Starting phenix.real_space_refine on Sat Dec 28 16:04:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7x_28912/12_2024/8f7x_28912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7x_28912/12_2024/8f7x_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_28912/12_2024/8f7x_28912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7x_28912/12_2024/8f7x_28912.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7x_28912/12_2024/8f7x_28912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7x_28912/12_2024/8f7x_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-5532/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: 5.78, per 1000 atoms: 0.65 Number of scatterers: 8902 At special positions: 0 Unit cell: (100.8, 111.72, 134.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1666 8.00 N 1519 7.00 C 5653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 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: 2.29 Time building geometry restraints manager: 2.91 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: 0.950 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.470 Find NCS groups from input model: 0.110 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9076 Z= 0.275 Angle : 0.876 7.834 12288 Z= 0.514 Chirality : 0.053 0.281 1405 Planarity : 0.006 0.052 1558 Dihedral : 8.644 70.556 3264 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.10 % Allowed : 1.65 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1127 helix: 2.33 (0.22), residues: 397 sheet: 0.05 (0.31), residues: 278 loop : -1.27 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.033 0.003 PHE A 354 TYR 0.024 0.002 TYR R 132 ARG 0.013 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.967 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: 0.2412 time to fit residues: 79.5425 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 : 0.965 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 1.078 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8932 (m) cc_final: 0.8525 (t) REVERT: C 46 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7648 (tptp) REVERT: E 219 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7533 (ttp-110) outliers start: 29 outliers final: 17 residues processed: 195 average time/residue: 0.2501 time to fit residues: 64.6458 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 259 GLN E 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9076 Z= 0.397 Angle : 0.682 8.145 12288 Z= 0.359 Chirality : 0.046 0.147 1405 Planarity : 0.005 0.047 1558 Dihedral : 4.626 27.214 1239 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.71 % Allowed : 11.24 % Favored : 85.05 % 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: 0.70 (0.24), residues: 1127 helix: 2.64 (0.24), residues: 400 sheet: 0.07 (0.29), residues: 283 loop : -1.35 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.006 0.002 HIS A 322 PHE 0.031 0.002 PHE E 108 TYR 0.027 0.003 TYR B 85 ARG 0.006 0.001 ARG B 314 *********************** 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 184 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.9025 (m) cc_final: 0.8755 (t) REVERT: B 226 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8142 (mm-30) REVERT: C 46 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7621 (tptp) REVERT: E 219 ARG cc_start: 0.8086 (ttp-110) cc_final: 0.7537 (ttp-110) outliers start: 36 outliers final: 22 residues processed: 175 average time/residue: 0.2586 time to fit residues: 59.7404 Evaluate side-chains 150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 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 271 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain 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 233 CYS Chi-restraints excluded: chain B residue 275 SER 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 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 76 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 50.0000 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 ASN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9076 Z= 0.174 Angle : 0.528 7.498 12288 Z= 0.280 Chirality : 0.040 0.130 1405 Planarity : 0.004 0.039 1558 Dihedral : 4.110 24.867 1239 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.78 % Allowed : 13.20 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1127 helix: 3.11 (0.25), residues: 400 sheet: 0.09 (0.29), residues: 276 loop : -1.10 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.014 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 170 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: R 66 LEU cc_start: 0.8130 (mt) cc_final: 0.7874 (mt) REVERT: R 232 SER cc_start: 0.8489 (m) cc_final: 0.8215 (p) REVERT: A 190 THR cc_start: 0.9080 (m) cc_final: 0.8801 (t) REVERT: E 45 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7831 (mt) REVERT: E 219 ARG cc_start: 0.8030 (ttp-110) cc_final: 0.7528 (ttp-110) outliers start: 27 outliers final: 15 residues processed: 162 average time/residue: 0.2558 time to fit residues: 55.2838 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 317 ILE Chi-restraints excluded: chain R residue 329 CYS 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 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 318 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9076 Z= 0.170 Angle : 0.520 7.889 12288 Z= 0.272 Chirality : 0.040 0.131 1405 Planarity : 0.004 0.038 1558 Dihedral : 3.941 23.341 1239 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.09 % Allowed : 14.54 % Favored : 82.37 % 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: 3.21 (0.24), residues: 399 sheet: 0.17 (0.29), residues: 275 loop : -1.03 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.011 0.001 PHE B 241 TYR 0.014 0.001 TYR B 85 ARG 0.009 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 179 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 LEU cc_start: 0.8157 (mt) cc_final: 0.7876 (mt) REVERT: R 73 MET cc_start: 0.8387 (tpp) cc_final: 0.8146 (mtp) REVERT: R 232 SER cc_start: 0.8481 (m) cc_final: 0.8220 (p) REVERT: A 190 THR cc_start: 0.9080 (m) cc_final: 0.8819 (t) REVERT: B 42 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7772 (ttp80) REVERT: B 219 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7374 (ttm-80) REVERT: E 219 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7539 (ttp-110) outliers start: 30 outliers final: 24 residues processed: 172 average time/residue: 0.2521 time to fit residues: 57.2208 Evaluate side-chains 161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 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 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 184 THR 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 234 PHE 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 57 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 198 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9076 Z= 0.157 Angle : 0.516 11.217 12288 Z= 0.267 Chirality : 0.040 0.136 1405 Planarity : 0.003 0.038 1558 Dihedral : 3.863 22.122 1239 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.78 % Allowed : 15.88 % 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: 1.31 (0.25), residues: 1127 helix: 3.27 (0.25), residues: 401 sheet: 0.19 (0.29), residues: 274 loop : -0.97 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR B 85 ARG 0.009 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 174 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: R 66 LEU cc_start: 0.8118 (mt) cc_final: 0.7831 (mt) REVERT: R 232 SER cc_start: 0.8472 (m) cc_final: 0.8215 (p) REVERT: A 190 THR cc_start: 0.9079 (m) cc_final: 0.8860 (t) REVERT: B 219 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7373 (ttm-80) REVERT: B 325 MET cc_start: 0.8212 (tpp) cc_final: 0.7795 (mmt) outliers start: 27 outliers final: 21 residues processed: 167 average time/residue: 0.2652 time to fit residues: 58.4185 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 : 1.030 ------------------------------------------------------------------------------- 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 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 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE 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 E residue 21 SER Chi-restraints excluded: chain E residue 202 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4758 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= 0.173 Angle : 0.520 10.113 12288 Z= 0.269 Chirality : 0.040 0.164 1405 Planarity : 0.004 0.042 1558 Dihedral : 3.842 21.204 1239 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.89 % Allowed : 15.67 % 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: 1.35 (0.25), residues: 1127 helix: 3.29 (0.25), residues: 402 sheet: 0.17 (0.29), residues: 271 loop : -0.91 (0.27), residues: 454 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 A 189 TYR 0.013 0.001 TYR B 85 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: R 66 LEU cc_start: 0.8126 (mt) cc_final: 0.7824 (mt) REVERT: R 232 SER cc_start: 0.8481 (m) cc_final: 0.8224 (p) REVERT: A 190 THR cc_start: 0.9088 (m) cc_final: 0.8876 (t) REVERT: A 240 MET cc_start: 0.5631 (OUTLIER) cc_final: 0.5366 (mmt) REVERT: B 219 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7392 (ttm-80) outliers start: 28 outliers final: 26 residues processed: 160 average time/residue: 0.2593 time to fit residues: 55.0788 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 : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 209 LYS 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 98 SER Chi-restraints excluded: chain B residue 135 VAL 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 234 PHE 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 57 SER Chi-restraints excluded: chain E residue 21 SER 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 64 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9076 Z= 0.269 Angle : 0.586 14.032 12288 Z= 0.302 Chirality : 0.042 0.148 1405 Planarity : 0.004 0.043 1558 Dihedral : 4.111 23.178 1239 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.81 % Allowed : 14.95 % 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: 1.12 (0.25), residues: 1127 helix: 3.07 (0.25), residues: 400 sheet: 0.06 (0.28), residues: 289 loop : -1.03 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.012 0.001 PHE A 189 TYR 0.021 0.002 TYR B 85 ARG 0.010 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 171 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: R 66 LEU cc_start: 0.8069 (mt) cc_final: 0.7739 (mt) REVERT: R 232 SER cc_start: 0.8507 (m) cc_final: 0.8243 (p) REVERT: A 190 THR cc_start: 0.9112 (m) cc_final: 0.8884 (t) REVERT: A 240 MET cc_start: 0.5665 (OUTLIER) cc_final: 0.5435 (mmt) REVERT: B 219 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7430 (ttm-80) outliers start: 37 outliers final: 28 residues processed: 157 average time/residue: 0.2537 time to fit residues: 53.4161 Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 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 240 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9076 Z= 0.176 Angle : 0.531 10.193 12288 Z= 0.275 Chirality : 0.040 0.137 1405 Planarity : 0.004 0.059 1558 Dihedral : 3.935 22.023 1239 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.78 % Allowed : 16.08 % 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: 1.27 (0.25), residues: 1127 helix: 3.19 (0.25), residues: 400 sheet: 0.19 (0.29), residues: 275 loop : -0.95 (0.28), residues: 452 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 0.011 0.001 PHE B 241 TYR 0.014 0.001 TYR B 85 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 161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: R 66 LEU cc_start: 0.8043 (mt) cc_final: 0.7740 (mt) REVERT: R 232 SER cc_start: 0.8483 (m) cc_final: 0.8223 (p) REVERT: A 190 THR cc_start: 0.9082 (m) cc_final: 0.8868 (t) REVERT: A 240 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5664 (mmt) REVERT: A 349 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7888 (mtpp) REVERT: B 219 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7401 (ttm-80) REVERT: E 113 GLN cc_start: 0.7559 (mm110) cc_final: 0.7066 (mt0) outliers start: 27 outliers final: 24 residues processed: 153 average time/residue: 0.2530 time to fit residues: 51.7254 Evaluate side-chains 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 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 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 184 THR 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 234 PHE 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 198 SER Chi-restraints excluded: chain E residue 202 ASP 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 64 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.0980 chunk 88 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 0.0970 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9076 Z= 0.140 Angle : 0.504 11.885 12288 Z= 0.259 Chirality : 0.039 0.143 1405 Planarity : 0.004 0.057 1558 Dihedral : 3.704 20.135 1239 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.37 % Allowed : 16.91 % Favored : 80.72 % 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: 1.40 (0.25), residues: 1127 helix: 3.25 (0.25), residues: 401 sheet: 0.25 (0.30), residues: 272 loop : -0.82 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.010 0.001 PHE B 241 TYR 0.012 0.001 TYR R 132 ARG 0.014 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 170 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.047 Fit side-chains REVERT: R 66 LEU cc_start: 0.8118 (mt) cc_final: 0.7813 (mt) REVERT: R 232 SER cc_start: 0.8424 (m) cc_final: 0.8190 (p) REVERT: A 240 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5606 (tpt) REVERT: A 349 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7799 (mtpp) REVERT: B 219 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7396 (ttm-80) outliers start: 23 outliers final: 19 residues processed: 162 average time/residue: 0.2498 time to fit residues: 54.7737 Evaluate side-chains 158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134911 restraints weight = 10664.614| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.34 r_work: 0.3157 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 9076 Z= 0.275 Angle : 0.869 59.190 12288 Z= 0.502 Chirality : 0.042 0.536 1405 Planarity : 0.004 0.054 1558 Dihedral : 3.725 20.101 1239 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.58 % Allowed : 17.11 % Favored : 80.31 % Cbeta Deviations : 0.09 % 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: 1.41 (0.25), residues: 1127 helix: 3.24 (0.25), residues: 401 sheet: 0.27 (0.30), residues: 272 loop : -0.81 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.010 0.001 PHE R 91 TYR 0.012 0.001 TYR R 132 ARG 0.012 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.31 seconds wall clock time: 41 minutes 4.09 seconds (2464.09 seconds total)