Starting phenix.real_space_refine on Thu Feb 13 06:50:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7x_28912/02_2025/8f7x_28912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7x_28912/02_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_28912/02_2025/8f7x_28912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7x_28912/02_2025/8f7x_28912.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7x_28912/02_2025/8f7x_28912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7x_28912/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.18, per 1000 atoms: 0.58 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 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: 1.09 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: 2.70 Time building geometry restraints manager: 2.39 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: 0.720 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- 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 : 1.010 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: 0.2474 time to fit residues: 82.1395 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 : 0.782 ------------------------------------------------------------------------------- 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 = 0.121098 restraints weight = 10790.936| |-----------------------------------------------------------------------------| 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 : 1.012 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: 0.6873 (ttm110) cc_final: 0.6660 (ttt180) REVERT: B 175 GLN cc_start: 0.8458 (mt0) cc_final: 0.8180 (mm110) REVERT: C 46 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7646 (tptp) REVERT: E 219 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7579 (ttp-110) outliers start: 29 outliers final: 17 residues processed: 195 average time/residue: 0.2472 time to fit residues: 63.8304 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 : 0.995 ------------------------------------------------------------------------------- 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: 3.9990 chunk 109 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 E 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.159865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121661 restraints weight = 11060.323| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.77 r_work: 0.3127 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9076 Z= 0.251 Angle : 0.590 7.521 12288 Z= 0.311 Chirality : 0.042 0.136 1405 Planarity : 0.004 0.041 1558 Dihedral : 4.253 24.512 1239 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.78 % Allowed : 11.65 % Favored : 85.57 % 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: 1.07 (0.25), residues: 1127 helix: 3.09 (0.24), residues: 400 sheet: 0.07 (0.29), residues: 288 loop : -1.16 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS E 233 PHE 0.016 0.002 PHE E 108 TYR 0.019 0.002 TYR B 85 ARG 0.004 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 173 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9068 (m) cc_final: 0.8746 (t) REVERT: B 175 GLN cc_start: 0.8350 (mt0) cc_final: 0.8121 (mm110) REVERT: E 219 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7559 (ttp-110) outliers start: 27 outliers final: 22 residues processed: 166 average time/residue: 0.2596 time to fit residues: 57.3626 Evaluate side-chains 158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 193 VAL Chi-restraints excluded: chain R residue 266 LEU 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 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 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 156 VAL Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.162611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124294 restraints weight = 10835.966| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.70 r_work: 0.3126 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4116 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= 0.163 Angle : 0.530 13.469 12288 Z= 0.275 Chirality : 0.040 0.128 1405 Planarity : 0.004 0.039 1558 Dihedral : 3.930 23.364 1239 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.61 % Allowed : 12.27 % Favored : 84.12 % 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: 3.42 (0.24), residues: 395 sheet: 0.06 (0.29), residues: 281 loop : -0.97 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.013 0.001 PHE P 1 TYR 0.014 0.001 TYR B 85 ARG 0.005 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 185 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9059 (m) cc_final: 0.8775 (t) REVERT: B 175 GLN cc_start: 0.8239 (mt0) cc_final: 0.7898 (mm110) REVERT: B 219 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7772 (ttm-80) REVERT: E 45 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7879 (mt) REVERT: E 219 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7527 (ttp-110) outliers start: 35 outliers final: 22 residues processed: 173 average time/residue: 0.2494 time to fit residues: 57.4772 Evaluate side-chains 161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 176 GLN 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 57 SER 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: 5.9990 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 81 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 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 = 0.3746 r_free = 0.3746 target = 0.158387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120490 restraints weight = 10830.868| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.77 r_work: 0.3065 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9076 Z= 0.246 Angle : 0.575 11.564 12288 Z= 0.296 Chirality : 0.042 0.137 1405 Planarity : 0.004 0.039 1558 Dihedral : 4.098 24.504 1239 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.71 % Allowed : 13.51 % Favored : 82.78 % 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: 1.16 (0.25), residues: 1127 helix: 3.17 (0.24), residues: 401 sheet: 0.02 (0.28), residues: 289 loop : -1.03 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.013 0.001 PHE E 108 TYR 0.020 0.002 TYR B 85 ARG 0.007 0.000 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 181 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9173 (m) cc_final: 0.8882 (t) REVERT: B 219 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7815 (ttm-80) REVERT: E 45 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7894 (mt) REVERT: E 219 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7559 (ttp-110) outliers start: 36 outliers final: 28 residues processed: 169 average time/residue: 0.2440 time to fit residues: 55.1075 Evaluate side-chains 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 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 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN 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 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: 2.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.156625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118797 restraints weight = 10937.280| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.68 r_work: 0.3082 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9076 Z= 0.265 Angle : 0.586 10.060 12288 Z= 0.306 Chirality : 0.042 0.138 1405 Planarity : 0.004 0.039 1558 Dihedral : 4.202 24.829 1239 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.02 % Allowed : 13.71 % Favored : 82.27 % 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: 1.07 (0.25), residues: 1127 helix: 3.08 (0.24), residues: 399 sheet: 0.01 (0.28), residues: 289 loop : -1.08 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.012 0.002 PHE E 108 TYR 0.019 0.002 TYR B 85 ARG 0.007 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 180 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: R 232 SER cc_start: 0.8744 (m) cc_final: 0.8463 (p) REVERT: A 190 THR cc_start: 0.9203 (m) cc_final: 0.8927 (t) REVERT: E 45 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7854 (mt) REVERT: E 219 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7585 (ttp-110) outliers start: 39 outliers final: 26 residues processed: 166 average time/residue: 0.2617 time to fit residues: 56.9948 Evaluate side-chains 160 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain R residue 100 VAL 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 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 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 156 VAL Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.168652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131114 restraints weight = 10781.008| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.43 r_work: 0.3073 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9076 Z= 0.185 Angle : 0.543 10.984 12288 Z= 0.281 Chirality : 0.040 0.162 1405 Planarity : 0.004 0.038 1558 Dihedral : 3.998 22.830 1239 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.40 % Allowed : 14.85 % 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: 1.23 (0.25), residues: 1127 helix: 3.22 (0.25), residues: 399 sheet: 0.11 (0.29), residues: 275 loop : -0.99 (0.27), 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 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR B 85 ARG 0.010 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 181 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 232 SER cc_start: 0.8854 (m) cc_final: 0.8529 (p) REVERT: A 190 THR cc_start: 0.9223 (m) cc_final: 0.8973 (t) REVERT: A 349 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8199 (mtpp) REVERT: B 219 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7930 (ttm-80) REVERT: E 45 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7841 (mt) REVERT: E 247 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7026 (mt-10) outliers start: 33 outliers final: 28 residues processed: 170 average time/residue: 0.2602 time to fit residues: 57.9650 Evaluate side-chains 169 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain R residue 100 VAL 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 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN 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 290 ASP 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 155 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 202 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 0.0050 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.161928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123792 restraints weight = 11108.743| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.66 r_work: 0.3137 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9076 Z= 0.161 Angle : 0.529 10.504 12288 Z= 0.273 Chirality : 0.040 0.142 1405 Planarity : 0.004 0.051 1558 Dihedral : 3.880 21.423 1239 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.20 % Allowed : 15.36 % Favored : 81.44 % 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: 1.28 (0.25), residues: 1127 helix: 3.26 (0.25), residues: 400 sheet: 0.10 (0.30), residues: 269 loop : -0.93 (0.28), residues: 458 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 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR B 59 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 175 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: R 232 SER cc_start: 0.8724 (m) cc_final: 0.8403 (p) REVERT: A 190 THR cc_start: 0.9182 (m) cc_final: 0.8945 (t) REVERT: A 349 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7982 (mtpp) REVERT: B 175 GLN cc_start: 0.8644 (mm110) cc_final: 0.8353 (mm110) REVERT: B 219 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7751 (ttm-80) REVERT: B 325 MET cc_start: 0.8637 (tpp) cc_final: 0.8256 (mmt) REVERT: E 45 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7763 (mt) outliers start: 31 outliers final: 27 residues processed: 165 average time/residue: 0.2632 time to fit residues: 57.1553 Evaluate side-chains 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 100 VAL 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 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 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 290 ASP 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 21 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 202 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.0030 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 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 = 0.3793 r_free = 0.3793 target = 0.162612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124403 restraints weight = 10983.956| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.68 r_work: 0.3138 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9076 Z= 0.156 Angle : 0.524 11.310 12288 Z= 0.269 Chirality : 0.040 0.142 1405 Planarity : 0.004 0.058 1558 Dihedral : 3.825 21.120 1239 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.89 % Allowed : 15.77 % Favored : 81.34 % 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: 3.24 (0.25), residues: 402 sheet: 0.07 (0.29), residues: 273 loop : -0.84 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.010 0.001 PHE B 241 TYR 0.011 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 169 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.038 Fit side-chains REVERT: R 232 SER cc_start: 0.8716 (m) cc_final: 0.8390 (p) REVERT: A 190 THR cc_start: 0.9172 (m) cc_final: 0.8945 (t) REVERT: B 175 GLN cc_start: 0.8627 (mm110) cc_final: 0.8053 (mm110) REVERT: B 219 ARG cc_start: 0.8074 (mmm160) cc_final: 0.7723 (ttm-80) REVERT: B 325 MET cc_start: 0.8624 (tpp) cc_final: 0.8184 (mmt) REVERT: E 45 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7690 (mt) outliers start: 28 outliers final: 26 residues processed: 160 average time/residue: 0.2836 time to fit residues: 59.5439 Evaluate side-chains 163 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 100 VAL 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 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 176 GLN 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 290 ASP 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 21 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 202 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 87 optimal weight: 0.0030 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.159603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121174 restraints weight = 10995.964| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.65 r_work: 0.3078 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9076 Z= 0.206 Angle : 0.559 11.070 12288 Z= 0.288 Chirality : 0.041 0.136 1405 Planarity : 0.004 0.058 1558 Dihedral : 3.936 21.570 1239 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.89 % Allowed : 15.98 % Favored : 81.13 % 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: 3.20 (0.25), residues: 402 sheet: 0.06 (0.29), residues: 285 loop : -0.91 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.011 0.001 PHE B 241 TYR 0.016 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 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: R 232 SER cc_start: 0.8883 (m) cc_final: 0.8544 (p) REVERT: A 190 THR cc_start: 0.9216 (m) cc_final: 0.8980 (t) REVERT: A 305 CYS cc_start: 0.7755 (m) cc_final: 0.7450 (p) REVERT: B 219 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7917 (ttm-80) REVERT: E 45 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7740 (mt) outliers start: 28 outliers final: 27 residues processed: 155 average time/residue: 0.2652 time to fit residues: 54.0935 Evaluate side-chains 163 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 100 VAL 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 135 VAL Chi-restraints excluded: chain B residue 176 GLN 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 290 ASP 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 21 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 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: 4.9990 chunk 105 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 28 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.171566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134041 restraints weight = 10767.432| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.34 r_work: 0.3171 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9076 Z= 0.150 Angle : 0.521 11.629 12288 Z= 0.268 Chirality : 0.040 0.140 1405 Planarity : 0.004 0.060 1558 Dihedral : 3.781 20.872 1239 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.37 % Allowed : 16.39 % Favored : 81.24 % 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: 1.37 (0.25), residues: 1127 helix: 3.29 (0.25), residues: 401 sheet: 0.13 (0.30), residues: 272 loop : -0.81 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.009 0.001 PHE A 189 TYR 0.012 0.001 TYR R 132 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: 4614.64 seconds wall clock time: 82 minutes 36.33 seconds (4956.33 seconds total)