Starting phenix.real_space_refine on Thu Mar 13 09:04:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7x_28912/03_2025/8f7x_28912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7x_28912/03_2025/8f7x_28912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7x_28912/03_2025/8f7x_28912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7x_28912/03_2025/8f7x_28912.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7x_28912/03_2025/8f7x_28912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7x_28912/03_2025/8f7x_28912.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 64 5.16 5 C 5653 2.51 5 N 1519 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8902 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2211 Classifications: {'peptide': 285} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 273} Chain: "P" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 105 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1782 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 436 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1792 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 5.76, per 1000 atoms: 0.65 Number of scatterers: 8902 At special positions: 0 Unit cell: (100.8, 111.72, 134.4, 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 64 16.00 O 1666 8.00 N 1519 7.00 C 5653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 49 through 78 Processing helix chain 'R' and resid 84 through 102 Processing helix chain 'R' and resid 103 through 114 removed outlier: 3.501A pdb=" N THR R 109 " --> pdb=" O PRO R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 154 Processing helix chain 'R' and resid 157 through 162 removed outlier: 3.603A pdb=" N VAL R 161 " --> pdb=" O ARG R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 189 Proline residue: R 184 - end of helix Processing helix chain 'R' and resid 207 through 245 Proline residue: R 213 - end of helix removed outlier: 4.836A pdb=" N VAL R 226 " --> pdb=" O PHE R 222 " (cutoff:3.500A) Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 251 through 288 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 294 through 320 removed outlier: 3.757A pdb=" N VAL R 298 " --> pdb=" O SER R 294 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN R 311 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER R 312 " --> pdb=" O GLY R 308 " (cutoff:3.500A) Proline residue: R 316 - end of helix Processing helix chain 'R' and resid 323 through 333 removed outlier: 3.620A pdb=" N PHE R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 14 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.822A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.554A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.792A pdb=" N LEU A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.333A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.727A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.749A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 25 removed outlier: 3.503A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.560A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.757A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.133A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 221 through 225 removed outlier: 3.720A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.536A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.548A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.857A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.835A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.533A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.552A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.880A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.879A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.401A pdb=" N VAL E 148 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1314 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: 2.52 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2879 1.35 - 1.46: 2111 1.46 - 1.58: 3995 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 9076 Sorted by residual: bond pdb=" C THR R 277 " pdb=" N PRO R 278 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.36e-02 5.41e+03 4.59e+00 bond pdb=" C VAL R 183 " pdb=" N PRO R 184 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.61e+00 bond pdb=" C LEU R 104 " pdb=" N PRO R 105 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.44e-02 4.82e+03 3.56e+00 bond pdb=" CA THR R 277 " pdb=" C THR R 277 " ideal model delta sigma weight residual 1.521 1.542 -0.021 1.14e-02 7.69e+03 3.35e+00 bond pdb=" C TYR E 236 " pdb=" N PRO E 237 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.12e+00 ... (remaining 9071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 11477 1.57 - 3.13: 646 3.13 - 4.70: 120 4.70 - 6.27: 29 6.27 - 7.83: 16 Bond angle restraints: 12288 Sorted by residual: angle pdb=" N GLY R 182 " pdb=" CA GLY R 182 " pdb=" C GLY R 182 " ideal model delta sigma weight residual 112.83 120.42 -7.59 1.22e+00 6.72e-01 3.88e+01 angle pdb=" C VAL R 181 " pdb=" N GLY R 182 " pdb=" CA GLY R 182 " ideal model delta sigma weight residual 120.03 125.95 -5.92 1.12e+00 7.97e-01 2.79e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 122.07 127.98 -5.91 1.43e+00 4.89e-01 1.71e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 122.61 128.93 -6.32 1.56e+00 4.11e-01 1.64e+01 angle pdb=" N GLY R 189 " pdb=" CA GLY R 189 " pdb=" C GLY R 189 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.17e+00 7.31e-01 1.60e+01 ... (remaining 12283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 5126 14.11 - 28.22: 223 28.22 - 42.33: 46 42.33 - 56.45: 5 56.45 - 70.56: 1 Dihedral angle restraints: 5401 sinusoidal: 2098 harmonic: 3303 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA GLU E 235 " pdb=" C GLU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta harmonic sigma weight residual 180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1081 0.056 - 0.112: 256 0.112 - 0.169: 57 0.169 - 0.225: 9 0.225 - 0.281: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB THR E 91 " pdb=" CA THR E 91 " pdb=" OG1 THR E 91 " pdb=" CG2 THR E 91 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1402 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 129 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ILE R 129 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE R 129 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP R 130 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.020 2.00e-02 2.50e+03 1.39e-02 4.82e+00 pdb=" CG TRP B 82 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO C 55 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.029 5.00e-02 4.00e+02 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1882 2.80 - 3.32: 7899 3.32 - 3.85: 14056 3.85 - 4.37: 15829 4.37 - 4.90: 28745 Nonbonded interactions: 68411 Sorted by model distance: nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.321 3.040 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.342 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.344 3.040 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.347 3.040 ... (remaining 68406 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.350 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.048 9076 Z= 0.275 Angle : 0.876 7.834 12288 Z= 0.514 Chirality : 0.053 0.281 1405 Planarity : 0.006 0.052 1558 Dihedral : 8.644 70.556 3264 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.10 % Allowed : 1.65 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1127 helix: 2.33 (0.22), residues: 397 sheet: 0.05 (0.31), residues: 278 loop : -1.27 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.033 0.003 PHE A 354 TYR 0.024 0.002 TYR R 132 ARG 0.013 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8556 (m) cc_final: 0.8302 (t) REVERT: B 138 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 212 ASP cc_start: 0.8038 (t70) cc_final: 0.7710 (t70) REVERT: E 219 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7485 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2483 time to fit residues: 82.5054 Evaluate side-chains 142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 0.0470 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN R 154 HIS ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 322 HIS B 259 GLN E 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.160228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121097 restraints weight = 10790.935| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.83 r_work: 0.3027 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9076 Z= 0.387 Angle : 0.683 8.321 12288 Z= 0.365 Chirality : 0.046 0.155 1405 Planarity : 0.005 0.044 1558 Dihedral : 4.475 24.525 1239 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.99 % Allowed : 9.48 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1127 helix: 2.95 (0.23), residues: 394 sheet: -0.01 (0.30), residues: 293 loop : -1.24 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.007 0.002 HIS E 233 PHE 0.019 0.002 PHE P 1 TYR 0.027 0.003 TYR B 85 ARG 0.006 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9021 (m) cc_final: 0.8626 (t) REVERT: A 313 ARG cc_start: 0.6870 (ttm110) cc_final: 0.6657 (ttt180) REVERT: B 175 GLN cc_start: 0.8455 (mt0) cc_final: 0.8179 (mm110) REVERT: C 46 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7645 (tptp) REVERT: E 219 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7576 (ttp-110) outliers start: 29 outliers final: 17 residues processed: 195 average time/residue: 0.2834 time to fit residues: 72.5966 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 109 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.164407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126682 restraints weight = 11026.743| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.72 r_work: 0.3107 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9076 Z= 0.165 Angle : 0.544 7.824 12288 Z= 0.287 Chirality : 0.041 0.128 1405 Planarity : 0.004 0.040 1558 Dihedral : 4.065 22.299 1239 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.37 % Allowed : 11.75 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1127 helix: 3.36 (0.24), residues: 396 sheet: 0.09 (0.30), residues: 272 loop : -1.02 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE P 1 TYR 0.015 0.001 TYR B 85 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8949 (m) cc_final: 0.8648 (t) REVERT: B 175 GLN cc_start: 0.8363 (mt0) cc_final: 0.8082 (mm110) REVERT: E 214 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7813 (t) REVERT: E 219 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7504 (ttp-110) outliers start: 23 outliers final: 17 residues processed: 164 average time/residue: 0.2307 time to fit residues: 50.8179 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 0.0470 chunk 96 optimal weight: 0.8980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 188 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133535 restraints weight = 10795.465| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.54 r_work: 0.3179 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9076 Z= 0.146 Angle : 0.504 7.314 12288 Z= 0.264 Chirality : 0.039 0.127 1405 Planarity : 0.004 0.039 1558 Dihedral : 3.802 20.609 1239 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.68 % Allowed : 13.30 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1127 helix: 3.53 (0.24), residues: 395 sheet: 0.08 (0.29), residues: 283 loop : -0.88 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.009 0.001 HIS A 188 PHE 0.012 0.001 PHE P 1 TYR 0.013 0.001 TYR B 85 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: R 73 MET cc_start: 0.8465 (tpp) cc_final: 0.8242 (mmm) REVERT: A 190 THR cc_start: 0.8974 (m) cc_final: 0.8698 (t) REVERT: B 205 ASP cc_start: 0.7061 (t0) cc_final: 0.6855 (t0) REVERT: B 219 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7723 (ttm-80) REVERT: E 45 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7897 (mt) REVERT: E 219 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7532 (ttp-110) outliers start: 26 outliers final: 18 residues processed: 160 average time/residue: 0.2388 time to fit residues: 51.0790 Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 175 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118032 restraints weight = 10876.371| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.81 r_work: 0.3075 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9076 Z= 0.332 Angle : 0.622 7.982 12288 Z= 0.325 Chirality : 0.043 0.150 1405 Planarity : 0.004 0.044 1558 Dihedral : 4.307 24.438 1239 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.81 % Allowed : 12.89 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1127 helix: 3.00 (0.24), residues: 400 sheet: 0.05 (0.29), residues: 293 loop : -1.08 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.002 HIS A 188 PHE 0.020 0.002 PHE E 108 TYR 0.024 0.002 TYR B 59 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9183 (m) cc_final: 0.8895 (t) REVERT: B 219 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7788 (mtp180) REVERT: C 46 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7532 (tptp) REVERT: E 45 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7815 (mt) REVERT: E 219 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7576 (ttp-110) outliers start: 37 outliers final: 25 residues processed: 167 average time/residue: 0.2451 time to fit residues: 54.1003 Evaluate side-chains 158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130402 restraints weight = 10665.877| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.40 r_work: 0.3132 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9076 Z= 0.164 Angle : 0.533 10.920 12288 Z= 0.276 Chirality : 0.040 0.127 1405 Planarity : 0.004 0.037 1558 Dihedral : 3.987 23.138 1239 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.30 % Allowed : 14.74 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1127 helix: 3.26 (0.25), residues: 399 sheet: 0.13 (0.29), residues: 275 loop : -0.99 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.011 0.001 PHE P 1 TYR 0.013 0.001 TYR B 59 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.110 Fit side-chains REVERT: R 66 LEU cc_start: 0.8129 (mt) cc_final: 0.7849 (mt) REVERT: R 232 SER cc_start: 0.8845 (m) cc_final: 0.8531 (p) REVERT: A 190 THR cc_start: 0.9185 (m) cc_final: 0.8941 (t) REVERT: B 42 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.8091 (ttp80) REVERT: B 219 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7894 (ttm-80) REVERT: E 45 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7872 (mt) REVERT: E 219 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7572 (ttp-110) outliers start: 32 outliers final: 25 residues processed: 164 average time/residue: 0.3163 time to fit residues: 68.2858 Evaluate side-chains 158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 202 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127817 restraints weight = 10793.314| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.39 r_work: 0.3070 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9076 Z= 0.272 Angle : 0.599 14.356 12288 Z= 0.307 Chirality : 0.042 0.162 1405 Planarity : 0.004 0.043 1558 Dihedral : 4.196 23.825 1239 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.99 % Allowed : 15.15 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1127 helix: 3.04 (0.24), residues: 399 sheet: 0.00 (0.28), residues: 293 loop : -0.98 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.002 HIS A 188 PHE 0.012 0.001 PHE B 241 TYR 0.019 0.002 TYR B 85 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.029 Fit side-chains REVERT: R 66 LEU cc_start: 0.8154 (mt) cc_final: 0.7880 (mt) REVERT: R 177 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7849 (tt) REVERT: R 232 SER cc_start: 0.8872 (m) cc_final: 0.8579 (p) REVERT: A 46 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7938 (mtpt) REVERT: A 190 THR cc_start: 0.9229 (m) cc_final: 0.8981 (t) REVERT: B 42 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8031 (ttp80) REVERT: B 219 ARG cc_start: 0.8328 (mmm160) cc_final: 0.7954 (ttm-80) REVERT: E 45 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7891 (mt) outliers start: 29 outliers final: 25 residues processed: 158 average time/residue: 0.2615 time to fit residues: 54.3758 Evaluate side-chains 160 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 310 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 0.0170 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132643 restraints weight = 10889.204| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.40 r_work: 0.3134 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9076 Z= 0.153 Angle : 0.526 9.460 12288 Z= 0.272 Chirality : 0.040 0.139 1405 Planarity : 0.004 0.050 1558 Dihedral : 3.910 21.942 1239 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.47 % Allowed : 15.67 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1127 helix: 3.27 (0.25), residues: 398 sheet: 0.07 (0.29), residues: 276 loop : -0.93 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR B 85 ARG 0.012 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.987 Fit side-chains REVERT: R 66 LEU cc_start: 0.8238 (mt) cc_final: 0.7938 (mt) REVERT: R 232 SER cc_start: 0.8807 (m) cc_final: 0.8507 (p) REVERT: A 190 THR cc_start: 0.9214 (m) cc_final: 0.8987 (t) REVERT: A 240 MET cc_start: 0.5946 (mmp) cc_final: 0.5570 (mmt) REVERT: A 349 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8102 (mtpp) REVERT: B 42 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7937 (ttp80) REVERT: B 129 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7700 (mtp180) REVERT: B 219 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7874 (ttm-80) REVERT: E 45 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7868 (mt) outliers start: 24 outliers final: 20 residues processed: 157 average time/residue: 0.2635 time to fit residues: 54.0955 Evaluate side-chains 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 202 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.0170 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 78 optimal weight: 0.1980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 GLN A 269 ASN B 175 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.173406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136185 restraints weight = 10767.475| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.41 r_work: 0.3183 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9076 Z= 0.143 Angle : 0.517 12.508 12288 Z= 0.265 Chirality : 0.040 0.140 1405 Planarity : 0.004 0.063 1558 Dihedral : 3.733 20.180 1239 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.16 % Allowed : 15.98 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1127 helix: 3.29 (0.25), residues: 399 sheet: 0.14 (0.29), residues: 273 loop : -0.83 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.010 0.001 PHE B 241 TYR 0.012 0.001 TYR R 132 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.906 Fit side-chains REVERT: R 66 LEU cc_start: 0.8299 (mt) cc_final: 0.7978 (mt) REVERT: R 73 MET cc_start: 0.8405 (mtp) cc_final: 0.7910 (mmm) REVERT: R 139 PHE cc_start: 0.8616 (m-10) cc_final: 0.8333 (m-10) REVERT: R 232 SER cc_start: 0.8784 (m) cc_final: 0.8492 (p) REVERT: A 190 THR cc_start: 0.9191 (m) cc_final: 0.8986 (t) REVERT: A 240 MET cc_start: 0.5973 (mmp) cc_final: 0.5658 (mmt) REVERT: A 305 CYS cc_start: 0.7745 (m) cc_final: 0.7438 (p) REVERT: A 349 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8011 (mtpp) REVERT: B 219 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7865 (ttm-80) REVERT: E 45 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7796 (mt) outliers start: 21 outliers final: 20 residues processed: 160 average time/residue: 0.2493 time to fit residues: 52.5543 Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 202 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131748 restraints weight = 10779.498| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.39 r_work: 0.3126 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9076 Z= 0.198 Angle : 0.554 12.335 12288 Z= 0.284 Chirality : 0.041 0.175 1405 Planarity : 0.004 0.058 1558 Dihedral : 3.891 20.420 1239 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.58 % Allowed : 15.67 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1127 helix: 3.26 (0.25), residues: 398 sheet: 0.12 (0.30), residues: 272 loop : -0.85 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.027 0.001 PHE P 1 TYR 0.014 0.001 TYR B 85 ARG 0.014 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.982 Fit side-chains REVERT: R 66 LEU cc_start: 0.8239 (mt) cc_final: 0.7930 (mt) REVERT: R 232 SER cc_start: 0.8854 (m) cc_final: 0.8547 (p) REVERT: A 190 THR cc_start: 0.9231 (m) cc_final: 0.8988 (t) REVERT: A 240 MET cc_start: 0.5998 (mmp) cc_final: 0.5709 (mmt) REVERT: A 349 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8146 (mtpp) REVERT: B 42 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.8008 (ttp80) REVERT: B 129 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7792 (mtp180) REVERT: B 219 ARG cc_start: 0.8241 (mmm160) cc_final: 0.7884 (ttm-80) REVERT: E 45 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7787 (mt) outliers start: 25 outliers final: 21 residues processed: 156 average time/residue: 0.2505 time to fit residues: 51.6871 Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 202 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.169921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132268 restraints weight = 10798.118| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.39 r_work: 0.3125 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9076 Z= 0.185 Angle : 0.546 11.928 12288 Z= 0.280 Chirality : 0.040 0.164 1405 Planarity : 0.004 0.060 1558 Dihedral : 3.872 20.015 1239 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.47 % Allowed : 15.67 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1127 helix: 3.28 (0.25), residues: 398 sheet: 0.08 (0.29), residues: 274 loop : -0.88 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.026 0.001 PHE P 1 TYR 0.014 0.001 TYR B 85 ARG 0.014 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4843.58 seconds wall clock time: 85 minutes 30.91 seconds (5130.91 seconds total)