Starting phenix.real_space_refine on Thu Jul 2 16:43:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24xz_69905/07_2026/24xz_69905.cif Found real_map, /net/cci-nas-00/data/ceres_data/24xz_69905/07_2026/24xz_69905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24xz_69905/07_2026/24xz_69905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24xz_69905/07_2026/24xz_69905.map" model { file = "/net/cci-nas-00/data/ceres_data/24xz_69905/07_2026/24xz_69905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24xz_69905/07_2026/24xz_69905.cif" } resolution = 2.93 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= 1.174 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 61 5.16 5 C 5758 2.51 5 N 1506 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9002 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2405 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "A" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1799 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.60, per 1000 atoms: 0.18 Number of scatterers: 9002 At special positions: 0 Unit cell: (88.5333, 123.783, 127.062, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 2 15.00 O 1675 8.00 N 1506 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 172 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 0.52 Conformation dependent library (CDL) restraints added in 367.3 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 37.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.667A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.980A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.713A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.602A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 23 Processing helix chain 'R' and resid 23 through 49 removed outlier: 3.939A pdb=" N VAL R 27 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR R 49 " --> pdb=" O TRP R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 83 removed outlier: 3.688A pdb=" N ILE R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Proline residue: R 75 - end of helix removed outlier: 3.658A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 96 removed outlier: 3.530A pdb=" N VAL R 91 " --> pdb=" O TRP R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 124 Processing helix chain 'R' and resid 137 through 159 Proline residue: R 155 - end of helix Processing helix chain 'R' and resid 177 through 214 removed outlier: 3.663A pdb=" N LYS R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU R 200 " --> pdb=" O TRP R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 247 removed outlier: 3.657A pdb=" N VAL R 247 " --> pdb=" O PHE R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 262 Processing helix chain 'R' and resid 266 through 286 Processing helix chain 'R' and resid 286 through 295 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 309 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.534A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 4.729A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.599A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.253A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.905A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.775A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.661A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.817A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.627A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.716A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.025A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.843A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.684A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.683A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.998A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.550A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.713A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.401A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 129 through 130 removed outlier: 3.526A pdb=" N THR S 129 " --> pdb=" O ARG S 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS S 147 " --> pdb=" O PHE S 200 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.982A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1245 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: 1.23 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2489 1.34 - 1.46: 2375 1.46 - 1.59: 4242 1.59 - 1.71: 3 1.71 - 1.84: 88 Bond restraints: 9197 Sorted by residual: bond pdb=" N VAL R 50 " pdb=" CA VAL R 50 " ideal model delta sigma weight residual 1.460 1.495 -0.035 9.30e-03 1.16e+04 1.39e+01 bond pdb=" N VAL A 201 " pdb=" CA VAL A 201 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.04e-02 9.25e+03 1.31e+01 bond pdb=" N PHE R 74 " pdb=" CA PHE R 74 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.29e+01 bond pdb=" O3A UDP R 801 " pdb=" PB UDP R 801 " ideal model delta sigma weight residual 1.584 1.617 -0.033 1.00e-02 1.00e+04 1.08e+01 bond pdb=" N VAL R 124 " pdb=" CA VAL R 124 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 ... (remaining 9192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 11954 2.75 - 5.49: 409 5.49 - 8.24: 63 8.24 - 10.98: 16 10.98 - 13.73: 5 Bond angle restraints: 12447 Sorted by residual: angle pdb=" O3A UDP R 801 " pdb=" PB UDP R 801 " pdb=" O3B UDP R 801 " ideal model delta sigma weight residual 112.01 104.56 7.45 1.00e+00 1.00e+00 5.55e+01 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 113.18 107.18 6.00 1.21e+00 6.83e-01 2.46e+01 angle pdb=" C ALA A 338 " pdb=" N VAL A 339 " pdb=" CA VAL A 339 " ideal model delta sigma weight residual 121.55 114.52 7.03 1.42e+00 4.96e-01 2.45e+01 angle pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 112.60 117.50 -4.90 1.00e+00 1.00e+00 2.40e+01 angle pdb=" C PRO S 41 " pdb=" N GLU S 42 " pdb=" CA GLU S 42 " ideal model delta sigma weight residual 122.46 129.20 -6.74 1.41e+00 5.03e-01 2.29e+01 ... (remaining 12442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4989 17.12 - 34.24: 413 34.24 - 51.35: 61 51.35 - 68.47: 13 68.47 - 85.59: 9 Dihedral angle restraints: 5485 sinusoidal: 2175 harmonic: 3310 Sorted by residual: dihedral pdb=" CB CYS R 94 " pdb=" SG CYS R 94 " pdb=" SG CYS R 172 " pdb=" CB CYS R 172 " ideal model delta sinusoidal sigma weight residual -86.00 -163.10 77.10 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 160.30 -67.30 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 144.53 -51.53 1 1.00e+01 1.00e-02 3.63e+01 ... (remaining 5482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1271 0.112 - 0.224: 125 0.224 - 0.336: 8 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CB VAL R 154 " pdb=" CA VAL R 154 " pdb=" CG1 VAL R 154 " pdb=" CG2 VAL R 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CB VAL A 342 " pdb=" CA VAL A 342 " pdb=" CG1 VAL A 342 " pdb=" CG2 VAL A 342 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL R 143 " pdb=" CA VAL R 143 " pdb=" CG1 VAL R 143 " pdb=" CG2 VAL R 143 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1402 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C THR A 340 " 0.069 2.00e-02 2.50e+03 pdb=" O THR A 340 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP A 341 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 337 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASP A 337 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP A 337 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 338 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 87 " 0.013 2.00e-02 2.50e+03 1.99e-02 9.92e+00 pdb=" CG TRP R 87 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP R 87 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP R 87 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 87 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 87 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 87 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 87 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 87 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 87 " -0.001 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2704 2.84 - 3.35: 7318 3.35 - 3.87: 14686 3.87 - 4.38: 16446 4.38 - 4.90: 28922 Nonbonded interactions: 70076 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.321 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.355 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.357 3.040 nonbonded pdb=" O ILE R 203 " pdb=" OG1 THR R 207 " model vdw 2.376 3.040 nonbonded pdb=" O VAL S 127 " pdb=" OG SER S 150 " model vdw 2.385 3.040 ... (remaining 70071 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: 2.390 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.006 0.084 9201 Z= 0.353 Angle : 1.194 13.725 12455 Z= 0.676 Chirality : 0.067 0.560 1405 Planarity : 0.009 0.121 1558 Dihedral : 13.068 85.591 3337 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.10 % Allowed : 0.50 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.22), residues: 1123 helix: -2.56 (0.18), residues: 371 sheet: -0.04 (0.32), residues: 274 loop : -1.84 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 197 TYR 0.029 0.003 TYR S 216 PHE 0.049 0.003 PHE R 56 TRP 0.052 0.002 TRP R 87 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.35 ( 9197) covalent geometry : angle 1.19411 / 0.68 (12447) SS BOND : bond 0.00734 / 0.38 ( 4) SS BOND : angle 1.49238 / 0.70 ( 8) hydrogen bonds : bond 0.15067 / 10.23 ( 436) hydrogen bonds : angle 7.39351 / 5.12 ( 1245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7683 (mmm-85) REVERT: B 44 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7584 (tp-100) REVERT: B 129 ARG cc_start: 0.8442 (ttp-170) cc_final: 0.8113 (ttm170) REVERT: B 188 MET cc_start: 0.8685 (mmm) cc_final: 0.8335 (mmm) REVERT: B 214 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.8263 (mtm-85) REVERT: B 247 ASP cc_start: 0.7083 (t0) cc_final: 0.6500 (t0) REVERT: B 289 TYR cc_start: 0.7697 (m-80) cc_final: 0.7463 (m-80) REVERT: B 303 ASP cc_start: 0.7164 (m-30) cc_final: 0.6764 (m-30) REVERT: R 79 LEU cc_start: 0.9320 (tt) cc_final: 0.9041 (tt) REVERT: R 167 VAL cc_start: 0.8987 (m) cc_final: 0.8622 (t) REVERT: A 193 ASP cc_start: 0.8948 (m-30) cc_final: 0.8580 (m-30) REVERT: A 240 MET cc_start: 0.7587 (ptt) cc_final: 0.7014 (pp-130) REVERT: A 248 LYS cc_start: 0.8696 (pttt) cc_final: 0.8355 (ptmt) REVERT: A 333 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7420 (tm-30) REVERT: S 134 SER cc_start: 0.8561 (p) cc_final: 0.8332 (t) REVERT: S 162 LEU cc_start: 0.7608 (tt) cc_final: 0.7344 (tp) REVERT: S 206 ARG cc_start: 0.8571 (mtm110) cc_final: 0.8282 (mtm110) REVERT: S 211 ASP cc_start: 0.9022 (m-30) cc_final: 0.8596 (m-30) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.4209 time to fit residues: 131.6252 Evaluate side-chains 225 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 ASN B 340 ASN R 62 ASN R 162 GLN R 184 HIS S 82 GLN S 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.153063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116152 restraints weight = 12561.289| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.27 r_work: 0.3279 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9201 Z= 0.158 Angle : 0.632 7.680 12455 Z= 0.336 Chirality : 0.044 0.234 1405 Planarity : 0.005 0.048 1558 Dihedral : 5.910 84.687 1259 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.53 % Allowed : 13.82 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1123 helix: 0.27 (0.25), residues: 381 sheet: 0.22 (0.32), residues: 273 loop : -1.42 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.023 0.002 TYR R 106 PHE 0.021 0.002 PHE R 56 TRP 0.013 0.001 TRP R 87 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9197) covalent geometry : angle 0.63156 / 0.34 (12447) SS BOND : bond 0.00481 / 0.25 ( 4) SS BOND : angle 1.29550 / 0.81 ( 8) hydrogen bonds : bond 0.04929 / 3.29 ( 436) hydrogen bonds : angle 4.86474 / 3.40 ( 1245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8053 (mmm-85) REVERT: B 44 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7677 (tp-100) REVERT: B 129 ARG cc_start: 0.8674 (ttp-170) cc_final: 0.8457 (ttp-170) REVERT: B 130 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 163 ASP cc_start: 0.7737 (t0) cc_final: 0.7400 (t0) REVERT: B 188 MET cc_start: 0.8716 (mmm) cc_final: 0.8468 (mmm) REVERT: B 214 ARG cc_start: 0.8726 (mtt-85) cc_final: 0.8395 (mtt-85) REVERT: B 247 ASP cc_start: 0.7672 (t0) cc_final: 0.7257 (t0) REVERT: B 262 MET cc_start: 0.5419 (mmm) cc_final: 0.5131 (mmm) REVERT: B 289 TYR cc_start: 0.8116 (m-80) cc_final: 0.7914 (m-80) REVERT: B 303 ASP cc_start: 0.6978 (m-30) cc_final: 0.6572 (m-30) REVERT: R 166 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7665 (tm-30) REVERT: R 167 VAL cc_start: 0.8921 (m) cc_final: 0.8527 (t) REVERT: R 230 LYS cc_start: 0.8505 (mtpp) cc_final: 0.8266 (mtpp) REVERT: R 232 SER cc_start: 0.8004 (m) cc_final: 0.7759 (p) REVERT: R 304 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8677 (mt-10) REVERT: A 193 ASP cc_start: 0.9026 (m-30) cc_final: 0.8757 (m-30) REVERT: A 297 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7191 (mp0) REVERT: A 337 ASP cc_start: 0.7601 (m-30) cc_final: 0.7093 (m-30) REVERT: A 340 THR cc_start: 0.9002 (m) cc_final: 0.8763 (p) REVERT: S 89 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7271 (tm-30) REVERT: S 151 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8046 (ptmt) REVERT: S 211 ASP cc_start: 0.8987 (m-30) cc_final: 0.8515 (m-30) outliers start: 35 outliers final: 20 residues processed: 286 average time/residue: 0.4209 time to fit residues: 130.1576 Evaluate side-chains 250 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 268 ASN R 22 GLN R 162 GLN R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 306 GLN S 39 GLN S 82 GLN S 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115111 restraints weight = 12558.128| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.26 r_work: 0.3262 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9201 Z= 0.139 Angle : 0.596 8.679 12455 Z= 0.314 Chirality : 0.043 0.173 1405 Planarity : 0.004 0.050 1558 Dihedral : 5.611 83.307 1259 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.13 % Allowed : 17.66 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1123 helix: 1.23 (0.27), residues: 383 sheet: 0.12 (0.32), residues: 277 loop : -1.19 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 46 TYR 0.017 0.001 TYR R 106 PHE 0.020 0.002 PHE R 56 TRP 0.009 0.001 TRP S 36 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9197) covalent geometry : angle 0.59567 / 0.31 (12447) SS BOND : bond 0.00721 / 0.37 ( 4) SS BOND : angle 1.26374 / 0.75 ( 8) hydrogen bonds : bond 0.04399 / 2.92 ( 436) hydrogen bonds : angle 4.55122 / 3.19 ( 1245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8011 (mmm-85) REVERT: B 44 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7715 (tp-100) REVERT: B 163 ASP cc_start: 0.7951 (t0) cc_final: 0.7608 (t0) REVERT: B 188 MET cc_start: 0.8741 (mmm) cc_final: 0.8526 (mmm) REVERT: B 214 ARG cc_start: 0.8700 (mtt-85) cc_final: 0.8297 (mtt90) REVERT: B 247 ASP cc_start: 0.7939 (t0) cc_final: 0.7437 (t0) REVERT: B 303 ASP cc_start: 0.6987 (m-30) cc_final: 0.6543 (m-30) REVERT: R 117 PHE cc_start: 0.8076 (t80) cc_final: 0.7870 (t80) REVERT: R 167 VAL cc_start: 0.8909 (m) cc_final: 0.8551 (t) REVERT: R 230 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8202 (mtpp) REVERT: R 304 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8629 (mt-10) REVERT: A 205 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8533 (mtp85) REVERT: A 245 GLU cc_start: 0.8120 (tp30) cc_final: 0.7656 (tp30) REVERT: A 248 LYS cc_start: 0.8011 (ptmt) cc_final: 0.7278 (pttp) REVERT: A 297 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7203 (mp0) REVERT: A 337 ASP cc_start: 0.7570 (m-30) cc_final: 0.7061 (m-30) REVERT: A 340 THR cc_start: 0.8968 (m) cc_final: 0.8735 (p) REVERT: S 89 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7284 (tm-30) REVERT: S 211 ASP cc_start: 0.8898 (m-30) cc_final: 0.8441 (m-30) outliers start: 31 outliers final: 17 residues processed: 257 average time/residue: 0.3768 time to fit residues: 104.9877 Evaluate side-chains 246 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 60 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 0.0770 chunk 62 optimal weight: 0.3980 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN R 162 GLN R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 306 GLN A 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119206 restraints weight = 12653.750| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.30 r_work: 0.3311 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9201 Z= 0.104 Angle : 0.562 8.053 12455 Z= 0.291 Chirality : 0.042 0.159 1405 Planarity : 0.004 0.045 1558 Dihedral : 5.401 85.476 1259 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 20.59 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1123 helix: 1.78 (0.27), residues: 384 sheet: 0.07 (0.32), residues: 280 loop : -1.03 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.011 0.001 TYR R 106 PHE 0.015 0.001 PHE R 56 TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9197) covalent geometry : angle 0.56176 / 0.29 (12447) SS BOND : bond 0.00668 / 0.35 ( 4) SS BOND : angle 0.79022 / 0.45 ( 8) hydrogen bonds : bond 0.03707 / 2.45 ( 436) hydrogen bonds : angle 4.26573 / 2.98 ( 1245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8118 (ptp-170) REVERT: B 44 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7703 (tp-100) REVERT: B 46 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7863 (ttp-110) REVERT: B 163 ASP cc_start: 0.7923 (t0) cc_final: 0.7585 (t0) REVERT: B 169 TRP cc_start: 0.8833 (m100) cc_final: 0.8548 (m100) REVERT: B 247 ASP cc_start: 0.8015 (t0) cc_final: 0.7519 (t0) REVERT: B 289 TYR cc_start: 0.8361 (m-80) cc_final: 0.7893 (m-80) REVERT: B 303 ASP cc_start: 0.7008 (m-30) cc_final: 0.6652 (m-30) REVERT: R 31 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6282 (mpt) REVERT: R 56 PHE cc_start: 0.7385 (t80) cc_final: 0.6896 (t80) REVERT: R 118 ASP cc_start: 0.8386 (t70) cc_final: 0.7996 (t0) REVERT: R 162 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7210 (mm-40) REVERT: R 166 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7508 (tm-30) REVERT: R 167 VAL cc_start: 0.8862 (m) cc_final: 0.8473 (t) REVERT: R 230 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8204 (mtpp) REVERT: A 240 MET cc_start: 0.7353 (ptm) cc_final: 0.6601 (pp-130) REVERT: A 245 GLU cc_start: 0.8125 (tp30) cc_final: 0.7753 (tp30) REVERT: A 248 LYS cc_start: 0.8003 (ptmt) cc_final: 0.7330 (mtmt) REVERT: A 297 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7145 (mp0) REVERT: A 337 ASP cc_start: 0.7490 (m-30) cc_final: 0.6979 (m-30) REVERT: S 89 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7414 (tm-30) REVERT: S 151 LYS cc_start: 0.8315 (ptmt) cc_final: 0.8012 (ptmm) REVERT: S 211 ASP cc_start: 0.8924 (m-30) cc_final: 0.8515 (m-30) outliers start: 25 outliers final: 10 residues processed: 257 average time/residue: 0.4024 time to fit residues: 111.6897 Evaluate side-chains 239 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 31 MET Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 GLN Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 67 optimal weight: 0.0060 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 62 ASN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 306 GLN A 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115176 restraints weight = 12681.471| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.28 r_work: 0.3266 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9201 Z= 0.132 Angle : 0.584 8.216 12455 Z= 0.303 Chirality : 0.043 0.164 1405 Planarity : 0.004 0.045 1558 Dihedral : 5.348 82.965 1259 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.14 % Allowed : 20.28 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1123 helix: 1.95 (0.27), residues: 383 sheet: 0.11 (0.32), residues: 280 loop : -0.96 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 313 TYR 0.023 0.001 TYR B 145 PHE 0.018 0.001 PHE R 56 TRP 0.010 0.001 TRP S 36 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9197) covalent geometry : angle 0.58319 / 0.30 (12447) SS BOND : bond 0.00357 / 0.18 ( 4) SS BOND : angle 0.96237 / 0.61 ( 8) hydrogen bonds : bond 0.04115 / 2.72 ( 436) hydrogen bonds : angle 4.30968 / 3.01 ( 1245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8344 (mpp80) REVERT: B 44 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7719 (tp-100) REVERT: B 46 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7773 (ttm110) REVERT: B 163 ASP cc_start: 0.7933 (t0) cc_final: 0.7622 (t0) REVERT: B 169 TRP cc_start: 0.8939 (m100) cc_final: 0.8661 (m100) REVERT: B 247 ASP cc_start: 0.7962 (t0) cc_final: 0.7494 (t0) REVERT: B 289 TYR cc_start: 0.8417 (m-80) cc_final: 0.8032 (m-80) REVERT: B 303 ASP cc_start: 0.7055 (m-30) cc_final: 0.6663 (m-30) REVERT: R 117 PHE cc_start: 0.8104 (t80) cc_final: 0.7711 (t80) REVERT: R 166 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7253 (tm-30) REVERT: R 167 VAL cc_start: 0.8878 (m) cc_final: 0.8491 (t) REVERT: R 230 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8179 (mtpp) REVERT: R 232 SER cc_start: 0.7945 (m) cc_final: 0.7707 (p) REVERT: R 304 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8693 (mt-10) REVERT: A 240 MET cc_start: 0.7199 (ptm) cc_final: 0.6557 (pp-130) REVERT: A 248 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7492 (ptpp) REVERT: A 337 ASP cc_start: 0.7352 (m-30) cc_final: 0.7105 (m-30) REVERT: S 38 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6841 (ptt180) REVERT: S 89 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7463 (tm-30) REVERT: S 151 LYS cc_start: 0.8286 (ptmt) cc_final: 0.7987 (ptmm) REVERT: S 211 ASP cc_start: 0.8857 (m-30) cc_final: 0.8441 (m-30) outliers start: 41 outliers final: 22 residues processed: 254 average time/residue: 0.3912 time to fit residues: 108.0194 Evaluate side-chains 245 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 72 optimal weight: 0.0570 chunk 12 optimal weight: 0.0770 chunk 109 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 306 GLN A 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119132 restraints weight = 12496.163| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.27 r_work: 0.3312 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9201 Z= 0.104 Angle : 0.578 8.985 12455 Z= 0.295 Chirality : 0.042 0.161 1405 Planarity : 0.004 0.043 1558 Dihedral : 5.285 84.536 1259 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.62 % Allowed : 22.60 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1123 helix: 2.13 (0.27), residues: 378 sheet: 0.35 (0.32), residues: 266 loop : -0.94 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 206 TYR 0.011 0.001 TYR R 106 PHE 0.015 0.001 PHE R 56 TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9197) covalent geometry : angle 0.57821 / 0.29 (12447) SS BOND : bond 0.00278 / 0.14 ( 4) SS BOND : angle 0.63558 / 0.38 ( 8) hydrogen bonds : bond 0.03699 / 2.43 ( 436) hydrogen bonds : angle 4.22700 / 2.94 ( 1245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8204 (mpp80) REVERT: B 44 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7663 (tp-100) REVERT: B 46 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7747 (ttm110) REVERT: B 163 ASP cc_start: 0.7895 (t0) cc_final: 0.7607 (t0) REVERT: B 169 TRP cc_start: 0.8803 (m100) cc_final: 0.8497 (m100) REVERT: B 214 ARG cc_start: 0.8694 (mtt-85) cc_final: 0.8365 (mtt-85) REVERT: B 247 ASP cc_start: 0.7926 (t0) cc_final: 0.7462 (t0) REVERT: B 289 TYR cc_start: 0.8323 (m-80) cc_final: 0.7749 (m-80) REVERT: B 303 ASP cc_start: 0.7026 (m-30) cc_final: 0.6619 (m-30) REVERT: B 325 MET cc_start: 0.8549 (mmt) cc_final: 0.8336 (mmm) REVERT: R 56 PHE cc_start: 0.7327 (t80) cc_final: 0.6461 (t80) REVERT: R 117 PHE cc_start: 0.7963 (t80) cc_final: 0.7599 (t80) REVERT: R 166 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7238 (tm-30) REVERT: R 167 VAL cc_start: 0.8881 (m) cc_final: 0.8509 (t) REVERT: R 230 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8311 (mtpp) REVERT: R 293 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7951 (mp) REVERT: R 304 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8700 (mt-10) REVERT: A 205 ARG cc_start: 0.8993 (mtp85) cc_final: 0.8665 (mpp80) REVERT: A 240 MET cc_start: 0.7125 (ptm) cc_final: 0.6577 (pp-130) REVERT: A 248 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7420 (ptpp) REVERT: A 297 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7114 (mp0) REVERT: A 309 ASP cc_start: 0.8768 (t0) cc_final: 0.8510 (t0) REVERT: A 337 ASP cc_start: 0.7277 (m-30) cc_final: 0.7034 (m-30) REVERT: S 38 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6630 (ptt180) REVERT: S 89 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7464 (tm-30) REVERT: S 151 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7994 (ptmm) REVERT: S 211 ASP cc_start: 0.8915 (m-30) cc_final: 0.8517 (m-30) outliers start: 26 outliers final: 17 residues processed: 253 average time/residue: 0.4638 time to fit residues: 126.9613 Evaluate side-chains 241 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 212 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 237 ASN B 295 ASN R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 306 GLN A 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113276 restraints weight = 12656.369| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.26 r_work: 0.3237 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9201 Z= 0.151 Angle : 0.611 9.437 12455 Z= 0.317 Chirality : 0.043 0.167 1405 Planarity : 0.004 0.045 1558 Dihedral : 5.382 81.779 1259 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.14 % Allowed : 22.00 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1123 helix: 2.02 (0.27), residues: 384 sheet: 0.25 (0.32), residues: 273 loop : -0.93 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 313 TYR 0.020 0.001 TYR R 106 PHE 0.021 0.002 PHE R 56 TRP 0.011 0.001 TRP S 36 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9197) covalent geometry : angle 0.61072 / 0.32 (12447) SS BOND : bond 0.00361 / 0.18 ( 4) SS BOND : angle 1.04689 / 0.63 ( 8) hydrogen bonds : bond 0.04392 / 2.91 ( 436) hydrogen bonds : angle 4.35214 / 3.03 ( 1245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8247 (mpp80) REVERT: B 44 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7742 (tp-100) REVERT: B 46 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7800 (ttm110) REVERT: B 163 ASP cc_start: 0.7997 (t0) cc_final: 0.7756 (t0) REVERT: B 169 TRP cc_start: 0.8968 (m100) cc_final: 0.8673 (m100) REVERT: B 247 ASP cc_start: 0.7930 (t0) cc_final: 0.7573 (t0) REVERT: B 289 TYR cc_start: 0.8346 (m-80) cc_final: 0.7989 (m-80) REVERT: B 303 ASP cc_start: 0.6980 (m-30) cc_final: 0.6568 (m-30) REVERT: B 325 MET cc_start: 0.8567 (mmt) cc_final: 0.8339 (mmm) REVERT: R 117 PHE cc_start: 0.8178 (t80) cc_final: 0.7934 (t80) REVERT: R 167 VAL cc_start: 0.8876 (m) cc_final: 0.8576 (t) REVERT: R 232 SER cc_start: 0.7988 (m) cc_final: 0.7729 (p) REVERT: R 293 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7965 (mp) REVERT: R 304 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8622 (mt-10) REVERT: A 205 ARG cc_start: 0.9026 (mtp85) cc_final: 0.8675 (mpp80) REVERT: A 240 MET cc_start: 0.7088 (ptm) cc_final: 0.6562 (pp-130) REVERT: A 248 LYS cc_start: 0.8000 (ptmt) cc_final: 0.7473 (ptpp) REVERT: A 309 ASP cc_start: 0.8817 (t0) cc_final: 0.8533 (t0) REVERT: S 38 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6860 (ptt180) REVERT: S 89 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7483 (tm-30) REVERT: S 151 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7986 (ptmm) REVERT: S 211 ASP cc_start: 0.8847 (m-30) cc_final: 0.8434 (m-30) outliers start: 41 outliers final: 25 residues processed: 262 average time/residue: 0.4361 time to fit residues: 124.2321 Evaluate side-chains 261 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 220 GLN B 268 ASN B 340 ASN R 62 ASN R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 306 GLN A 347 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.150313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113690 restraints weight = 12670.145| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.27 r_work: 0.3246 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9201 Z= 0.140 Angle : 0.615 10.209 12455 Z= 0.318 Chirality : 0.043 0.166 1405 Planarity : 0.004 0.053 1558 Dihedral : 5.393 82.506 1259 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.23 % Allowed : 22.91 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1123 helix: 2.03 (0.27), residues: 384 sheet: 0.16 (0.31), residues: 275 loop : -0.90 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 313 TYR 0.017 0.001 TYR R 106 PHE 0.018 0.001 PHE R 56 TRP 0.010 0.001 TRP S 36 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9197) covalent geometry : angle 0.61335 / 0.32 (12447) SS BOND : bond 0.00368 / 0.19 ( 4) SS BOND : angle 1.75038 / 0.81 ( 8) hydrogen bonds : bond 0.04303 / 2.85 ( 436) hydrogen bonds : angle 4.36127 / 3.04 ( 1245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8217 (mpp80) REVERT: B 44 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7708 (tp-100) REVERT: B 46 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7857 (ttm110) REVERT: B 163 ASP cc_start: 0.8021 (t0) cc_final: 0.7802 (t0) REVERT: B 169 TRP cc_start: 0.8958 (m100) cc_final: 0.8639 (m100) REVERT: B 247 ASP cc_start: 0.7910 (t0) cc_final: 0.7605 (t0) REVERT: B 289 TYR cc_start: 0.8391 (m-80) cc_final: 0.7905 (m-80) REVERT: B 303 ASP cc_start: 0.6952 (m-30) cc_final: 0.6544 (m-30) REVERT: B 325 MET cc_start: 0.8543 (mmt) cc_final: 0.8264 (mmm) REVERT: R 117 PHE cc_start: 0.8130 (t80) cc_final: 0.7910 (t80) REVERT: R 162 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7223 (mm-40) REVERT: R 167 VAL cc_start: 0.8863 (m) cc_final: 0.8547 (t) REVERT: R 230 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8233 (mtpp) REVERT: R 232 SER cc_start: 0.7992 (m) cc_final: 0.7746 (p) REVERT: R 293 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7947 (mp) REVERT: R 304 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8616 (mt-10) REVERT: A 205 ARG cc_start: 0.9024 (mtp85) cc_final: 0.8667 (mpp80) REVERT: A 240 MET cc_start: 0.7059 (ptm) cc_final: 0.6394 (pp-130) REVERT: A 248 LYS cc_start: 0.8033 (ptmt) cc_final: 0.7524 (ptpp) REVERT: A 309 ASP cc_start: 0.8851 (t0) cc_final: 0.8576 (t0) REVERT: S 38 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6770 (ptt180) REVERT: S 89 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7422 (tm-30) REVERT: S 151 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8008 (ptmm) REVERT: S 211 ASP cc_start: 0.8867 (m-30) cc_final: 0.8474 (m-30) outliers start: 32 outliers final: 23 residues processed: 255 average time/residue: 0.4414 time to fit residues: 122.2379 Evaluate side-chains 255 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 62 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 ASN R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114747 restraints weight = 12608.316| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.27 r_work: 0.3261 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9201 Z= 0.127 Angle : 0.618 11.065 12455 Z= 0.319 Chirality : 0.043 0.169 1405 Planarity : 0.004 0.058 1558 Dihedral : 5.394 83.548 1259 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.13 % Allowed : 23.92 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1123 helix: 2.11 (0.27), residues: 384 sheet: 0.16 (0.31), residues: 273 loop : -0.93 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 313 TYR 0.015 0.001 TYR R 106 PHE 0.017 0.001 PHE R 56 TRP 0.008 0.001 TRP S 36 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9197) covalent geometry : angle 0.61712 / 0.32 (12447) SS BOND : bond 0.00407 / 0.20 ( 4) SS BOND : angle 1.31086 / 0.61 ( 8) hydrogen bonds : bond 0.04133 / 2.73 ( 436) hydrogen bonds : angle 4.34402 / 3.03 ( 1245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8233 (mpp80) REVERT: B 44 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7753 (tp-100) REVERT: B 46 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7828 (ttm110) REVERT: B 59 TYR cc_start: 0.7407 (m-80) cc_final: 0.7172 (m-80) REVERT: B 88 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7574 (m110) REVERT: B 163 ASP cc_start: 0.8030 (t0) cc_final: 0.7826 (t0) REVERT: B 169 TRP cc_start: 0.8912 (m100) cc_final: 0.8603 (m100) REVERT: B 247 ASP cc_start: 0.7955 (t0) cc_final: 0.7664 (t0) REVERT: B 289 TYR cc_start: 0.8427 (m-80) cc_final: 0.8025 (m-80) REVERT: B 303 ASP cc_start: 0.6939 (m-30) cc_final: 0.6558 (m-30) REVERT: B 325 MET cc_start: 0.8516 (mmt) cc_final: 0.8233 (mmm) REVERT: B 327 VAL cc_start: 0.7670 (t) cc_final: 0.7192 (p) REVERT: R 117 PHE cc_start: 0.7983 (t80) cc_final: 0.7755 (t80) REVERT: R 162 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7179 (mm-40) REVERT: R 167 VAL cc_start: 0.8866 (m) cc_final: 0.8606 (t) REVERT: R 232 SER cc_start: 0.7927 (m) cc_final: 0.7667 (p) REVERT: R 304 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8617 (mt-10) REVERT: A 205 ARG cc_start: 0.9023 (mtp85) cc_final: 0.8669 (mpp80) REVERT: A 240 MET cc_start: 0.6925 (ptm) cc_final: 0.6316 (pp-130) REVERT: A 248 LYS cc_start: 0.8028 (ptmt) cc_final: 0.7529 (ptpp) REVERT: A 309 ASP cc_start: 0.8858 (t0) cc_final: 0.8578 (t0) REVERT: A 337 ASP cc_start: 0.7378 (m-30) cc_final: 0.7123 (m-30) REVERT: S 18 ARG cc_start: 0.7621 (tpp80) cc_final: 0.7359 (tpp80) REVERT: S 38 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6665 (ptt180) REVERT: S 89 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7461 (tm-30) REVERT: S 151 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8017 (ptmm) REVERT: S 211 ASP cc_start: 0.8842 (m-30) cc_final: 0.8441 (m-30) outliers start: 31 outliers final: 21 residues processed: 256 average time/residue: 0.4460 time to fit residues: 123.9393 Evaluate side-chains 252 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.0270 chunk 77 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.0050 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 125 ASN B 268 ASN R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113920 restraints weight = 12627.250| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.28 r_work: 0.3247 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9201 Z= 0.133 Angle : 0.625 12.208 12455 Z= 0.323 Chirality : 0.044 0.174 1405 Planarity : 0.004 0.061 1558 Dihedral : 5.378 83.364 1259 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.43 % Allowed : 23.92 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1123 helix: 2.14 (0.27), residues: 383 sheet: 0.23 (0.32), residues: 270 loop : -0.94 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 313 TYR 0.016 0.001 TYR R 106 PHE 0.020 0.001 PHE S 227 TRP 0.010 0.001 TRP S 36 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9197) covalent geometry : angle 0.62467 / 0.32 (12447) SS BOND : bond 0.00243 / 0.12 ( 4) SS BOND : angle 1.33294 / 0.62 ( 8) hydrogen bonds : bond 0.04205 / 2.76 ( 436) hydrogen bonds : angle 4.30939 / 3.01 ( 1245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8192 (mpp80) REVERT: B 44 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7748 (tp-100) REVERT: B 46 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7789 (ttm110) REVERT: B 59 TYR cc_start: 0.7774 (m-80) cc_final: 0.7401 (m-80) REVERT: B 163 ASP cc_start: 0.8021 (t0) cc_final: 0.7810 (t0) REVERT: B 169 TRP cc_start: 0.8883 (m100) cc_final: 0.8572 (m100) REVERT: B 289 TYR cc_start: 0.8400 (m-80) cc_final: 0.7904 (m-80) REVERT: B 303 ASP cc_start: 0.6807 (m-30) cc_final: 0.6417 (m-30) REVERT: B 325 MET cc_start: 0.8505 (mmt) cc_final: 0.8209 (mmm) REVERT: B 327 VAL cc_start: 0.7663 (t) cc_final: 0.7191 (p) REVERT: R 117 PHE cc_start: 0.7959 (t80) cc_final: 0.7735 (t80) REVERT: R 162 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7095 (mm-40) REVERT: R 167 VAL cc_start: 0.8836 (m) cc_final: 0.8596 (t) REVERT: R 232 SER cc_start: 0.7928 (m) cc_final: 0.7691 (p) REVERT: R 293 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7944 (mp) REVERT: A 205 ARG cc_start: 0.9035 (mtp85) cc_final: 0.8671 (mpp80) REVERT: A 240 MET cc_start: 0.6932 (ptm) cc_final: 0.6357 (pp-130) REVERT: A 248 LYS cc_start: 0.7997 (ptmt) cc_final: 0.7509 (ptpp) REVERT: A 309 ASP cc_start: 0.8847 (t0) cc_final: 0.8570 (t0) REVERT: A 337 ASP cc_start: 0.7348 (m-30) cc_final: 0.7104 (m-30) REVERT: S 38 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6674 (ptt180) REVERT: S 89 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7434 (tm-30) REVERT: S 151 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7957 (ptmm) REVERT: S 211 ASP cc_start: 0.8821 (m-30) cc_final: 0.8415 (m-30) outliers start: 34 outliers final: 23 residues processed: 257 average time/residue: 0.4425 time to fit residues: 123.3674 Evaluate side-chains 250 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 64 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 82 optimal weight: 0.0040 overall best weight: 0.2890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 ASN R 188 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118793 restraints weight = 12489.344| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.25 r_work: 0.3313 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9201 Z= 0.113 Angle : 0.619 12.582 12455 Z= 0.318 Chirality : 0.043 0.171 1405 Planarity : 0.004 0.060 1558 Dihedral : 5.304 86.136 1259 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.62 % Allowed : 24.52 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1123 helix: 2.24 (0.27), residues: 390 sheet: 0.22 (0.32), residues: 268 loop : -0.89 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 313 TYR 0.011 0.001 TYR R 106 PHE 0.014 0.001 PHE R 56 TRP 0.008 0.001 TRP B 339 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9197) covalent geometry : angle 0.61900 / 0.32 (12447) SS BOND : bond 0.00206 / 0.10 ( 4) SS BOND : angle 0.88625 / 0.42 ( 8) hydrogen bonds : bond 0.03729 / 2.45 ( 436) hydrogen bonds : angle 4.19709 / 2.92 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.13 seconds wall clock time: 60 minutes 54.75 seconds (3654.75 seconds total)