Starting phenix.real_space_refine on Thu Jul 2 12:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.map" model { file = "/net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e32_30974/07_2026/7e32_30974.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5615 2.51 5 N 1493 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 8797 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2273 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "R" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CLR': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 8797 At special positions: 0 Unit cell: (108.68, 117.04, 109.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1631 8.00 N 1493 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 188 " distance=2.03 Simple disulfide: pdb=" SG CYS R 327 " - pdb=" SG CYS R 331 " distance=2.03 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: 0.78 Conformation dependent library (CDL) restraints added in 446.8 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 41.2% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.612A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.059A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.859A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.844A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.672A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.028A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.911A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix 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 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.880A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 35 through 66 removed outlier: 3.939A pdb=" N ILE R 39 " --> pdb=" O GLN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 70 Processing helix chain 'R' and resid 71 through 91 Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.745A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 142 removed outlier: 4.268A pdb=" N LEU R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 150 removed outlier: 4.045A pdb=" N LYS R 148 " --> pdb=" O LEU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 171 Processing helix chain 'R' and resid 171 through 177 removed outlier: 4.150A pdb=" N PHE R 175 " --> pdb=" O ILE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 206 removed outlier: 3.718A pdb=" N THR R 198 " --> pdb=" O GLN R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 230 Processing helix chain 'R' and resid 285 through 327 removed outlier: 3.652A pdb=" N PHE R 310 " --> pdb=" O ILE R 306 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS R 313 " --> pdb=" O ALA R 309 " (cutoff:3.500A) Proline residue: R 316 - end of helix removed outlier: 3.653A pdb=" N VAL R 320 " --> pdb=" O PRO R 316 " (cutoff:3.500A) Proline residue: R 325 - end of helix Processing helix chain 'R' and resid 334 through 359 removed outlier: 3.658A pdb=" N ASN R 348 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER R 349 " --> pdb=" O GLY R 345 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU R 350 " --> pdb=" O TYR R 346 " (cutoff:3.500A) Proline residue: R 353 - end of helix removed outlier: 3.953A pdb=" N PHE R 359 " --> pdb=" O ILE R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.838A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.524A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.120A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.866A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.488A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.605A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.230A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.645A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.641A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.641A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.527A pdb=" N SER E 206 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.721A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.721A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1275 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: 1.54 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2812 1.35 - 1.46: 2162 1.46 - 1.58: 3928 1.58 - 1.70: 2 1.70 - 1.81: 80 Bond restraints: 8984 Sorted by residual: bond pdb=" C17 CLR R 402 " pdb=" C20 CLR R 402 " ideal model delta sigma weight residual 1.535 1.596 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" N PHE R 317 " pdb=" CA PHE R 317 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.30e-02 5.92e+03 4.94e+00 bond pdb=" C23 CLR R 402 " pdb=" C24 CLR R 402 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" C24 CLR R 402 " pdb=" C25 CLR R 402 " ideal model delta sigma weight residual 1.530 1.573 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C22 CLR R 402 " pdb=" C23 CLR R 402 " ideal model delta sigma weight residual 1.525 1.567 -0.042 2.00e-02 2.50e+03 4.50e+00 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 12011 1.40 - 2.79: 107 2.79 - 4.19: 54 4.19 - 5.58: 6 5.58 - 6.98: 4 Bond angle restraints: 12182 Sorted by residual: angle pdb=" CA PHE A 354 " pdb=" CB PHE A 354 " pdb=" CG PHE A 354 " ideal model delta sigma weight residual 113.80 117.02 -3.22 1.00e+00 1.00e+00 1.04e+01 angle pdb=" C12 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C18 CLR R 402 " ideal model delta sigma weight residual 111.01 104.03 6.98 3.00e+00 1.11e-01 5.41e+00 angle pdb=" N ILE R 312 " pdb=" CA ILE R 312 " pdb=" C ILE R 312 " ideal model delta sigma weight residual 112.98 110.13 2.85 1.25e+00 6.40e-01 5.20e+00 angle pdb=" C PHE A 354 " pdb=" CA PHE A 354 " pdb=" CB PHE A 354 " ideal model delta sigma weight residual 110.10 114.40 -4.30 1.90e+00 2.77e-01 5.13e+00 angle pdb=" C14 CLR R 402 " pdb=" C8 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 110.19 116.91 -6.72 3.00e+00 1.11e-01 5.01e+00 ... (remaining 12177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4936 17.97 - 35.95: 319 35.95 - 53.92: 47 53.92 - 71.90: 9 71.90 - 89.87: 9 Dihedral angle restraints: 5320 sinusoidal: 2076 harmonic: 3244 Sorted by residual: dihedral pdb=" CB CYS R 327 " pdb=" SG CYS R 327 " pdb=" SG CYS R 331 " pdb=" CB CYS R 331 " ideal model delta sinusoidal sigma weight residual 93.00 46.74 46.26 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " pdb=" CD GLU A 298 " pdb=" OE1 GLU A 298 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU G 47 " pdb=" CG GLU G 47 " pdb=" CD GLU G 47 " pdb=" OE1 GLU G 47 " ideal model delta sinusoidal sigma weight residual 0.00 -88.27 88.27 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 5317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1237 0.060 - 0.119: 147 0.119 - 0.179: 8 0.179 - 0.239: 1 0.239 - 0.299: 2 Chirality restraints: 1395 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 2.85 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C20 CLR R 402 " pdb=" C17 CLR R 402 " pdb=" C21 CLR R 402 " pdb=" C22 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.59 2.79 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 1392 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 353 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C LEU A 353 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 353 " 0.031 2.00e-02 2.50e+03 pdb=" N PHE A 354 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR R 71 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO R 72 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 316 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C PRO R 316 " -0.022 2.00e-02 2.50e+03 pdb=" O PRO R 316 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE R 317 " 0.007 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 58 2.56 - 3.14: 7225 3.14 - 3.73: 13898 3.73 - 4.31: 19809 4.31 - 4.90: 33277 Nonbonded interactions: 74267 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.013 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.037 3.040 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.122 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.124 3.040 ... (remaining 74262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.003 0.061 8988 Z= 0.134 Angle : 0.454 6.979 12190 Z= 0.244 Chirality : 0.040 0.299 1395 Planarity : 0.002 0.047 1520 Dihedral : 12.558 89.872 3212 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.27), residues: 1097 helix: 2.80 (0.27), residues: 389 sheet: 1.22 (0.32), residues: 265 loop : 0.40 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 42 TYR 0.009 0.001 TYR R 197 PHE 0.011 0.001 PHE A 354 TRP 0.008 0.001 TRP R 343 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 8984) covalent geometry : angle 0.45397 / 0.24 (12182) SS BOND : bond 0.00072 / 0.03 ( 4) SS BOND : angle 0.55188 / 0.33 ( 8) hydrogen bonds : bond 0.18554 / 12.66 ( 450) hydrogen bonds : angle 6.56487 / 4.71 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.321 Fit side-chains REVERT: A 354 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.4824 (m-80) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.3963 time to fit residues: 67.8937 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 18 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115683 restraints weight = 10021.723| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.33 r_work: 0.3249 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8988 Z= 0.176 Angle : 0.559 8.165 12190 Z= 0.298 Chirality : 0.043 0.155 1395 Planarity : 0.004 0.047 1520 Dihedral : 5.298 77.116 1225 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.61 % Allowed : 8.98 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.26), residues: 1097 helix: 2.12 (0.26), residues: 399 sheet: 0.81 (0.31), residues: 272 loop : 0.31 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.014 0.002 TYR B 59 PHE 0.016 0.002 PHE B 151 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 8984) covalent geometry : angle 0.55881 / 0.30 (12182) SS BOND : bond 0.00350 / 0.17 ( 4) SS BOND : angle 1.16391 / 0.68 ( 8) hydrogen bonds : bond 0.03571 / 2.43 ( 450) hydrogen bonds : angle 4.84538 / 3.45 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.272 Fit side-chains REVERT: A 198 MET cc_start: 0.8333 (ttm) cc_final: 0.7902 (ttm) REVERT: A 354 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.4770 (m-80) REVERT: B 19 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7674 (ttp80) REVERT: B 119 ASN cc_start: 0.8254 (m110) cc_final: 0.7782 (m-40) REVERT: B 163 ASP cc_start: 0.7191 (t0) cc_final: 0.6874 (t0) REVERT: B 164 THR cc_start: 0.8556 (m) cc_final: 0.8281 (m) REVERT: B 184 THR cc_start: 0.8161 (p) cc_final: 0.7946 (p) outliers start: 25 outliers final: 11 residues processed: 146 average time/residue: 0.4079 time to fit residues: 64.5233 Evaluate side-chains 140 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110348 restraints weight = 9900.260| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.39 r_work: 0.3165 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8988 Z= 0.147 Angle : 0.514 5.466 12190 Z= 0.275 Chirality : 0.042 0.154 1395 Planarity : 0.004 0.051 1520 Dihedral : 5.290 73.708 1225 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.19 % Allowed : 12.53 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.26), residues: 1097 helix: 1.92 (0.26), residues: 404 sheet: 0.59 (0.31), residues: 272 loop : 0.20 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 32 TYR 0.018 0.001 TYR R 197 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8984) covalent geometry : angle 0.51383 / 0.27 (12182) SS BOND : bond 0.00320 / 0.16 ( 4) SS BOND : angle 0.88590 / 0.52 ( 8) hydrogen bonds : bond 0.03434 / 2.33 ( 450) hydrogen bonds : angle 4.68599 / 3.31 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.308 Fit side-chains REVERT: A 198 MET cc_start: 0.8391 (ttm) cc_final: 0.7958 (ttm) REVERT: B 19 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7638 (ttp80) REVERT: B 42 ARG cc_start: 0.7010 (tpp-160) cc_final: 0.6696 (tpp-160) REVERT: B 120 ILE cc_start: 0.8212 (pt) cc_final: 0.7997 (mp) REVERT: B 164 THR cc_start: 0.8487 (m) cc_final: 0.8256 (m) REVERT: B 184 THR cc_start: 0.8236 (p) cc_final: 0.8013 (p) REVERT: B 197 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7920 (mtp85) REVERT: E 83 MET cc_start: 0.8424 (mtm) cc_final: 0.8037 (mtp) REVERT: E 140 MET cc_start: 0.8870 (mmm) cc_final: 0.8133 (mmm) outliers start: 21 outliers final: 6 residues processed: 149 average time/residue: 0.4479 time to fit residues: 72.3356 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 119 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109862 restraints weight = 10052.756| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.41 r_work: 0.3155 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8988 Z= 0.131 Angle : 0.506 6.409 12190 Z= 0.270 Chirality : 0.041 0.149 1395 Planarity : 0.004 0.055 1520 Dihedral : 4.995 74.780 1221 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.67 % Allowed : 14.51 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1097 helix: 1.86 (0.26), residues: 404 sheet: 0.36 (0.31), residues: 276 loop : 0.15 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.016 0.001 TYR R 197 PHE 0.016 0.001 PHE E 68 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8984) covalent geometry : angle 0.50586 / 0.27 (12182) SS BOND : bond 0.00309 / 0.15 ( 4) SS BOND : angle 0.85625 / 0.50 ( 8) hydrogen bonds : bond 0.03182 / 2.16 ( 450) hydrogen bonds : angle 4.58897 / 3.23 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.267 Fit side-chains REVERT: A 198 MET cc_start: 0.8402 (ttm) cc_final: 0.8000 (ttm) REVERT: B 19 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7657 (ttp80) REVERT: B 120 ILE cc_start: 0.8306 (pt) cc_final: 0.8095 (mp) REVERT: B 184 THR cc_start: 0.8304 (p) cc_final: 0.8065 (p) REVERT: E 140 MET cc_start: 0.8911 (mmm) cc_final: 0.8111 (mmm) outliers start: 16 outliers final: 9 residues processed: 134 average time/residue: 0.4383 time to fit residues: 63.3406 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109263 restraints weight = 10074.446| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.39 r_work: 0.3096 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8988 Z= 0.132 Angle : 0.501 5.323 12190 Z= 0.269 Chirality : 0.041 0.150 1395 Planarity : 0.004 0.056 1520 Dihedral : 4.995 74.721 1221 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.61 % Allowed : 14.30 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1097 helix: 1.85 (0.26), residues: 406 sheet: 0.19 (0.31), residues: 277 loop : 0.10 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.017 0.001 TYR R 197 PHE 0.017 0.001 PHE E 68 TRP 0.010 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8984) covalent geometry : angle 0.50049 / 0.27 (12182) SS BOND : bond 0.00347 / 0.17 ( 4) SS BOND : angle 0.84235 / 0.50 ( 8) hydrogen bonds : bond 0.03142 / 2.13 ( 450) hydrogen bonds : angle 4.54938 / 3.20 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.289 Fit side-chains REVERT: A 318 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 19 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7700 (ttp80) REVERT: B 42 ARG cc_start: 0.7559 (tpt170) cc_final: 0.7299 (tpt-90) REVERT: B 120 ILE cc_start: 0.8228 (pt) cc_final: 0.8026 (mp) REVERT: B 163 ASP cc_start: 0.7341 (t0) cc_final: 0.7131 (t0) REVERT: B 267 ASP cc_start: 0.8130 (m-30) cc_final: 0.7850 (m-30) REVERT: B 325 MET cc_start: 0.8743 (tpp) cc_final: 0.8542 (mmm) REVERT: E 83 MET cc_start: 0.8454 (mtm) cc_final: 0.8085 (mtp) REVERT: E 140 MET cc_start: 0.8986 (mmm) cc_final: 0.8028 (mmm) REVERT: G 19 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7365 (mt) outliers start: 25 outliers final: 13 residues processed: 143 average time/residue: 0.4188 time to fit residues: 64.9109 Evaluate side-chains 142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115160 restraints weight = 10023.392| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.45 r_work: 0.3260 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8988 Z= 0.133 Angle : 0.504 5.663 12190 Z= 0.271 Chirality : 0.041 0.149 1395 Planarity : 0.004 0.056 1520 Dihedral : 4.996 74.393 1221 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 16.60 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1097 helix: 1.81 (0.26), residues: 408 sheet: 0.03 (0.30), residues: 278 loop : 0.12 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.017 0.001 TYR R 197 PHE 0.015 0.001 PHE E 68 TRP 0.011 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8984) covalent geometry : angle 0.50326 / 0.27 (12182) SS BOND : bond 0.00294 / 0.14 ( 4) SS BOND : angle 0.79553 / 0.47 ( 8) hydrogen bonds : bond 0.03109 / 2.10 ( 450) hydrogen bonds : angle 4.52978 / 3.18 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.335 Fit side-chains REVERT: A 197 LYS cc_start: 0.8025 (ptmt) cc_final: 0.7631 (mtpt) REVERT: A 313 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6586 (ptm160) REVERT: B 19 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7781 (ttp80) REVERT: B 42 ARG cc_start: 0.7457 (tpt170) cc_final: 0.7202 (tpt-90) REVERT: B 163 ASP cc_start: 0.7473 (t0) cc_final: 0.7242 (t0) REVERT: B 197 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8116 (mtp85) REVERT: B 267 ASP cc_start: 0.8217 (m-30) cc_final: 0.7936 (m-30) REVERT: B 273 ILE cc_start: 0.8983 (mp) cc_final: 0.8768 (mm) REVERT: B 325 MET cc_start: 0.8815 (tpp) cc_final: 0.8574 (mmm) REVERT: E 83 MET cc_start: 0.8627 (mtm) cc_final: 0.8244 (mtp) REVERT: E 140 MET cc_start: 0.8997 (mmm) cc_final: 0.7990 (mmm) REVERT: G 19 LEU cc_start: 0.7885 (mt) cc_final: 0.7629 (mt) outliers start: 23 outliers final: 13 residues processed: 140 average time/residue: 0.4601 time to fit residues: 69.7174 Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 102 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.104171 restraints weight = 10083.787| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.38 r_work: 0.3071 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8988 Z= 0.192 Angle : 0.561 8.745 12190 Z= 0.299 Chirality : 0.043 0.153 1395 Planarity : 0.004 0.058 1520 Dihedral : 5.193 73.238 1221 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.40 % Allowed : 17.43 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1097 helix: 1.64 (0.26), residues: 408 sheet: -0.16 (0.30), residues: 283 loop : 0.01 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.017 0.002 TYR R 197 PHE 0.018 0.001 PHE E 68 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 8984) covalent geometry : angle 0.56064 / 0.30 (12182) SS BOND : bond 0.00327 / 0.16 ( 4) SS BOND : angle 0.96129 / 0.56 ( 8) hydrogen bonds : bond 0.03445 / 2.35 ( 450) hydrogen bonds : angle 4.72625 / 3.32 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.328 Fit side-chains REVERT: A 198 MET cc_start: 0.8301 (ttm) cc_final: 0.7891 (ttm) REVERT: B 197 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7944 (mtp85) REVERT: B 267 ASP cc_start: 0.8326 (m-30) cc_final: 0.8068 (m-30) REVERT: B 325 MET cc_start: 0.8844 (tpp) cc_final: 0.8627 (mmm) REVERT: E 83 MET cc_start: 0.8401 (mtm) cc_final: 0.8107 (mtp) REVERT: E 140 MET cc_start: 0.9086 (mmm) cc_final: 0.7832 (mmm) REVERT: G 19 LEU cc_start: 0.7756 (mt) cc_final: 0.7546 (mt) REVERT: R 189 LEU cc_start: 0.8063 (pp) cc_final: 0.7855 (pp) outliers start: 23 outliers final: 13 residues processed: 140 average time/residue: 0.3858 time to fit residues: 58.8634 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 85 optimal weight: 0.4980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133225 restraints weight = 9601.942| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.19 r_work: 0.3377 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8988 Z= 0.114 Angle : 0.524 8.633 12190 Z= 0.280 Chirality : 0.041 0.141 1395 Planarity : 0.004 0.059 1520 Dihedral : 5.081 75.206 1221 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.88 % Allowed : 18.68 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1097 helix: 1.86 (0.26), residues: 407 sheet: -0.11 (0.30), residues: 281 loop : 0.06 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 32 TYR 0.018 0.001 TYR R 197 PHE 0.013 0.001 PHE E 68 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8984) covalent geometry : angle 0.52424 / 0.28 (12182) SS BOND : bond 0.00272 / 0.13 ( 4) SS BOND : angle 0.69392 / 0.41 ( 8) hydrogen bonds : bond 0.03043 / 2.04 ( 450) hydrogen bonds : angle 4.51942 / 3.15 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.339 Fit side-chains REVERT: A 197 LYS cc_start: 0.7937 (ptmt) cc_final: 0.7550 (mtpt) REVERT: A 275 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: B 197 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8109 (mtp85) REVERT: B 267 ASP cc_start: 0.8329 (m-30) cc_final: 0.8045 (m-30) REVERT: B 325 MET cc_start: 0.8825 (tpp) cc_final: 0.8584 (mmm) REVERT: E 83 MET cc_start: 0.8674 (mtm) cc_final: 0.8311 (mtp) REVERT: E 140 MET cc_start: 0.8996 (mmm) cc_final: 0.7976 (mmm) REVERT: G 19 LEU cc_start: 0.8081 (mt) cc_final: 0.7875 (mt) REVERT: R 189 LEU cc_start: 0.8218 (pp) cc_final: 0.8010 (pp) outliers start: 18 outliers final: 12 residues processed: 139 average time/residue: 0.4300 time to fit residues: 65.2668 Evaluate side-chains 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131129 restraints weight = 9576.133| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.20 r_work: 0.3347 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8988 Z= 0.144 Angle : 0.542 9.463 12190 Z= 0.289 Chirality : 0.041 0.149 1395 Planarity : 0.004 0.059 1520 Dihedral : 5.088 73.899 1221 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.77 % Allowed : 19.42 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1097 helix: 1.76 (0.26), residues: 408 sheet: -0.13 (0.30), residues: 276 loop : -0.05 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.017 0.001 TYR R 197 PHE 0.014 0.001 PHE E 68 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8984) covalent geometry : angle 0.54132 / 0.29 (12182) SS BOND : bond 0.00295 / 0.14 ( 4) SS BOND : angle 0.79586 / 0.47 ( 8) hydrogen bonds : bond 0.03142 / 2.13 ( 450) hydrogen bonds : angle 4.58749 / 3.20 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.340 Fit side-chains REVERT: A 197 LYS cc_start: 0.7998 (ptmt) cc_final: 0.7631 (mtpt) REVERT: B 197 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8083 (mtp85) REVERT: B 267 ASP cc_start: 0.8366 (m-30) cc_final: 0.8080 (m-30) REVERT: B 325 MET cc_start: 0.8830 (tpp) cc_final: 0.8603 (mmm) REVERT: E 83 MET cc_start: 0.8594 (mtm) cc_final: 0.8192 (mtp) REVERT: E 140 MET cc_start: 0.9019 (mmm) cc_final: 0.7835 (mmm) REVERT: G 19 LEU cc_start: 0.8121 (mt) cc_final: 0.7919 (mt) REVERT: G 21 MET cc_start: 0.7318 (tmm) cc_final: 0.6913 (tmm) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.3635 time to fit residues: 53.7825 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 104 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133125 restraints weight = 9575.216| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.27 r_work: 0.3371 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8988 Z= 0.125 Angle : 0.545 8.682 12190 Z= 0.286 Chirality : 0.041 0.146 1395 Planarity : 0.004 0.059 1520 Dihedral : 5.057 73.734 1221 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.36 % Allowed : 20.15 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1097 helix: 1.83 (0.26), residues: 408 sheet: -0.10 (0.30), residues: 275 loop : -0.08 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.017 0.001 TYR R 197 PHE 0.012 0.001 PHE E 68 TRP 0.013 0.001 TRP B 211 HIS 0.001 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8984) covalent geometry : angle 0.54453 / 0.29 (12182) SS BOND : bond 0.00284 / 0.14 ( 4) SS BOND : angle 0.73238 / 0.43 ( 8) hydrogen bonds : bond 0.03046 / 2.05 ( 450) hydrogen bonds : angle 4.54157 / 3.16 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.334 Fit side-chains REVERT: A 197 LYS cc_start: 0.7945 (ptmt) cc_final: 0.7572 (mtpt) REVERT: A 198 MET cc_start: 0.8336 (ttm) cc_final: 0.7971 (ttm) REVERT: B 197 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8028 (mtp85) REVERT: B 267 ASP cc_start: 0.8357 (m-30) cc_final: 0.8070 (m-30) REVERT: B 303 ASP cc_start: 0.7700 (m-30) cc_final: 0.7105 (p0) REVERT: B 325 MET cc_start: 0.8811 (tpp) cc_final: 0.8579 (mmm) REVERT: E 83 MET cc_start: 0.8591 (mtm) cc_final: 0.8192 (mtp) REVERT: E 140 MET cc_start: 0.8971 (mmm) cc_final: 0.7880 (mmm) REVERT: G 19 LEU cc_start: 0.8087 (mt) cc_final: 0.7885 (mt) REVERT: G 21 MET cc_start: 0.7327 (tmm) cc_final: 0.6941 (tmm) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.4465 time to fit residues: 61.5964 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.0020 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131178 restraints weight = 9518.836| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.19 r_work: 0.3350 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8988 Z= 0.147 Angle : 0.548 9.880 12190 Z= 0.289 Chirality : 0.042 0.149 1395 Planarity : 0.004 0.059 1520 Dihedral : 5.107 72.815 1221 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.57 % Allowed : 20.04 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1097 helix: 1.78 (0.26), residues: 408 sheet: -0.21 (0.30), residues: 276 loop : -0.08 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.017 0.001 TYR R 197 PHE 0.013 0.001 PHE E 68 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8984) covalent geometry : angle 0.54827 / 0.29 (12182) SS BOND : bond 0.00306 / 0.15 ( 4) SS BOND : angle 0.78780 / 0.46 ( 8) hydrogen bonds : bond 0.03131 / 2.12 ( 450) hydrogen bonds : angle 4.60953 / 3.22 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.39 seconds wall clock time: 58 minutes 46.66 seconds (3526.66 seconds total)