Starting phenix.real_space_refine on Sat Aug 23 00:26:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7x_28912/08_2025/8f7x_28912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7x_28912/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f7x_28912/08_2025/8f7x_28912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7x_28912/08_2025/8f7x_28912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f7x_28912/08_2025/8f7x_28912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7x_28912/08_2025/8f7x_28912.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.61, per 1000 atoms: 0.18 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: 0.51 Conformation dependent library (CDL) restraints added in 400.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 1.11 Time building geometry restraints manager: 0.70 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: 1.030 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.580 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- 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 9079 Z= 0.231 Angle : 0.876 7.834 12294 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (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 ARG 0.013 0.001 ARG B 150 TYR 0.024 0.002 TYR R 132 PHE 0.033 0.003 PHE A 354 TRP 0.037 0.002 TRP B 82 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9076) covalent geometry : angle 0.87567 (12288) SS BOND : bond 0.00961 ( 3) SS BOND : angle 1.75496 ( 6) hydrogen bonds : bond 0.11302 ( 447) hydrogen bonds : angle 5.87607 ( 1314) *********************** 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 : 0.203 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: 0.0916 time to fit residues: 30.5355 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 : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.0870 overall best weight: 2.7564 ------------------------------------------------------------------------------- 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** R 311 ASN A 269 ASN A 322 HIS B 259 GLN E 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.161189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122638 restraints weight = 10837.407| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.91 r_work: 0.3030 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9079 Z= 0.235 Angle : 0.674 8.529 12294 Z= 0.360 Chirality : 0.045 0.151 1405 Planarity : 0.005 0.043 1558 Dihedral : 4.424 24.211 1239 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.20 % Allowed : 9.18 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.24), residues: 1127 helix: 3.01 (0.23), residues: 394 sheet: 0.04 (0.30), residues: 283 loop : -1.25 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.025 0.003 TYR B 85 PHE 0.020 0.002 PHE P 1 TRP 0.023 0.002 TRP B 82 HIS 0.007 0.002 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 9076) covalent geometry : angle 0.67315 (12288) SS BOND : bond 0.00619 ( 3) SS BOND : angle 1.69611 ( 6) hydrogen bonds : bond 0.06042 ( 447) hydrogen bonds : angle 4.73966 ( 1314) *********************** 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 206 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 188 HIS cc_start: 0.7447 (p-80) cc_final: 0.7210 (t-90) REVERT: A 190 THR cc_start: 0.9006 (m) cc_final: 0.8625 (t) REVERT: A 313 ARG cc_start: 0.6853 (ttm110) cc_final: 0.6598 (ttt180) REVERT: B 136 SER cc_start: 0.8982 (t) cc_final: 0.8661 (p) REVERT: B 175 GLN cc_start: 0.8443 (mt0) cc_final: 0.8165 (mm110) REVERT: C 46 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7581 (tptp) REVERT: E 219 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7547 (ttp-110) outliers start: 31 outliers final: 17 residues processed: 196 average time/residue: 0.0927 time to fit residues: 24.2338 Evaluate side-chains 156 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 6 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 14 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.171299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134199 restraints weight = 10548.788| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.30 r_work: 0.3176 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9079 Z= 0.140 Angle : 0.567 8.000 12294 Z= 0.298 Chirality : 0.041 0.133 1405 Planarity : 0.004 0.040 1558 Dihedral : 4.148 22.655 1239 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.47 % Allowed : 11.86 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1127 helix: 3.32 (0.24), residues: 396 sheet: 0.09 (0.30), residues: 277 loop : -1.05 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.017 0.002 TYR B 85 PHE 0.014 0.001 PHE P 1 TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS E 233 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9076) covalent geometry : angle 0.56454 (12288) SS BOND : bond 0.00828 ( 3) SS BOND : angle 2.42856 ( 6) hydrogen bonds : bond 0.04753 ( 447) hydrogen bonds : angle 4.26808 ( 1314) *********************** 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: 24 poor density : 147 time to evaluate : 0.356 Fit side-chains REVERT: A 190 THR cc_start: 0.9032 (m) cc_final: 0.8731 (t) REVERT: B 175 GLN cc_start: 0.8432 (mt0) cc_final: 0.8158 (mm110) REVERT: B 205 ASP cc_start: 0.7349 (t0) cc_final: 0.7145 (t0) REVERT: E 219 ARG cc_start: 0.8111 (ttp-110) cc_final: 0.7573 (ttp-110) outliers start: 24 outliers final: 21 residues processed: 163 average time/residue: 0.0886 time to fit residues: 19.3149 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 : 0.231 ------------------------------------------------------------------------------- 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 247 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 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 198 SER 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 9 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.163316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125267 restraints weight = 10998.196| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.77 r_work: 0.3152 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9079 Z= 0.116 Angle : 0.532 13.089 12294 Z= 0.275 Chirality : 0.040 0.129 1405 Planarity : 0.004 0.040 1558 Dihedral : 3.923 21.396 1239 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.71 % Allowed : 11.96 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.25), residues: 1127 helix: 3.51 (0.24), residues: 394 sheet: 0.09 (0.29), residues: 286 loop : -0.96 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.015 0.001 TYR B 85 PHE 0.012 0.001 PHE P 1 TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9076) covalent geometry : angle 0.53108 (12288) SS BOND : bond 0.00493 ( 3) SS BOND : angle 1.38898 ( 6) hydrogen bonds : bond 0.04201 ( 447) hydrogen bonds : angle 3.97542 ( 1314) *********************** 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 180 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9078 (m) cc_final: 0.8761 (t) REVERT: B 175 GLN cc_start: 0.8266 (mt0) cc_final: 0.7983 (mm110) REVERT: B 205 ASP cc_start: 0.7127 (t0) cc_final: 0.6921 (t0) REVERT: B 219 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7780 (ttm-80) REVERT: E 45 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7858 (mt) REVERT: E 219 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7511 (ttp-110) outliers start: 36 outliers final: 23 residues processed: 169 average time/residue: 0.0950 time to fit residues: 21.6957 Evaluate side-chains 156 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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 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 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 198 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.158933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120991 restraints weight = 11004.283| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.71 r_work: 0.3048 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9079 Z= 0.157 Angle : 0.569 10.953 12294 Z= 0.294 Chirality : 0.041 0.138 1405 Planarity : 0.004 0.039 1558 Dihedral : 4.066 22.990 1239 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.23 % Allowed : 13.20 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.25), residues: 1127 helix: 3.20 (0.24), residues: 401 sheet: 0.04 (0.29), residues: 294 loop : -1.01 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.020 0.002 TYR B 59 PHE 0.015 0.002 PHE E 108 TRP 0.020 0.002 TRP B 82 HIS 0.008 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9076) covalent geometry : angle 0.56861 (12288) SS BOND : bond 0.00606 ( 3) SS BOND : angle 1.52934 ( 6) hydrogen bonds : bond 0.04874 ( 447) hydrogen bonds : angle 4.10587 ( 1314) *********************** 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 190 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.351 Fit side-chains REVERT: R 177 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 190 THR cc_start: 0.9180 (m) cc_final: 0.8915 (t) REVERT: A 327 THR cc_start: 0.7243 (m) cc_final: 0.6945 (p) REVERT: B 205 ASP cc_start: 0.7286 (t0) cc_final: 0.7054 (t0) REVERT: B 219 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7908 (ttm-80) REVERT: E 45 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7920 (mt) REVERT: E 219 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7569 (ttp-110) outliers start: 41 outliers final: 30 residues processed: 176 average time/residue: 0.1129 time to fit residues: 26.5818 Evaluate side-chains 167 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 266 LEU 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 86 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 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 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 83 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122724 restraints weight = 10998.228| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.66 r_work: 0.3021 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9079 Z= 0.232 Angle : 0.654 10.714 12294 Z= 0.340 Chirality : 0.044 0.144 1405 Planarity : 0.005 0.043 1558 Dihedral : 4.486 25.945 1239 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.33 % Allowed : 14.12 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.24), residues: 1127 helix: 2.77 (0.24), residues: 400 sheet: -0.04 (0.28), residues: 294 loop : -1.16 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.023 0.002 TYR B 85 PHE 0.018 0.002 PHE E 240 TRP 0.018 0.002 TRP B 82 HIS 0.007 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 9076) covalent geometry : angle 0.65236 (12288) SS BOND : bond 0.00838 ( 3) SS BOND : angle 2.11083 ( 6) hydrogen bonds : bond 0.05932 ( 447) hydrogen bonds : angle 4.45299 ( 1314) *********************** 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 182 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.214 Fit side-chains REVERT: R 66 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7949 (mt) REVERT: R 232 SER cc_start: 0.8932 (m) cc_final: 0.8602 (p) REVERT: A 190 THR cc_start: 0.9226 (m) cc_final: 0.8974 (t) REVERT: B 129 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7744 (mtp180) REVERT: B 219 ARG cc_start: 0.8381 (mmm160) cc_final: 0.7791 (mtp180) REVERT: B 226 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 46 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7542 (tptp) REVERT: E 45 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7817 (mt) REVERT: E 219 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7527 (ttp-110) outliers start: 42 outliers final: 30 residues processed: 167 average time/residue: 0.1230 time to fit residues: 26.9006 Evaluate side-chains 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 271 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 143 THR 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 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 79 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 104 optimal weight: 0.0370 chunk 53 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.161618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123786 restraints weight = 11078.823| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.70 r_work: 0.3120 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9079 Z= 0.107 Angle : 0.530 10.840 12294 Z= 0.275 Chirality : 0.040 0.158 1405 Planarity : 0.004 0.038 1558 Dihedral : 3.994 22.939 1239 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 15.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.25), residues: 1127 helix: 3.19 (0.25), residues: 399 sheet: 0.09 (0.29), residues: 267 loop : -1.06 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.013 0.001 TYR E 191 PHE 0.010 0.001 PHE P 1 TRP 0.022 0.001 TRP B 82 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9076) covalent geometry : angle 0.52951 (12288) SS BOND : bond 0.00568 ( 3) SS BOND : angle 1.02638 ( 6) hydrogen bonds : bond 0.03897 ( 447) hydrogen bonds : angle 3.98029 ( 1314) *********************** 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 177 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.351 Fit side-chains REVERT: R 232 SER cc_start: 0.8707 (m) cc_final: 0.8433 (p) REVERT: R 326 PHE cc_start: 0.7945 (t80) cc_final: 0.7729 (t80) REVERT: A 190 THR cc_start: 0.9182 (m) cc_final: 0.8955 (t) REVERT: A 327 THR cc_start: 0.7280 (m) cc_final: 0.7035 (p) REVERT: A 349 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8023 (mtpp) REVERT: B 219 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7792 (ttm-80) REVERT: B 325 MET cc_start: 0.8689 (tpp) cc_final: 0.8303 (mmt) REVERT: E 45 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7825 (mt) outliers start: 26 outliers final: 21 residues processed: 168 average time/residue: 0.1237 time to fit residues: 27.1793 Evaluate side-chains 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 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 143 THR Chi-restraints excluded: chain B residue 176 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 GLN A 52 GLN A 269 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121543 restraints weight = 11040.127| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.64 r_work: 0.3083 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9079 Z= 0.126 Angle : 0.554 11.214 12294 Z= 0.285 Chirality : 0.041 0.142 1405 Planarity : 0.004 0.051 1558 Dihedral : 3.998 22.532 1239 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.09 % Allowed : 15.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1127 helix: 3.19 (0.25), residues: 399 sheet: 0.03 (0.29), residues: 271 loop : -0.99 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.015 0.001 TYR B 85 PHE 0.012 0.001 PHE B 241 TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9076) covalent geometry : angle 0.55338 (12288) SS BOND : bond 0.00563 ( 3) SS BOND : angle 1.13885 ( 6) hydrogen bonds : bond 0.04214 ( 447) hydrogen bonds : angle 3.98778 ( 1314) *********************** 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 169 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.358 Fit side-chains REVERT: R 232 SER cc_start: 0.8757 (m) cc_final: 0.8421 (p) REVERT: A 190 THR cc_start: 0.9164 (m) cc_final: 0.8938 (t) REVERT: A 240 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5565 (mmt) REVERT: A 327 THR cc_start: 0.7290 (m) cc_final: 0.7034 (p) REVERT: A 349 LYS cc_start: 0.8457 (mtpt) cc_final: 0.7989 (mtpp) REVERT: B 42 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7790 (ttp80) REVERT: B 219 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7755 (ttm-80) REVERT: E 45 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7703 (mt) outliers start: 30 outliers final: 27 residues processed: 158 average time/residue: 0.1244 time to fit residues: 25.7216 Evaluate side-chains 165 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 A residue 240 MET 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 318 LEU Chi-restraints excluded: chain B residue 327 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125194 restraints weight = 10991.722| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.74 r_work: 0.3017 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9079 Z= 0.144 Angle : 0.569 10.877 12294 Z= 0.292 Chirality : 0.041 0.136 1405 Planarity : 0.004 0.059 1558 Dihedral : 4.068 22.368 1239 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.30 % Allowed : 15.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.25), residues: 1127 helix: 3.07 (0.25), residues: 400 sheet: -0.02 (0.29), residues: 283 loop : -0.96 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 134 TYR 0.017 0.002 TYR B 85 PHE 0.011 0.001 PHE B 241 TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9076) covalent geometry : angle 0.56822 (12288) SS BOND : bond 0.00605 ( 3) SS BOND : angle 1.27116 ( 6) hydrogen bonds : bond 0.04544 ( 447) hydrogen bonds : angle 4.02386 ( 1314) *********************** 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: 32 poor density : 134 time to evaluate : 0.350 Fit side-chains REVERT: R 66 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7907 (mt) REVERT: R 177 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7715 (tt) REVERT: R 232 SER cc_start: 0.8780 (m) cc_final: 0.8431 (p) REVERT: A 190 THR cc_start: 0.9179 (m) cc_final: 0.8945 (t) REVERT: A 240 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.5545 (mmt) REVERT: A 313 ARG cc_start: 0.7855 (ttt90) cc_final: 0.7537 (ttt90) REVERT: A 318 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: B 219 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7776 (ttm-80) REVERT: E 45 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7703 (mt) outliers start: 32 outliers final: 27 residues processed: 154 average time/residue: 0.1257 time to fit residues: 25.3021 Evaluate side-chains 165 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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 209 LYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 318 GLU 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 294 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 21 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 119 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.159678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121780 restraints weight = 11008.770| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.61 r_work: 0.3069 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9079 Z= 0.122 Angle : 0.552 11.568 12294 Z= 0.284 Chirality : 0.041 0.137 1405 Planarity : 0.004 0.058 1558 Dihedral : 3.985 21.774 1239 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.20 % Allowed : 15.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1127 helix: 3.14 (0.25), residues: 400 sheet: 0.11 (0.29), residues: 269 loop : -0.94 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.015 0.001 TYR B 85 PHE 0.011 0.001 PHE B 241 TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9076) covalent geometry : angle 0.55183 (12288) SS BOND : bond 0.00560 ( 3) SS BOND : angle 1.11083 ( 6) hydrogen bonds : bond 0.04196 ( 447) hydrogen bonds : angle 3.95773 ( 1314) ********************** 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: 31 poor density : 133 time to evaluate : 0.340 Fit side-chains REVERT: R 66 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7899 (mt) REVERT: R 232 SER cc_start: 0.8749 (m) cc_final: 0.8411 (p) REVERT: A 190 THR cc_start: 0.9170 (m) cc_final: 0.8950 (t) REVERT: A 240 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5428 (tpt) REVERT: A 313 ARG cc_start: 0.7725 (ttt90) cc_final: 0.7408 (ttt90) REVERT: A 318 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: B 42 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7737 (ttp80) REVERT: B 219 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7739 (ttm-80) REVERT: B 325 MET cc_start: 0.8674 (tpp) cc_final: 0.8443 (mmt) REVERT: E 45 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7699 (mt) outliers start: 31 outliers final: 26 residues processed: 153 average time/residue: 0.1268 time to fit residues: 25.2745 Evaluate side-chains 163 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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 209 LYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 318 GLU 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 318 LEU Chi-restraints excluded: chain B residue 327 VAL 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 119 VAL 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 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 0.0470 chunk 100 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.162164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124545 restraints weight = 10864.510| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.45 r_work: 0.3105 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9079 Z= 0.103 Angle : 0.527 10.759 12294 Z= 0.271 Chirality : 0.040 0.140 1405 Planarity : 0.004 0.058 1558 Dihedral : 3.799 20.576 1239 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.99 % Allowed : 15.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.25), residues: 1127 helix: 3.23 (0.25), residues: 401 sheet: 0.12 (0.29), residues: 269 loop : -0.88 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.013 0.001 TYR E 191 PHE 0.010 0.001 PHE A 189 TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9076) covalent geometry : angle 0.52656 (12288) SS BOND : bond 0.00496 ( 3) SS BOND : angle 0.86962 ( 6) hydrogen bonds : bond 0.03655 ( 447) hydrogen bonds : angle 3.81963 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.02 seconds wall clock time: 39 minutes 58.26 seconds (2398.26 seconds total)