geometry restraints manager: 1.30 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: 3963 1.33 - 1.45: 1949 1.45 - 1.57: 7131 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 13091 Sorted by residual: bond pdb=" C LEU B 212 " pdb=" N PRO B 213 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.30e-02 5.92e+03 4.95e+00 bond pdb=" C GLU E 270 " pdb=" N PRO E 271 " ideal model delta sigma weight residual 1.340 1.390 -0.050 2.76e-02 1.31e+03 3.25e+00 bond pdb=" CB LYS B 174 " pdb=" CG LYS B 174 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CB LYS C 174 " pdb=" CG LYS C 174 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" C ALA D 24 " pdb=" N THR D 25 " ideal model delta sigma weight residual 1.333 1.311 0.022 1.61e-02 3.86e+03 1.92e+00 ... (remaining 13086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 17249 1.96 - 3.91: 451 3.91 - 5.87: 59 5.87 - 7.83: 29 7.83 - 9.79: 12 Bond angle restraints: 17800 Sorted by residual: angle pdb=" CB LYS B 174 " pdb=" CG LYS B 174 " pdb=" CD LYS B 174 " ideal model delta sigma weight residual 111.30 121.09 -9.79 2.30e+00 1.89e-01 1.81e+01 angle pdb=" N VAL D 272 " pdb=" CA VAL D 272 " pdb=" C VAL D 272 " ideal model delta sigma weight residual 113.22 108.12 5.10 1.23e+00 6.61e-01 1.72e+01 angle pdb=" CB LYS C 174 " pdb=" CG LYS C 174 " pdb=" CD LYS C 174 " ideal model delta sigma weight residual 111.30 120.51 -9.21 2.30e+00 1.89e-01 1.60e+01 angle pdb=" CB LYS F 274 " pdb=" CG LYS F 274 " pdb=" CD LYS F 274 " ideal model delta sigma weight residual 111.30 119.46 -8.16 2.30e+00 1.89e-01 1.26e+01 angle pdb=" N GLY E 38 " pdb=" CA GLY E 38 " pdb=" C GLY E 38 " ideal model delta sigma weight residual 113.18 121.25 -8.07 2.37e+00 1.78e-01 1.16e+01 ... (remaining 17795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 7033 16.82 - 33.65: 602 33.65 - 50.47: 140 50.47 - 67.29: 16 67.29 - 84.11: 2 Dihedral angle restraints: 7793 sinusoidal: 2927 harmonic: 4866 Sorted by residual: dihedral pdb=" CA GLN C 186 " pdb=" C GLN C 186 " pdb=" N ILE C 187 " pdb=" CA ILE C 187 " ideal model delta harmonic sigma weight residual 180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLU C 185 " pdb=" C GLU C 185 " pdb=" N GLN C 186 " pdb=" CA GLN C 186 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" N LEU B 266 " pdb=" C LEU B 266 " pdb=" CA LEU B 266 " pdb=" CB LEU B 266 " ideal model delta harmonic sigma weight residual 122.80 131.62 -8.82 0 2.50e+00 1.60e-01 1.24e+01 ... (remaining 7790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1764 0.065 - 0.130: 295 0.130 - 0.195: 9 0.195 - 0.260: 1 0.260 - 0.325: 1 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CA LEU B 266 " pdb=" N LEU B 266 " pdb=" C LEU B 266 " pdb=" CB LEU B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB THR E 67 " pdb=" CA THR E 67 " pdb=" OG1 THR E 67 " pdb=" CG2 THR E 67 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL A 5 " pdb=" CA VAL A 5 " pdb=" CG1 VAL A 5 " pdb=" CG2 VAL A 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 2067 not shown) Planarity restraints: 2303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 116 " 0.019 2.00e-02 2.50e+03 2.04e-02 7.26e+00 pdb=" CG PHE C 116 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 116 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 116 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 116 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 116 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 116 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 47 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 48 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 270 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 271 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.026 5.00e-02 4.00e+02 ... (remaining 2300 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5761 2.93 - 3.42: 11169 3.42 - 3.92: 18828 3.92 - 4.41: 20224 4.41 - 4.90: 36969 Nonbonded interactions: 92951 Sorted by model distance: nonbonded pdb=" O ASN E 218 " pdb=" OD1 ASN E 218 " model vdw 2.440 3.040 nonbonded pdb=" O ASN B 183 " pdb=" OD1 ASN B 183 " model vdw 2.442 3.040 nonbonded pdb=" O SER F 215 " pdb=" OD1 ASN F 216 " model vdw 2.473 3.040 nonbonded pdb=" N ASP E 139 " pdb=" OD1 ASP E 139 " model vdw 2.531 3.120 nonbonded pdb=" O SER E 215 " pdb=" OD1 ASN E 216 " model vdw 2.546 3.040 ... (remaining 92946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'C' and (resid 2 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and (resid 2 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'E' and (resid 2 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'F' and (resid 2 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )))) } 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: 0.980 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.060 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.004 0.050 13091 Z= 0.194 Angle : 0.813 9.786 17800 Z= 0.438 Chirality : 0.046 0.325 2070 Planarity : 0.004 0.055 2303 Dihedral : 13.015 84.113 4661 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.20 % Favored : 92.26 % Rotamer: Outliers : 3.77 % Allowed : 25.85 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.21), residues: 1680 helix: -2.80 (0.66), residues: 42 sheet: -0.83 (0.16), residues: 1092 loop : -2.94 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 124 TYR 0.020 0.002 TYR E 247 PHE 0.047 0.002 PHE C 116 TRP 0.008 0.001 TRP D 75 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00370 (13091) covalent geometry : angle 0.81343 (17800) hydrogen bonds : bond 0.17218 ( 723) hydrogen bonds : angle 7.94712 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 481 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8657 (p) REVERT: A 116 PHE cc_start: 0.8290 (t80) cc_final: 0.7838 (t80) REVERT: A 118 GLN cc_start: 0.7732 (pt0) cc_final: 0.7385 (pt0) REVERT: A 249 GLN cc_start: 0.8130 (tp40) cc_final: 0.7809 (tp40) REVERT: A 252 ARG cc_start: 0.7334 (tmm-80) cc_final: 0.7072 (ptm-80) REVERT: B 22 TYR cc_start: 0.8520 (m-80) cc_final: 0.8104 (m-80) REVERT: B 240 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 20 ASP cc_start: 0.7993 (m-30) cc_final: 0.7699 (m-30) REVERT: C 84 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8367 (ttmm) REVERT: C 91 THR cc_start: 0.7210 (OUTLIER) cc_final: 0.6897 (p) REVERT: C 124 ARG cc_start: 0.8816 (ptt90) cc_final: 0.8154 (ptt90) REVERT: C 230 SER cc_start: 0.8698 (t) cc_final: 0.8344 (p) REVERT: D 75 TRP cc_start: 0.7493 (t-100) cc_final: 0.7242 (t-100) REVERT: D 209 ASN cc_start: 0.8276 (t0) cc_final: 0.7591 (t0) REVERT: E 108 LYS cc_start: 0.7943 (pttt) cc_final: 0.7541 (pttt) REVERT: E 175 ASP cc_start: 0.7631 (p0) cc_final: 0.7094 (p0) REVERT: E 274 LYS cc_start: 0.7585 (mppt) cc_final: 0.7328 (mppt) REVERT: F 175 ASP cc_start: 0.7297 (p0) cc_final: 0.6845 (p0) outliers start: 53 outliers final: 45 residues processed: 498 average time/residue: 0.0852 time to fit residues: 63.5868 Evaluate side-chains 524 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 476 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN D 186 GLN E 66 GLN E 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.188197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120765 restraints weight = 15403.783| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.63 r_work: 0.3400 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 13091 Z= 0.429 Angle : 0.860 9.190 17800 Z= 0.440 Chirality : 0.051 0.170 2070 Planarity : 0.005 0.070 2303 Dihedral : 7.731 57.613 1850 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.60 % Favored : 88.93 % Rotamer: Outliers : 11.18 % Allowed : 17.24 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.21), residues: 1680 helix: -2.99 (0.59), residues: 42 sheet: -0.76 (0.16), residues: 1098 loop : -3.03 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 224 TYR 0.023 0.002 TYR A 6 PHE 0.037 0.003 PHE A 193 TRP 0.009 0.002 TRP E 75 HIS 0.011 0.002 HIS D 273 Details of bonding type rmsd covalent geometry : bond 0.00941 (13091) covalent geometry : angle 0.85955 (17800) hydrogen bonds : bond 0.04002 ( 723) hydrogen bonds : angle 6.32690 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 472 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.6713 (p90) REVERT: A 40 LYS cc_start: 0.7844 (tttm) cc_final: 0.7462 (tmtt) REVERT: A 118 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: A 124 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7752 (mtm-85) REVERT: A 182 LEU cc_start: 0.8706 (tt) cc_final: 0.8358 (mp) REVERT: A 249 GLN cc_start: 0.8245 (tp40) cc_final: 0.7647 (tp40) REVERT: A 252 ARG cc_start: 0.7988 (tmm-80) cc_final: 0.7455 (ptm160) REVERT: A 264 ASP cc_start: 0.8403 (t0) cc_final: 0.8133 (t0) REVERT: B 63 ASN cc_start: 0.8311 (t0) cc_final: 0.8008 (t0) REVERT: B 220 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8499 (mt-10) REVERT: C 20 ASP cc_start: 0.9047 (m-30) cc_final: 0.8811 (m-30) REVERT: C 91 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7219 (p) REVERT: C 124 ARG cc_start: 0.7874 (ptt90) cc_final: 0.7510 (ptt180) REVERT: C 228 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7525 (p0) REVERT: C 230 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8552 (p) REVERT: D 73 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6571 (tm-30) REVERT: D 75 TRP cc_start: 0.7511 (t-100) cc_final: 0.5781 (m-90) REVERT: E 66 GLN cc_start: 0.5917 (OUTLIER) cc_final: 0.5617 (pp30) REVERT: E 73 GLN cc_start: 0.8459 (tp40) cc_final: 0.8108 (tp40) REVERT: E 84 LYS cc_start: 0.7544 (mtpt) cc_final: 0.7191 (tttp) REVERT: E 108 LYS cc_start: 0.7618 (pttt) cc_final: 0.7144 (pttt) REVERT: E 175 ASP cc_start: 0.7816 (p0) cc_final: 0.7231 (p0) REVERT: E 226 LEU cc_start: 0.8535 (tt) cc_final: 0.8327 (tt) REVERT: E 274 LYS cc_start: 0.6000 (mppt) cc_final: 0.5758 (mppt) REVERT: F 73 GLN cc_start: 0.8266 (tp40) cc_final: 0.7881 (tp-100) REVERT: F 175 ASP cc_start: 0.7478 (p0) cc_final: 0.6824 (p0) REVERT: F 195 ASN cc_start: 0.6881 (t0) cc_final: 0.6478 (t0) REVERT: F 274 LYS cc_start: 0.7164 (mmmt) cc_final: 0.6869 (mmtm) outliers start: 157 outliers final: 114 residues processed: 536 average time/residue: 0.0866 time to fit residues: 69.3019 Evaluate side-chains 576 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 456 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN C 14 ASN C 82 GLN C 273 HIS D 186 GLN E 66 GLN E 249 GLN F 66 GLN F 232 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127280 restraints weight = 15320.131| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.70 r_work: 0.3474 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13091 Z= 0.153 Angle : 0.690 9.027 17800 Z= 0.343 Chirality : 0.045 0.140 2070 Planarity : 0.004 0.062 2303 Dihedral : 5.974 56.220 1811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.86 % Favored : 91.61 % Rotamer: Outliers : 7.62 % Allowed : 22.58 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.21), residues: 1680 helix: -2.82 (0.60), residues: 42 sheet: -0.53 (0.16), residues: 1094 loop : -2.80 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 11 TYR 0.011 0.001 TYR E 6 PHE 0.022 0.002 PHE C 221 TRP 0.007 0.001 TRP B 75 HIS 0.006 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00316 (13091) covalent geometry : angle 0.69039 (17800) hydrogen bonds : bond 0.03215 ( 723) hydrogen bonds : angle 5.87196 ( 1983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 504 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6186 (p90) REVERT: A 40 LYS cc_start: 0.7827 (tttm) cc_final: 0.7498 (tmtt) REVERT: A 69 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6454 (tm) REVERT: A 116 PHE cc_start: 0.8175 (t80) cc_final: 0.7768 (t80) REVERT: A 124 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7578 (mtm-85) REVERT: A 174 LYS cc_start: 0.9161 (tppt) cc_final: 0.8881 (tppt) REVERT: A 249 GLN cc_start: 0.8343 (tp40) cc_final: 0.7693 (tp40) REVERT: A 264 ASP cc_start: 0.8451 (t0) cc_final: 0.8184 (t0) REVERT: B 22 TYR cc_start: 0.8988 (m-80) cc_final: 0.8645 (m-80) REVERT: B 62 LEU cc_start: 0.8219 (pp) cc_final: 0.7923 (pt) REVERT: B 75 TRP cc_start: 0.7045 (m-90) cc_final: 0.6712 (m-90) REVERT: B 220 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8447 (mt-10) REVERT: B 264 ASP cc_start: 0.8641 (t0) cc_final: 0.8323 (t70) REVERT: C 124 ARG cc_start: 0.7921 (ptt90) cc_final: 0.7413 (ptt90) REVERT: C 228 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7329 (p0) REVERT: C 230 SER cc_start: 0.8964 (t) cc_final: 0.8421 (p) REVERT: C 249 GLN cc_start: 0.8098 (tp40) cc_final: 0.7736 (tp40) REVERT: C 262 SER cc_start: 0.8449 (t) cc_final: 0.8101 (p) REVERT: D 220 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8690 (mt-10) REVERT: D 264 ASP cc_start: 0.8580 (t70) cc_final: 0.8202 (t70) REVERT: E 66 GLN cc_start: 0.6081 (OUTLIER) cc_final: 0.5751 (pp30) REVERT: E 73 GLN cc_start: 0.8345 (tp40) cc_final: 0.7895 (tp-100) REVERT: E 84 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7122 (tttp) REVERT: E 108 LYS cc_start: 0.7571 (pttt) cc_final: 0.7187 (pttt) REVERT: E 175 ASP cc_start: 0.7753 (p0) cc_final: 0.6982 (p0) REVERT: E 195 ASN cc_start: 0.7004 (t0) cc_final: 0.6629 (t0) REVERT: E 278 SER cc_start: 0.9174 (t) cc_final: 0.8950 (p) REVERT: F 11 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7351 (ttm-80) REVERT: F 174 LYS cc_start: 0.9320 (tppt) cc_final: 0.8726 (pttm) REVERT: F 175 ASP cc_start: 0.7393 (p0) cc_final: 0.6699 (p0) REVERT: F 195 ASN cc_start: 0.6785 (t0) cc_final: 0.6397 (t0) REVERT: F 274 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6982 (mmtm) outliers start: 107 outliers final: 86 residues processed: 537 average time/residue: 0.0933 time to fit residues: 74.9612 Evaluate side-chains 558 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 468 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 113 ASN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 82 GLN C 273 HIS D 73 GLN E 47 GLN E 249 GLN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126663 restraints weight = 15228.302| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.64 r_work: 0.3467 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13091 Z= 0.160 Angle : 0.672 10.772 17800 Z= 0.332 Chirality : 0.045 0.144 2070 Planarity : 0.004 0.056 2303 Dihedral : 5.422 50.862 1804 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.98 % Favored : 91.49 % Rotamer: Outliers : 8.69 % Allowed : 22.15 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.21), residues: 1680 helix: -2.27 (0.96), residues: 18 sheet: -0.44 (0.16), residues: 1096 loop : -2.64 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 164 TYR 0.012 0.001 TYR E 6 PHE 0.018 0.002 PHE E 153 TRP 0.005 0.001 TRP B 75 HIS 0.007 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00344 (13091) covalent geometry : angle 0.67201 (17800) hydrogen bonds : bond 0.02921 ( 723) hydrogen bonds : angle 5.56722 ( 1983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 489 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.6266 (p90) REVERT: A 40 LYS cc_start: 0.7813 (tttm) cc_final: 0.7470 (tmtt) REVERT: A 69 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6739 (tm) REVERT: A 116 PHE cc_start: 0.8173 (t80) cc_final: 0.7799 (t80) REVERT: A 124 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: A 174 LYS cc_start: 0.9164 (tppt) cc_final: 0.8935 (tptp) REVERT: A 249 GLN cc_start: 0.8237 (tp40) cc_final: 0.7606 (tp40) REVERT: A 264 ASP cc_start: 0.8444 (t0) cc_final: 0.8226 (t0) REVERT: B 22 TYR cc_start: 0.9014 (m-80) cc_final: 0.8652 (m-80) REVERT: B 62 LEU cc_start: 0.8243 (pp) cc_final: 0.7910 (pt) REVERT: B 63 ASN cc_start: 0.8327 (t0) cc_final: 0.7814 (t0) REVERT: B 75 TRP cc_start: 0.7059 (m-90) cc_final: 0.6750 (m-90) REVERT: B 220 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 240 SER cc_start: 0.9542 (m) cc_final: 0.9185 (p) REVERT: B 264 ASP cc_start: 0.8704 (t0) cc_final: 0.8265 (t70) REVERT: C 124 ARG cc_start: 0.7864 (ptt90) cc_final: 0.7336 (ptt90) REVERT: C 228 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7376 (p0) REVERT: C 230 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8450 (p) REVERT: C 249 GLN cc_start: 0.8137 (tp40) cc_final: 0.7682 (tp40) REVERT: C 262 SER cc_start: 0.8404 (t) cc_final: 0.8060 (p) REVERT: D 62 LEU cc_start: 0.8216 (pp) cc_final: 0.7972 (pt) REVERT: D 220 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8663 (mt-10) REVERT: D 264 ASP cc_start: 0.8571 (t70) cc_final: 0.8253 (t70) REVERT: E 66 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5869 (pp30) REVERT: E 73 GLN cc_start: 0.8176 (tp40) cc_final: 0.7795 (tp40) REVERT: E 84 LYS cc_start: 0.7515 (mtpt) cc_final: 0.7288 (ttmt) REVERT: E 108 LYS cc_start: 0.7587 (pttt) cc_final: 0.7193 (pttt) REVERT: E 174 LYS cc_start: 0.9298 (tppt) cc_final: 0.8893 (pttm) REVERT: E 175 ASP cc_start: 0.7648 (p0) cc_final: 0.6995 (p0) REVERT: E 278 SER cc_start: 0.9178 (t) cc_final: 0.8931 (p) REVERT: F 11 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7353 (ttm-80) REVERT: F 51 ASP cc_start: 0.8664 (t0) cc_final: 0.8403 (m-30) REVERT: F 174 LYS cc_start: 0.9298 (tppt) cc_final: 0.8749 (pttm) REVERT: F 274 LYS cc_start: 0.7280 (mmmt) cc_final: 0.7052 (mmtm) outliers start: 122 outliers final: 99 residues processed: 534 average time/residue: 0.0858 time to fit residues: 69.0803 Evaluate side-chains 574 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 470 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 32 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 113 ASN A 118 GLN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 183 ASN C 273 HIS D 73 GLN E 66 GLN E 249 GLN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.195846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129960 restraints weight = 15207.069| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.69 r_work: 0.3478 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13091 Z= 0.131 Angle : 0.668 9.899 17800 Z= 0.325 Chirality : 0.044 0.146 2070 Planarity : 0.004 0.053 2303 Dihedral : 5.171 46.509 1800 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.56 % Favored : 91.96 % Rotamer: Outliers : 8.83 % Allowed : 21.72 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1680 helix: -2.26 (0.94), residues: 18 sheet: -0.34 (0.16), residues: 1096 loop : -2.63 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 164 TYR 0.011 0.001 TYR E 6 PHE 0.024 0.001 PHE D 221 TRP 0.007 0.001 TRP B 75 HIS 0.007 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00278 (13091) covalent geometry : angle 0.66766 (17800) hydrogen bonds : bond 0.02761 ( 723) hydrogen bonds : angle 5.41513 ( 1983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 496 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.6093 (p90) REVERT: A 40 LYS cc_start: 0.7801 (tttm) cc_final: 0.7485 (tmtt) REVERT: A 69 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6828 (tm) REVERT: A 116 PHE cc_start: 0.8238 (t80) cc_final: 0.7922 (t80) REVERT: A 118 GLN cc_start: 0.7487 (pt0) cc_final: 0.7241 (pm20) REVERT: A 124 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7472 (mtm-85) REVERT: A 174 LYS cc_start: 0.9172 (tppt) cc_final: 0.8963 (tptp) REVERT: A 249 GLN cc_start: 0.8251 (tp40) cc_final: 0.7600 (tp40) REVERT: B 22 TYR cc_start: 0.9033 (m-80) cc_final: 0.8626 (m-80) REVERT: B 50 LYS cc_start: 0.7350 (ptpt) cc_final: 0.6939 (ptmm) REVERT: B 62 LEU cc_start: 0.8228 (pp) cc_final: 0.7902 (pt) REVERT: B 63 ASN cc_start: 0.8392 (t0) cc_final: 0.7886 (t0) REVERT: B 73 GLN cc_start: 0.7849 (pt0) cc_final: 0.7237 (tm-30) REVERT: B 75 TRP cc_start: 0.7073 (m-90) cc_final: 0.6820 (m-90) REVERT: B 220 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8430 (mt-10) REVERT: B 240 SER cc_start: 0.9541 (m) cc_final: 0.9186 (p) REVERT: B 264 ASP cc_start: 0.8619 (t0) cc_final: 0.8058 (t70) REVERT: C 14 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8548 (t0) REVERT: C 20 ASP cc_start: 0.8962 (m-30) cc_final: 0.8450 (m-30) REVERT: C 91 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7433 (p) REVERT: C 124 ARG cc_start: 0.7849 (ptt90) cc_final: 0.7364 (ptt90) REVERT: C 174 LYS cc_start: 0.9148 (tppt) cc_final: 0.8877 (tptp) REVERT: C 228 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7356 (p0) REVERT: C 230 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8290 (p) REVERT: C 249 GLN cc_start: 0.8149 (tp40) cc_final: 0.7711 (tp40) REVERT: C 262 SER cc_start: 0.8394 (t) cc_final: 0.8082 (p) REVERT: D 220 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8666 (mt-10) REVERT: D 264 ASP cc_start: 0.8517 (t70) cc_final: 0.8186 (t70) REVERT: E 66 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5773 (pp30) REVERT: E 73 GLN cc_start: 0.8085 (tp40) cc_final: 0.7660 (tp40) REVERT: E 108 LYS cc_start: 0.7707 (pttt) cc_final: 0.7296 (pttt) REVERT: E 174 LYS cc_start: 0.9297 (tppt) cc_final: 0.8900 (pttm) REVERT: E 175 ASP cc_start: 0.7538 (p0) cc_final: 0.6898 (p0) REVERT: E 278 SER cc_start: 0.9175 (t) cc_final: 0.8927 (p) REVERT: F 11 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7363 (ttm-80) REVERT: F 175 ASP cc_start: 0.7369 (p0) cc_final: 0.6728 (p0) REVERT: F 252 ARG cc_start: 0.4784 (mtm180) cc_final: 0.3954 (mtm180) outliers start: 124 outliers final: 104 residues processed: 539 average time/residue: 0.0913 time to fit residues: 73.5680 Evaluate side-chains 593 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 482 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 34 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 113 ASN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 273 HIS E 249 GLN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.193294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127805 restraints weight = 15101.756| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.56 r_work: 0.3450 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13091 Z= 0.203 Angle : 0.684 9.529 17800 Z= 0.338 Chirality : 0.045 0.146 2070 Planarity : 0.004 0.053 2303 Dihedral : 5.130 49.517 1795 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.51 % Favored : 90.95 % Rotamer: Outliers : 9.62 % Allowed : 22.65 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.21), residues: 1680 helix: -2.75 (0.54), residues: 42 sheet: -0.34 (0.16), residues: 1100 loop : -2.69 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 164 TYR 0.012 0.001 TYR E 6 PHE 0.023 0.002 PHE C 116 TRP 0.004 0.001 TRP B 75 HIS 0.008 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00444 (13091) covalent geometry : angle 0.68407 (17800) hydrogen bonds : bond 0.02822 ( 723) hydrogen bonds : angle 5.41090 ( 1983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 474 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.6308 (p90) REVERT: A 40 LYS cc_start: 0.7844 (tttm) cc_final: 0.7517 (tmtt) REVERT: A 124 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: A 174 LYS cc_start: 0.9161 (tppt) cc_final: 0.8946 (tptp) REVERT: A 249 GLN cc_start: 0.8267 (tp40) cc_final: 0.7632 (tp40) REVERT: B 22 TYR cc_start: 0.9044 (m-80) cc_final: 0.8691 (m-80) REVERT: B 50 LYS cc_start: 0.7461 (ptpt) cc_final: 0.7043 (ptmm) REVERT: B 63 ASN cc_start: 0.8454 (t0) cc_final: 0.8072 (t0) REVERT: B 75 TRP cc_start: 0.7174 (m-90) cc_final: 0.6814 (m-90) REVERT: B 220 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8423 (mt-10) REVERT: B 240 SER cc_start: 0.9545 (m) cc_final: 0.9196 (p) REVERT: C 14 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8560 (t0) REVERT: C 91 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7562 (p) REVERT: C 124 ARG cc_start: 0.7858 (ptt90) cc_final: 0.7342 (ptt-90) REVERT: C 174 LYS cc_start: 0.9158 (tppt) cc_final: 0.8906 (tptp) REVERT: C 219 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7906 (pt) REVERT: C 228 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 230 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8479 (p) REVERT: C 249 GLN cc_start: 0.8196 (tp40) cc_final: 0.7740 (tp40) REVERT: C 262 SER cc_start: 0.8449 (t) cc_final: 0.8138 (p) REVERT: D 75 TRP cc_start: 0.7404 (t-100) cc_final: 0.7061 (t-100) REVERT: D 220 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8684 (mt-10) REVERT: D 264 ASP cc_start: 0.8560 (t70) cc_final: 0.8222 (t70) REVERT: E 73 GLN cc_start: 0.8139 (tp40) cc_final: 0.7720 (tp40) REVERT: E 108 LYS cc_start: 0.7660 (pttt) cc_final: 0.7309 (pttt) REVERT: E 175 ASP cc_start: 0.7560 (p0) cc_final: 0.6819 (p0) REVERT: E 278 SER cc_start: 0.9221 (t) cc_final: 0.8938 (p) REVERT: F 61 LYS cc_start: 0.7142 (ttmt) cc_final: 0.6432 (tmtt) outliers start: 135 outliers final: 117 residues processed: 525 average time/residue: 0.0980 time to fit residues: 77.4353 Evaluate side-chains 598 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 475 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 113 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS D 73 GLN E 249 GLN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.193022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.127855 restraints weight = 15014.524| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 4.54 r_work: 0.3448 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13091 Z= 0.179 Angle : 0.688 9.422 17800 Z= 0.337 Chirality : 0.045 0.149 2070 Planarity : 0.004 0.055 2303 Dihedral : 5.142 49.567 1795 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.10 % Favored : 91.37 % Rotamer: Outliers : 9.33 % Allowed : 23.22 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1680 helix: -2.74 (0.54), residues: 42 sheet: -0.31 (0.16), residues: 1098 loop : -2.66 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 164 TYR 0.013 0.001 TYR E 6 PHE 0.019 0.002 PHE E 193 TRP 0.006 0.001 TRP B 75 HIS 0.006 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00390 (13091) covalent geometry : angle 0.68843 (17800) hydrogen bonds : bond 0.02792 ( 723) hydrogen bonds : angle 5.37018 ( 1983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 490 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.6244 (p90) REVERT: A 40 LYS cc_start: 0.7786 (tttm) cc_final: 0.7528 (tmtt) REVERT: A 124 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7448 (mtt90) REVERT: A 144 HIS cc_start: 0.7952 (t-90) cc_final: 0.7512 (t-90) REVERT: A 249 GLN cc_start: 0.8272 (tp40) cc_final: 0.7619 (tp40) REVERT: B 22 TYR cc_start: 0.9020 (m-80) cc_final: 0.8696 (m-80) REVERT: B 50 LYS cc_start: 0.7527 (ptpt) cc_final: 0.7108 (ptmm) REVERT: B 63 ASN cc_start: 0.8462 (t0) cc_final: 0.8091 (t0) REVERT: B 73 GLN cc_start: 0.7880 (pt0) cc_final: 0.7289 (tm-30) REVERT: B 75 TRP cc_start: 0.7171 (m-90) cc_final: 0.6858 (m-90) REVERT: B 220 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8424 (mt-10) REVERT: B 240 SER cc_start: 0.9512 (m) cc_final: 0.9160 (p) REVERT: B 264 ASP cc_start: 0.8909 (t70) cc_final: 0.8702 (t0) REVERT: C 14 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8679 (t0) REVERT: C 32 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8416 (tp40) REVERT: C 91 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7569 (p) REVERT: C 116 PHE cc_start: 0.7633 (t80) cc_final: 0.7424 (t80) REVERT: C 124 ARG cc_start: 0.7855 (ptt90) cc_final: 0.7323 (ptt-90) REVERT: C 174 LYS cc_start: 0.9145 (tppt) cc_final: 0.8914 (tptp) REVERT: C 219 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7934 (pt) REVERT: C 228 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7429 (p0) REVERT: C 230 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8469 (p) REVERT: C 249 GLN cc_start: 0.8194 (tp40) cc_final: 0.7719 (tp40) REVERT: C 262 SER cc_start: 0.8436 (t) cc_final: 0.8122 (p) REVERT: D 62 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8090 (pt) REVERT: D 75 TRP cc_start: 0.7398 (t-100) cc_final: 0.6901 (t-100) REVERT: D 96 ASN cc_start: 0.8028 (t0) cc_final: 0.7734 (t0) REVERT: D 220 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8703 (mt-10) REVERT: D 264 ASP cc_start: 0.8558 (t70) cc_final: 0.8258 (t70) REVERT: E 73 GLN cc_start: 0.8133 (tp40) cc_final: 0.7712 (tp40) REVERT: E 108 LYS cc_start: 0.7658 (pttt) cc_final: 0.7308 (pttt) REVERT: E 174 LYS cc_start: 0.9320 (tppt) cc_final: 0.8922 (pttm) REVERT: E 175 ASP cc_start: 0.7431 (p0) cc_final: 0.6766 (p0) REVERT: E 278 SER cc_start: 0.9244 (t) cc_final: 0.8971 (p) REVERT: F 51 ASP cc_start: 0.8852 (t0) cc_final: 0.8608 (t0) REVERT: F 108 LYS cc_start: 0.7511 (pttt) cc_final: 0.7116 (pttt) REVERT: F 153 PHE cc_start: 0.8797 (p90) cc_final: 0.8543 (p90) REVERT: F 274 LYS cc_start: 0.7227 (mmmt) cc_final: 0.6942 (mmtm) outliers start: 131 outliers final: 119 residues processed: 533 average time/residue: 0.0945 time to fit residues: 75.1007 Evaluate side-chains 609 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 482 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 124 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 113 ASN C 77 ASN C 96 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN E 66 GLN E 249 GLN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.190291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125061 restraints weight = 14935.294| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 4.47 r_work: 0.3419 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13091 Z= 0.275 Angle : 0.726 9.307 17800 Z= 0.363 Chirality : 0.046 0.157 2070 Planarity : 0.004 0.055 2303 Dihedral : 5.419 48.349 1795 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.29 % Favored : 90.24 % Rotamer: Outliers : 10.26 % Allowed : 22.36 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.21), residues: 1680 helix: -2.76 (0.52), residues: 42 sheet: -0.34 (0.16), residues: 1098 loop : -2.70 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 164 TYR 0.013 0.002 TYR E 6 PHE 0.028 0.002 PHE D 221 TRP 0.005 0.001 TRP C 277 HIS 0.007 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00604 (13091) covalent geometry : angle 0.72645 (17800) hydrogen bonds : bond 0.02954 ( 723) hydrogen bonds : angle 5.47911 ( 1983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 486 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.6507 (p90) REVERT: A 40 LYS cc_start: 0.7859 (tttm) cc_final: 0.7577 (tmtt) REVERT: A 124 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7530 (mtm-85) REVERT: A 249 GLN cc_start: 0.8360 (tp40) cc_final: 0.7685 (tp40) REVERT: B 22 TYR cc_start: 0.9020 (m-80) cc_final: 0.8731 (m-80) REVERT: B 32 GLN cc_start: 0.8861 (mt0) cc_final: 0.8399 (mt0) REVERT: B 50 LYS cc_start: 0.7602 (ptpt) cc_final: 0.7034 (tmtt) REVERT: B 63 ASN cc_start: 0.8501 (t0) cc_final: 0.8139 (t0) REVERT: B 75 TRP cc_start: 0.7241 (m-90) cc_final: 0.6879 (m-90) REVERT: B 220 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 240 SER cc_start: 0.9477 (m) cc_final: 0.9151 (p) REVERT: B 264 ASP cc_start: 0.8972 (t70) cc_final: 0.8762 (t0) REVERT: C 32 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8389 (tp40) REVERT: C 91 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7680 (p) REVERT: C 124 ARG cc_start: 0.7861 (ptt90) cc_final: 0.7337 (ptt-90) REVERT: C 174 LYS cc_start: 0.9181 (tppt) cc_final: 0.8942 (tptp) REVERT: C 219 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8067 (pt) REVERT: C 228 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7496 (p0) REVERT: C 230 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8433 (p) REVERT: C 249 GLN cc_start: 0.8169 (tp40) cc_final: 0.7698 (tp40) REVERT: C 262 SER cc_start: 0.8458 (t) cc_final: 0.8147 (p) REVERT: D 22 TYR cc_start: 0.9288 (m-80) cc_final: 0.8565 (m-80) REVERT: D 73 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6057 (tm-30) REVERT: D 75 TRP cc_start: 0.7630 (t-100) cc_final: 0.5819 (m-90) REVERT: D 96 ASN cc_start: 0.8018 (t0) cc_final: 0.7673 (t0) REVERT: D 220 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8709 (mt-10) REVERT: D 264 ASP cc_start: 0.8631 (t70) cc_final: 0.8015 (t0) REVERT: E 66 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5605 (pp30) REVERT: E 73 GLN cc_start: 0.8155 (tp40) cc_final: 0.7740 (tp40) REVERT: E 108 LYS cc_start: 0.7790 (pttt) cc_final: 0.7433 (pttt) REVERT: E 174 LYS cc_start: 0.9314 (tppt) cc_final: 0.8917 (pttm) REVERT: E 175 ASP cc_start: 0.7452 (p0) cc_final: 0.6788 (p0) REVERT: F 51 ASP cc_start: 0.8938 (t0) cc_final: 0.8712 (t0) REVERT: F 108 LYS cc_start: 0.7651 (pttt) cc_final: 0.7254 (pttt) REVERT: F 153 PHE cc_start: 0.8811 (p90) cc_final: 0.8567 (p90) outliers start: 144 outliers final: 124 residues processed: 543 average time/residue: 0.0962 time to fit residues: 77.5611 Evaluate side-chains 602 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 471 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN A 113 ASN C 96 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.191189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126052 restraints weight = 15201.977| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.53 r_work: 0.3429 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13091 Z= 0.207 Angle : 0.711 9.289 17800 Z= 0.350 Chirality : 0.045 0.155 2070 Planarity : 0.004 0.058 2303 Dihedral : 5.371 48.678 1795 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.63 % Favored : 90.89 % Rotamer: Outliers : 8.97 % Allowed : 23.93 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.21), residues: 1680 helix: -2.69 (0.53), residues: 42 sheet: -0.32 (0.16), residues: 1098 loop : -2.67 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 164 TYR 0.015 0.001 TYR E 6 PHE 0.022 0.002 PHE E 193 TRP 0.008 0.001 TRP B 75 HIS 0.008 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00452 (13091) covalent geometry : angle 0.71121 (17800) hydrogen bonds : bond 0.02825 ( 723) hydrogen bonds : angle 5.42817 ( 1983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 485 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.6556 (p90) REVERT: A 124 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7521 (mtm-85) REVERT: A 144 HIS cc_start: 0.8081 (t-90) cc_final: 0.7627 (t-90) REVERT: A 249 GLN cc_start: 0.8261 (tp40) cc_final: 0.7633 (tp40) REVERT: B 22 TYR cc_start: 0.9004 (m-80) cc_final: 0.8740 (m-80) REVERT: B 32 GLN cc_start: 0.8871 (mt0) cc_final: 0.8460 (mt0) REVERT: B 50 LYS cc_start: 0.7615 (ptpt) cc_final: 0.7112 (tmtt) REVERT: B 63 ASN cc_start: 0.8476 (t0) cc_final: 0.8117 (t0) REVERT: B 73 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: B 75 TRP cc_start: 0.7169 (m-90) cc_final: 0.6849 (m-90) REVERT: B 220 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 240 SER cc_start: 0.9473 (m) cc_final: 0.9130 (p) REVERT: B 264 ASP cc_start: 0.8937 (t70) cc_final: 0.8727 (t0) REVERT: C 32 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8300 (tp40) REVERT: C 91 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7710 (p) REVERT: C 124 ARG cc_start: 0.7858 (ptt90) cc_final: 0.7325 (ptt-90) REVERT: C 174 LYS cc_start: 0.9173 (tppt) cc_final: 0.8924 (tptp) REVERT: C 219 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8066 (pt) REVERT: C 228 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7454 (p0) REVERT: C 230 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8469 (p) REVERT: C 249 GLN cc_start: 0.8188 (tp40) cc_final: 0.7730 (tp40) REVERT: C 262 SER cc_start: 0.8437 (t) cc_final: 0.8134 (p) REVERT: D 22 TYR cc_start: 0.9254 (m-80) cc_final: 0.8519 (m-80) REVERT: D 75 TRP cc_start: 0.7603 (t-100) cc_final: 0.7095 (t-100) REVERT: D 96 ASN cc_start: 0.7997 (t0) cc_final: 0.7696 (t0) REVERT: D 220 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8718 (mt-10) REVERT: D 264 ASP cc_start: 0.8627 (t70) cc_final: 0.8024 (t0) REVERT: E 73 GLN cc_start: 0.8159 (tp40) cc_final: 0.7740 (tp40) REVERT: E 108 LYS cc_start: 0.7771 (pttt) cc_final: 0.7424 (pttt) REVERT: E 174 LYS cc_start: 0.9314 (tppt) cc_final: 0.9064 (tppt) REVERT: E 175 ASP cc_start: 0.7407 (p0) cc_final: 0.6708 (p0) REVERT: F 50 LYS cc_start: 0.7342 (ptpp) cc_final: 0.5720 (tptt) REVERT: F 51 ASP cc_start: 0.8920 (t0) cc_final: 0.8609 (t0) REVERT: F 108 LYS cc_start: 0.7708 (pttt) cc_final: 0.7343 (pttt) REVERT: F 153 PHE cc_start: 0.8806 (p90) cc_final: 0.8545 (p90) outliers start: 126 outliers final: 115 residues processed: 532 average time/residue: 0.0871 time to fit residues: 70.3388 Evaluate side-chains 599 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 477 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 167 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN A 113 ASN C 96 ASN C 118 GLN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.190381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124778 restraints weight = 15104.914| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 4.55 r_work: 0.3444 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13091 Z= 0.175 Angle : 0.710 9.247 17800 Z= 0.348 Chirality : 0.045 0.192 2070 Planarity : 0.004 0.052 2303 Dihedral : 5.289 48.982 1795 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.21 % Favored : 91.25 % Rotamer: Outliers : 8.83 % Allowed : 24.29 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1680 helix: -2.61 (0.55), residues: 42 sheet: -0.31 (0.16), residues: 1096 loop : -2.56 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 164 TYR 0.015 0.001 TYR E 6 PHE 0.027 0.002 PHE C 116 TRP 0.008 0.001 TRP B 75 HIS 0.008 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00380 (13091) covalent geometry : angle 0.70982 (17800) hydrogen bonds : bond 0.02722 ( 723) hydrogen bonds : angle 5.37817 ( 1983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 496 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.6438 (p90) REVERT: A 40 LYS cc_start: 0.7890 (tttm) cc_final: 0.7333 (tmtt) REVERT: A 124 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7507 (mtm-85) REVERT: A 144 HIS cc_start: 0.8082 (t-90) cc_final: 0.7604 (t-90) REVERT: A 249 GLN cc_start: 0.8259 (tp40) cc_final: 0.7592 (tp40) REVERT: B 22 TYR cc_start: 0.8998 (m-80) cc_final: 0.8718 (m-80) REVERT: B 32 GLN cc_start: 0.8863 (mt0) cc_final: 0.8553 (mt0) REVERT: B 50 LYS cc_start: 0.7634 (ptpt) cc_final: 0.7148 (tmtt) REVERT: B 63 ASN cc_start: 0.8469 (t0) cc_final: 0.8117 (t0) REVERT: B 73 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: B 75 TRP cc_start: 0.7184 (m-90) cc_final: 0.6868 (m-90) REVERT: B 96 ASN cc_start: 0.8074 (t0) cc_final: 0.7729 (t0) REVERT: B 220 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 240 SER cc_start: 0.9472 (m) cc_final: 0.9124 (p) REVERT: C 32 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8269 (tp40) REVERT: C 91 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7751 (p) REVERT: C 124 ARG cc_start: 0.7868 (ptt90) cc_final: 0.7346 (ptt-90) REVERT: C 174 LYS cc_start: 0.9218 (tppt) cc_final: 0.8962 (tptp) REVERT: C 219 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8036 (pt) REVERT: C 228 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 230 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 249 GLN cc_start: 0.8150 (tp40) cc_final: 0.7688 (tp40) REVERT: C 262 SER cc_start: 0.8390 (t) cc_final: 0.8173 (p) REVERT: D 22 TYR cc_start: 0.9235 (m-80) cc_final: 0.8505 (m-80) REVERT: D 75 TRP cc_start: 0.7637 (t-100) cc_final: 0.7056 (t-100) REVERT: D 96 ASN cc_start: 0.7991 (t0) cc_final: 0.7692 (t0) REVERT: D 220 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8713 (mt-10) REVERT: D 264 ASP cc_start: 0.8648 (t70) cc_final: 0.8039 (t0) REVERT: E 73 GLN cc_start: 0.8175 (tp40) cc_final: 0.7750 (tp40) REVERT: E 108 LYS cc_start: 0.7758 (pttt) cc_final: 0.7397 (pttt) REVERT: F 50 LYS cc_start: 0.7232 (ptpp) cc_final: 0.5573 (tptt) REVERT: F 51 ASP cc_start: 0.8918 (t0) cc_final: 0.8608 (t0) REVERT: F 108 LYS cc_start: 0.7760 (pttt) cc_final: 0.7378 (pttt) REVERT: F 153 PHE cc_start: 0.8815 (p90) cc_final: 0.8562 (p90) outliers start: 124 outliers final: 116 residues processed: 541 average time/residue: 0.0958 time to fit residues: 77.9129 Evaluate side-chains 618 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 495 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 TYR Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 278 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN A 113 ASN C 14 ASN C 96 ASN E 63 ASN ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128032 restraints weight = 15089.532| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 4.59 r_work: 0.3460 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13091 Z= 0.128 Angle : 0.708 9.253 17800 Z= 0.341 Chirality : 0.045 0.173 2070 Planarity : 0.004 0.053 2303 Dihedral : 5.136 49.466 1795 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.20 % Favored : 92.26 % Rotamer: Outliers : 8.05 % Allowed : 25.50 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.22), residues: 1680 helix: -2.51 (0.58), residues: 42 sheet: -0.25 (0.16), residues: 1096 loop : -2.52 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 164 TYR 0.014 0.001 TYR E 6 PHE 0.038 0.002 PHE C 116 TRP 0.011 0.001 TRP B 75 HIS 0.009 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00273 (13091) covalent geometry : angle 0.70847 (17800) hydrogen bonds : bond 0.02624 ( 723) hydrogen bonds : angle 5.27936 ( 1983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.62 seconds wall clock time: 60 minutes 43.68 seconds (3643.68 seconds total)