Starting phenix.real_space_refine on Tue Mar 3 21:18:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e32_30974/03_2026/7e32_30974.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e32_30974/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2026/7e32_30974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2026/7e32_30974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2026/7e32_30974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2026/7e32_30974.map" } 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-5986/lib/python3.9/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: 2.24, per 1000 atoms: 0.25 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: 0.77 Conformation dependent library (CDL) restraints added in 342.5 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: 0.24 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: 1.28 Time building geometry restraints manager: 1.02 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 - 18.45: 4990 18.45 - 36.90: 319 36.90 - 55.35: 47 55.35 - 73.80: 9 73.80 - 92.25: 11 Dihedral angle restraints: 5376 sinusoidal: 2132 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=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" C4 CLR R 402 " pdb=" C5 CLR R 402 " ideal model delta sinusoidal sigma weight residual -55.03 37.22 -92.25 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" C5 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" C4 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sinusoidal sigma weight residual 175.64 83.89 91.75 1 3.00e+01 1.11e-03 1.10e+01 ... (remaining 5373 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.040 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 : 12.894 92.246 3268 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 covalent geometry : bond 0.00253 ( 8984) covalent geometry : angle 0.45397 (12182) SS BOND : bond 0.00072 ( 4) SS BOND : angle 0.55188 ( 8) hydrogen bonds : bond 0.18554 ( 450) hydrogen bonds : angle 6.56487 ( 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 : 0.340 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: 0.4935 time to fit residues: 83.9487 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 : 0.326 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 155 ASN ** G 59 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 = 0.3803 r_free = 0.3803 target = 0.160073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114924 restraints weight = 10008.105| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.33 r_work: 0.3210 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1919 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= 0.166 Angle : 0.560 7.650 12190 Z= 0.295 Chirality : 0.043 0.157 1395 Planarity : 0.004 0.046 1520 Dihedral : 5.023 76.638 1281 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.51 % Allowed : 9.19 % Favored : 88.31 % 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: 1.59 (0.26), residues: 1097 helix: 2.12 (0.26), residues: 399 sheet: 0.79 (0.31), residues: 272 loop : 0.31 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.014 0.001 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 covalent geometry : bond 0.00378 ( 8984) covalent geometry : angle 0.55898 (12182) SS BOND : bond 0.00354 ( 4) SS BOND : angle 1.14199 ( 8) hydrogen bonds : bond 0.03743 ( 450) hydrogen bonds : angle 4.84273 ( 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 162 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.351 Fit side-chains REVERT: A 198 MET cc_start: 0.8387 (ttm) cc_final: 0.7899 (ttm) REVERT: A 354 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.4729 (m-80) REVERT: B 19 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7658 (ttp80) REVERT: B 119 ASN cc_start: 0.8268 (m110) cc_final: 0.7789 (m-40) REVERT: B 163 ASP cc_start: 0.7212 (t0) cc_final: 0.6863 (t0) REVERT: B 164 THR cc_start: 0.8538 (m) cc_final: 0.8266 (m) REVERT: B 184 THR cc_start: 0.8164 (p) cc_final: 0.7953 (p) REVERT: B 197 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7906 (mtp85) outliers start: 24 outliers final: 9 residues processed: 144 average time/residue: 0.5015 time to fit residues: 77.9114 Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.160013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114605 restraints weight = 9894.473| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.34 r_work: 0.3244 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2198 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= 0.120 Angle : 0.493 5.402 12190 Z= 0.264 Chirality : 0.041 0.150 1395 Planarity : 0.004 0.051 1520 Dihedral : 4.751 75.650 1281 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.98 % Allowed : 12.73 % 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: 1.47 (0.26), residues: 1097 helix: 2.12 (0.26), residues: 399 sheet: 0.70 (0.31), residues: 270 loop : 0.16 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.015 0.001 TYR R 197 PHE 0.013 0.001 PHE R 175 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8984) covalent geometry : angle 0.49295 (12182) SS BOND : bond 0.00305 ( 4) SS BOND : angle 0.87398 ( 8) hydrogen bonds : bond 0.03321 ( 450) hydrogen bonds : angle 4.65068 ( 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 153 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.353 Fit side-chains REVERT: A 198 MET cc_start: 0.8343 (ttm) cc_final: 0.7904 (ttm) REVERT: A 261 ASP cc_start: 0.6786 (p0) cc_final: 0.6276 (t0) REVERT: A 354 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: B 19 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7654 (ttp80) REVERT: B 44 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: B 119 ASN cc_start: 0.8405 (m110) cc_final: 0.7867 (m-40) REVERT: B 120 ILE cc_start: 0.8132 (pt) cc_final: 0.7901 (mp) REVERT: B 163 ASP cc_start: 0.7153 (t0) cc_final: 0.6845 (t0) REVERT: B 164 THR cc_start: 0.8453 (m) cc_final: 0.8212 (m) REVERT: B 197 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7927 (mtp85) REVERT: E 83 MET cc_start: 0.8283 (mtm) cc_final: 0.7887 (mtp) outliers start: 19 outliers final: 5 residues processed: 143 average time/residue: 0.5073 time to fit residues: 78.2939 Evaluate side-chains 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110969 restraints weight = 10134.157| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.56 r_work: 0.2985 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8988 Z= 0.226 Angle : 0.578 6.215 12190 Z= 0.308 Chirality : 0.044 0.161 1395 Planarity : 0.004 0.054 1520 Dihedral : 5.041 73.837 1281 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.30 % Allowed : 13.57 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.26), residues: 1097 helix: 1.55 (0.26), residues: 407 sheet: 0.23 (0.31), residues: 276 loop : 0.11 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.016 0.002 TYR R 197 PHE 0.015 0.002 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 8984) covalent geometry : angle 0.57712 (12182) SS BOND : bond 0.00400 ( 4) SS BOND : angle 1.05566 ( 8) hydrogen bonds : bond 0.03759 ( 450) hydrogen bonds : angle 4.89808 ( 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 151 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.336 Fit side-chains REVERT: A 198 MET cc_start: 0.8304 (ttm) cc_final: 0.7883 (ttm) REVERT: A 354 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: B 19 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7673 (ttp80) REVERT: B 44 GLN cc_start: 0.7332 (tt0) cc_final: 0.7113 (tt0) REVERT: B 171 ILE cc_start: 0.8311 (mm) cc_final: 0.8027 (mt) REVERT: B 196 THR cc_start: 0.7750 (p) cc_final: 0.7531 (m) REVERT: B 267 ASP cc_start: 0.8163 (m-30) cc_final: 0.7879 (m-30) REVERT: E 83 MET cc_start: 0.8455 (mtm) cc_final: 0.8112 (mtp) REVERT: E 140 MET cc_start: 0.9084 (mmm) cc_final: 0.8398 (mmm) REVERT: G 19 LEU cc_start: 0.7725 (mt) cc_final: 0.7508 (mt) REVERT: R 113 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6741 (mp) REVERT: R 148 LYS cc_start: 0.8330 (mptt) cc_final: 0.8071 (mptp) outliers start: 22 outliers final: 7 residues processed: 140 average time/residue: 0.4946 time to fit residues: 74.7094 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 198 THR 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: 0.9990 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 106 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111162 restraints weight = 10092.311| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.45 r_work: 0.3116 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3160 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= 0.173 Angle : 0.547 8.523 12190 Z= 0.292 Chirality : 0.042 0.151 1395 Planarity : 0.004 0.056 1520 Dihedral : 4.905 74.792 1279 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.51 % Allowed : 15.45 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.26), residues: 1097 helix: 1.55 (0.26), residues: 406 sheet: 0.01 (0.31), residues: 276 loop : 0.01 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 18 TYR 0.016 0.001 TYR R 197 PHE 0.015 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8984) covalent geometry : angle 0.54656 (12182) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.95697 ( 8) hydrogen bonds : bond 0.03438 ( 450) hydrogen bonds : angle 4.81469 ( 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 145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.207 Fit side-chains REVERT: B 19 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7790 (ttp80) REVERT: B 171 ILE cc_start: 0.8478 (mm) cc_final: 0.8126 (mt) REVERT: E 83 MET cc_start: 0.8526 (mtm) cc_final: 0.8145 (mtp) REVERT: E 140 MET cc_start: 0.9112 (mmm) cc_final: 0.8283 (mmm) REVERT: G 19 LEU cc_start: 0.7838 (mt) cc_final: 0.7604 (mt) REVERT: R 113 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6816 (mp) outliers start: 24 outliers final: 14 residues processed: 133 average time/residue: 0.4657 time to fit residues: 66.9718 Evaluate side-chains 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU 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 155 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 113 ILE 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: 0.9980 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113057 restraints weight = 10008.856| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.51 r_work: 0.3055 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3176 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= 0.132 Angle : 0.514 6.424 12190 Z= 0.276 Chirality : 0.041 0.147 1395 Planarity : 0.004 0.057 1520 Dihedral : 4.613 75.920 1277 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.61 % Allowed : 16.18 % Favored : 81.21 % 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: 0.80 (0.26), residues: 1097 helix: 1.66 (0.26), residues: 406 sheet: -0.13 (0.30), residues: 275 loop : -0.00 (0.32), residues: 416 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 0.013 0.001 PHE B 151 TRP 0.012 0.001 TRP R 343 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8984) covalent geometry : angle 0.51393 (12182) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.85705 ( 8) hydrogen bonds : bond 0.03209 ( 450) hydrogen bonds : angle 4.65690 ( 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 149 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.404 Fit side-chains REVERT: B 19 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7759 (ttp80) REVERT: B 171 ILE cc_start: 0.8224 (mm) cc_final: 0.7817 (mt) REVERT: B 267 ASP cc_start: 0.8157 (m-30) cc_final: 0.7887 (m-30) REVERT: E 83 MET cc_start: 0.8453 (mtm) cc_final: 0.8142 (mtp) REVERT: E 140 MET cc_start: 0.9057 (mmm) cc_final: 0.8178 (mmm) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 0.4891 time to fit residues: 72.2954 Evaluate side-chains 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 198 LEU 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 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: 1.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 69 optimal weight: 0.0770 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 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 = 0.3751 r_free = 0.3751 target = 0.155064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109273 restraints weight = 10011.584| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.34 r_work: 0.3106 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3223 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= 0.122 Angle : 0.511 5.783 12190 Z= 0.273 Chirality : 0.041 0.147 1395 Planarity : 0.004 0.057 1520 Dihedral : 4.532 75.743 1277 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.30 % Allowed : 18.16 % Favored : 79.54 % 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: 1.76 (0.26), residues: 408 sheet: -0.17 (0.30), residues: 276 loop : 0.06 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.018 0.001 TYR R 197 PHE 0.013 0.001 PHE R 175 TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8984) covalent geometry : angle 0.51050 (12182) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.82093 ( 8) hydrogen bonds : bond 0.03109 ( 450) hydrogen bonds : angle 4.55728 ( 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 148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.336 Fit side-chains REVERT: A 318 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: B 44 GLN cc_start: 0.7267 (tt0) cc_final: 0.6983 (tt0) REVERT: B 196 THR cc_start: 0.7744 (p) cc_final: 0.7508 (m) REVERT: B 246 ASP cc_start: 0.8685 (m-30) cc_final: 0.8455 (m-30) REVERT: B 267 ASP cc_start: 0.8212 (m-30) cc_final: 0.7941 (m-30) REVERT: B 303 ASP cc_start: 0.7359 (m-30) cc_final: 0.6673 (p0) REVERT: E 83 MET cc_start: 0.8465 (mtm) cc_final: 0.8174 (mtp) REVERT: E 140 MET cc_start: 0.9021 (mmm) cc_final: 0.8118 (mmm) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 0.4764 time to fit residues: 71.2567 Evaluate side-chains 138 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 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 198 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131972 restraints weight = 9566.143| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.23 r_work: 0.3355 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3294 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= 0.124 Angle : 0.512 7.092 12190 Z= 0.273 Chirality : 0.041 0.147 1395 Planarity : 0.004 0.058 1520 Dihedral : 4.489 75.252 1277 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.77 % Allowed : 19.31 % Favored : 78.91 % 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: 0.88 (0.26), residues: 1097 helix: 1.76 (0.26), residues: 408 sheet: -0.05 (0.31), residues: 268 loop : -0.03 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.017 0.001 TYR R 197 PHE 0.013 0.001 PHE B 151 TRP 0.013 0.001 TRP R 343 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8984) covalent geometry : angle 0.51215 (12182) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.79077 ( 8) hydrogen bonds : bond 0.03095 ( 450) hydrogen bonds : angle 4.52220 ( 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 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.353 Fit side-chains REVERT: A 275 GLU cc_start: 0.8710 (pt0) cc_final: 0.7894 (tm-30) REVERT: A 313 ARG cc_start: 0.6930 (ptm160) cc_final: 0.6727 (ptp-110) REVERT: A 318 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: B 44 GLN cc_start: 0.7129 (tt0) cc_final: 0.6892 (tt0) REVERT: B 267 ASP cc_start: 0.8076 (m-30) cc_final: 0.7788 (m-30) REVERT: B 303 ASP cc_start: 0.7493 (m-30) cc_final: 0.6917 (p0) REVERT: E 83 MET cc_start: 0.8630 (mtm) cc_final: 0.8238 (mtp) REVERT: E 140 MET cc_start: 0.8960 (mmm) cc_final: 0.8150 (mmm) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.4780 time to fit residues: 68.8946 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 198 LEU 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 50 LEU 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: 5.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3991 r_free = 0.3991 target = 0.170585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132181 restraints weight = 9528.766| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.21 r_work: 0.3357 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3359 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= 0.126 Angle : 0.508 6.013 12190 Z= 0.273 Chirality : 0.041 0.148 1395 Planarity : 0.004 0.058 1520 Dihedral : 4.475 74.801 1277 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.98 % Allowed : 19.83 % Favored : 78.18 % 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: 0.88 (0.26), residues: 1097 helix: 1.79 (0.26), residues: 408 sheet: -0.11 (0.30), residues: 274 loop : -0.01 (0.32), residues: 415 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 R 175 TRP 0.012 0.001 TRP R 343 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8984) covalent geometry : angle 0.50827 (12182) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.75013 ( 8) hydrogen bonds : bond 0.03082 ( 450) hydrogen bonds : angle 4.50505 ( 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 142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.338 Fit side-chains REVERT: A 275 GLU cc_start: 0.8702 (pt0) cc_final: 0.7824 (tm-30) REVERT: A 313 ARG cc_start: 0.6983 (ptm160) cc_final: 0.6776 (ptp-170) REVERT: A 318 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: B 267 ASP cc_start: 0.8294 (m-30) cc_final: 0.8025 (m-30) REVERT: B 325 MET cc_start: 0.8826 (tpp) cc_final: 0.8579 (mmm) REVERT: E 83 MET cc_start: 0.8633 (mtm) cc_final: 0.8258 (mtp) REVERT: E 140 MET cc_start: 0.9050 (mmm) cc_final: 0.8111 (mmm) REVERT: G 21 MET cc_start: 0.7384 (tmm) cc_final: 0.6989 (tmm) outliers start: 19 outliers final: 15 residues processed: 134 average time/residue: 0.4656 time to fit residues: 67.4844 Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 198 LEU 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 50 LEU 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: 0.0770 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3993 r_free = 0.3993 target = 0.170873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132429 restraints weight = 9548.609| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.22 r_work: 0.3362 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3386 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= 0.122 Angle : 0.513 6.976 12190 Z= 0.276 Chirality : 0.041 0.147 1395 Planarity : 0.004 0.059 1520 Dihedral : 4.472 74.545 1277 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.67 % Allowed : 20.04 % Favored : 78.29 % 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: 0.91 (0.26), residues: 1097 helix: 1.82 (0.26), residues: 408 sheet: -0.10 (0.30), residues: 272 loop : -0.00 (0.32), residues: 417 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 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP B 211 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8984) covalent geometry : angle 0.51305 (12182) SS BOND : bond 0.00261 ( 4) SS BOND : angle 0.74278 ( 8) hydrogen bonds : bond 0.03070 ( 450) hydrogen bonds : angle 4.48031 ( 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 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.318 Fit side-chains REVERT: A 198 MET cc_start: 0.8318 (ttm) cc_final: 0.7950 (ttm) REVERT: B 267 ASP cc_start: 0.8272 (m-30) cc_final: 0.7993 (m-30) REVERT: B 303 ASP cc_start: 0.7620 (m-30) cc_final: 0.7064 (p0) REVERT: B 325 MET cc_start: 0.8815 (tpp) cc_final: 0.8570 (mmm) REVERT: E 83 MET cc_start: 0.8645 (mtm) cc_final: 0.8265 (mtp) REVERT: E 140 MET cc_start: 0.9029 (mmm) cc_final: 0.8104 (mmm) REVERT: G 21 MET cc_start: 0.7403 (tmm) cc_final: 0.7010 (tmm) outliers start: 16 outliers final: 16 residues processed: 131 average time/residue: 0.4499 time to fit residues: 64.1076 Evaluate side-chains 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE 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 50 LEU 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: 0.7980 chunk 91 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3967 r_free = 0.3967 target = 0.168591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130050 restraints weight = 9649.527| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.42 r_work: 0.3239 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8988 Z= 0.175 Angle : 0.553 6.322 12190 Z= 0.297 Chirality : 0.043 0.159 1395 Planarity : 0.004 0.059 1520 Dihedral : 4.651 72.832 1277 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.09 % Allowed : 19.94 % Favored : 77.97 % 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: 0.71 (0.26), residues: 1097 helix: 1.65 (0.26), residues: 408 sheet: -0.26 (0.30), residues: 274 loop : -0.07 (0.32), residues: 415 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 0.015 0.001 PHE R 175 TRP 0.012 0.001 TRP B 99 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8984) covalent geometry : angle 0.55280 (12182) SS BOND : bond 0.00298 ( 4) SS BOND : angle 0.88743 ( 8) hydrogen bonds : bond 0.03368 ( 450) hydrogen bonds : angle 4.66596 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3554.38 seconds wall clock time: 61 minutes 18.58 seconds (3678.58 seconds total)