Starting phenix.real_space_refine on Wed Aug 5 04:21:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t6n_55619/08_2026/9t6n_55619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t6n_55619/08_2026/9t6n_55619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t6n_55619/08_2026/9t6n_55619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t6n_55619/08_2026/9t6n_55619.map" model { file = "/net/cci-nas-00/data/ceres_data/9t6n_55619/08_2026/9t6n_55619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t6n_55619/08_2026/9t6n_55619.cif" } resolution = 3.0 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= 0.002 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 5264 2.51 5 N 1428 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8254 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1706 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3072 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 3 Chain: "D" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3027 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 421 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.43, per 1000 atoms: 0.17 Number of scatterers: 8254 At special positions: 0 Unit cell: (78.3104, 110.656, 120.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 2 15.00 Mg 1 11.99 O 1496 8.00 N 1428 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.53 Conformation dependent library (CDL) restraints added in 310.5 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 64.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.594A pdb=" N PHE B 50 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 51 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 69 through 82 removed outlier: 3.620A pdb=" N GLU B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Proline residue: B 77 - end of helix removed outlier: 3.826A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.688A pdb=" N VAL B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.946A pdb=" N ALA B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.580A pdb=" N LYS B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.546A pdb=" N ALA B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.893A pdb=" N GLU B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.559A pdb=" N ASP B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'C' and resid 103 through 121 removed outlier: 3.630A pdb=" N GLN C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.542A pdb=" N LYS C 130 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.576A pdb=" N GLU C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 4.123A pdb=" N ALA C 173 " --> pdb=" O HIS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 removed outlier: 3.894A pdb=" N LEU C 192 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 209 Processing helix chain 'C' and resid 216 through 238 removed outlier: 3.731A pdb=" N ARG C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP C 234 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 263 removed outlier: 3.860A pdb=" N LEU C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 263 " --> pdb=" O CYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 296 removed outlier: 3.645A pdb=" N ASN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 314 Processing helix chain 'C' and resid 320 through 326 removed outlier: 3.796A pdb=" N GLU C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.848A pdb=" N PHE C 340 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.894A pdb=" N GLN C 361 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.678A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 390 removed outlier: 3.510A pdb=" N ARG C 379 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP C 381 " --> pdb=" O GLN C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.680A pdb=" N ALA C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'D' and resid 5 through 19 Processing helix chain 'D' and resid 21 through 28 removed outlier: 3.703A pdb=" N CYS D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA D 26 " --> pdb=" O GLY D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 57 through 73 removed outlier: 3.846A pdb=" N MET D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 96 removed outlier: 3.854A pdb=" N LYS D 82 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 126 removed outlier: 3.664A pdb=" N ALA D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 4.038A pdb=" N SER D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 166 removed outlier: 4.118A pdb=" N TRP D 166 " --> pdb=" O SER D 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 166' Processing helix chain 'D' and resid 167 through 183 removed outlier: 4.101A pdb=" N LEU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 198 removed outlier: 4.500A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 223 removed outlier: 4.046A pdb=" N PHE D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.772A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 261 removed outlier: 3.515A pdb=" N LYS D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 267 through 274 removed outlier: 3.601A pdb=" N LEU D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 278 removed outlier: 6.011A pdb=" N GLN D 278 " --> pdb=" O HIS D 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 278' Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.612A pdb=" N VAL D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 301 removed outlier: 3.559A pdb=" N HIS D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 317 through 334 Processing helix chain 'D' and resid 340 through 350 removed outlier: 3.701A pdb=" N LEU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 371 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 50 through 63 removed outlier: 3.679A pdb=" N HIS E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.391A pdb=" N LEU B 117 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP B 196 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET B 119 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 85 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 398 through 401 removed outlier: 3.639A pdb=" N SER C 429 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR C 427 " --> pdb=" O GLU C 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 265 through 266 removed outlier: 3.780A pdb=" N MET D 265 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 339 389 hydrogen bonds defined for protein. 1122 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: 0.82 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2692 1.34 - 1.46: 1523 1.46 - 1.58: 4108 1.58 - 1.69: 3 1.69 - 1.81: 97 Bond restraints: 8423 Sorted by residual: bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" CA VAL D 36 " pdb=" CB VAL D 36 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.23e-01 bond pdb=" C GLU B 132 " pdb=" O GLU B 132 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.77e-01 bond pdb=" C THR C 245 " pdb=" O THR C 245 " ideal model delta sigma weight residual 1.236 1.243 -0.007 1.29e-02 6.01e+03 3.24e-01 bond pdb=" CA ILE D 87 " pdb=" CB ILE D 87 " ideal model delta sigma weight residual 1.540 1.546 -0.007 1.17e-02 7.31e+03 3.24e-01 ... (remaining 8418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 11148 1.17 - 2.35: 154 2.35 - 3.52: 43 3.52 - 4.69: 14 4.69 - 5.87: 7 Bond angle restraints: 11366 Sorted by residual: angle pdb=" N PHE B 136 " pdb=" CA PHE B 136 " pdb=" C PHE B 136 " ideal model delta sigma weight residual 111.36 113.56 -2.20 1.09e+00 8.42e-01 4.08e+00 angle pdb=" O2B ADP B 501 " pdb=" PB ADP B 501 " pdb=" O3B ADP B 501 " ideal model delta sigma weight residual 119.90 114.19 5.71 3.00e+00 1.11e-01 3.63e+00 angle pdb=" C1' ADP B 501 " pdb=" C2' ADP B 501 " pdb=" C3' ADP B 501 " ideal model delta sigma weight residual 111.00 105.36 5.64 3.00e+00 1.11e-01 3.54e+00 angle pdb=" C VAL D 88 " pdb=" CA VAL D 88 " pdb=" CB VAL D 88 " ideal model delta sigma weight residual 112.22 109.63 2.59 1.38e+00 5.25e-01 3.51e+00 angle pdb=" N TYR B 133 " pdb=" CA TYR B 133 " pdb=" CB TYR B 133 " ideal model delta sigma weight residual 110.12 112.85 -2.73 1.47e+00 4.63e-01 3.45e+00 ... (remaining 11361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4884 17.82 - 35.63: 199 35.63 - 53.45: 28 53.45 - 71.26: 0 71.26 - 89.08: 5 Dihedral angle restraints: 5116 sinusoidal: 2093 harmonic: 3023 Sorted by residual: dihedral pdb=" CA LEU C 421 " pdb=" C LEU C 421 " pdb=" N THR C 422 " pdb=" CA THR C 422 " ideal model delta harmonic sigma weight residual 180.00 164.38 15.62 0 5.00e+00 4.00e-02 9.76e+00 dihedral pdb=" CB GLU E 59 " pdb=" CG GLU E 59 " pdb=" CD GLU E 59 " pdb=" OE1 GLU E 59 " ideal model delta sinusoidal sigma weight residual 0.00 -79.61 79.61 1 3.00e+01 1.11e-03 8.74e+00 dihedral pdb=" CA GLN D 278 " pdb=" CB GLN D 278 " pdb=" CG GLN D 278 " pdb=" CD GLN D 278 " ideal model delta sinusoidal sigma weight residual 60.00 107.99 -47.99 3 1.50e+01 4.44e-03 8.57e+00 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 773 0.028 - 0.057: 346 0.057 - 0.085: 98 0.085 - 0.113: 40 0.113 - 0.141: 10 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA VAL C 162 " pdb=" N VAL C 162 " pdb=" C VAL C 162 " pdb=" CB VAL C 162 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL B 170 " pdb=" N VAL B 170 " pdb=" C VAL B 170 " pdb=" CB VAL B 170 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE B 168 " pdb=" N ILE B 168 " pdb=" C ILE B 168 " pdb=" CB ILE B 168 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 1264 not shown) Planarity restraints: 1451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 56 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO D 57 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 242 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO C 243 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 133 " 0.012 2.00e-02 2.50e+03 1.17e-02 2.74e+00 pdb=" CG TYR B 133 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 133 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 133 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 133 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 133 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 133 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 133 " -0.002 2.00e-02 2.50e+03 ... (remaining 1448 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 11 2.66 - 3.22: 7419 3.22 - 3.78: 11128 3.78 - 4.34: 15438 4.34 - 4.90: 26666 Nonbonded interactions: 60662 Sorted by model distance: nonbonded pdb=" O1B ADP B 501 " pdb="MG MG B 502 " model vdw 2.097 2.170 nonbonded pdb=" OG1 THR B 96 " pdb="MG MG B 502 " model vdw 2.230 2.170 nonbonded pdb=" O2' ADP B 501 " pdb=" O3' ADP B 501 " model vdw 2.498 2.432 nonbonded pdb=" N ASP C 242 " pdb=" O ASP C 242 " model vdw 2.624 2.496 nonbonded pdb=" N ILE B 154 " pdb=" N LYS B 155 " model vdw 2.627 2.560 ... (remaining 60657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.010 Find NCS groups from input model: 0.030 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:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.002 0.021 8423 Z= 0.085 Angle : 0.434 5.867 11366 Z= 0.227 Chirality : 0.037 0.141 1267 Planarity : 0.003 0.051 1451 Dihedral : 9.937 89.077 3138 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.27), residues: 1002 helix: 1.13 (0.23), residues: 560 sheet: 0.98 (0.73), residues: 66 loop : -0.33 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 67 TYR 0.029 0.001 TYR B 133 PHE 0.019 0.001 PHE C 307 TRP 0.011 0.001 TRP C 220 HIS 0.001 0.000 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.08 ( 8423) covalent geometry : angle 0.43356 / 0.23 (11366) hydrogen bonds : bond 0.22553 / 15.09 ( 389) hydrogen bonds : angle 5.88852 / 4.14 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.348 Fit side-chains REVERT: E 51 ASP cc_start: 0.8779 (p0) cc_final: 0.8506 (p0) REVERT: E 67 MET cc_start: 0.8864 (ttm) cc_final: 0.8514 (ttm) REVERT: E 68 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8808 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.5572 time to fit residues: 33.1022 Evaluate side-chains 49 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 8 GLN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** 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 = 0.3035 r_free = 0.3035 target = 0.053592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.038837 restraints weight = 28576.193| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 3.81 r_work: 0.2426 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 8423 Z= 0.228 Angle : 0.547 7.622 11366 Z= 0.284 Chirality : 0.042 0.137 1267 Planarity : 0.004 0.047 1451 Dihedral : 4.239 46.972 1112 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.56 % Allowed : 3.01 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.28), residues: 1002 helix: 1.25 (0.23), residues: 583 sheet: 1.43 (0.73), residues: 59 loop : -0.38 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 232 TYR 0.009 0.001 TYR B 13 PHE 0.025 0.002 PHE B 99 TRP 0.011 0.001 TRP C 220 HIS 0.003 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 ( 8423) covalent geometry : angle 0.54733 / 0.28 (11366) hydrogen bonds : bond 0.07003 / 4.70 ( 389) hydrogen bonds : angle 4.20377 / 3.01 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.306 Fit side-chains REVERT: B 83 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7886 (mmp) REVERT: E 51 ASP cc_start: 0.8721 (p0) cc_final: 0.8462 (p0) REVERT: E 67 MET cc_start: 0.9095 (ttm) cc_final: 0.8594 (ttm) REVERT: E 68 GLU cc_start: 0.9373 (tm-30) cc_final: 0.8910 (tm-30) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.5831 time to fit residues: 30.9169 Evaluate side-chains 51 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 239 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 0.0170 chunk 22 optimal weight: 6.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 212 GLN ** D 33 HIS ** 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 = 0.3051 r_free = 0.3051 target = 0.054473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.039824 restraints weight = 28410.633| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 3.80 r_work: 0.2449 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8423 Z= 0.151 Angle : 0.479 8.490 11366 Z= 0.244 Chirality : 0.040 0.139 1267 Planarity : 0.003 0.045 1451 Dihedral : 4.180 47.496 1112 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.56 % Allowed : 4.24 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.28), residues: 1002 helix: 1.42 (0.23), residues: 583 sheet: 1.27 (0.74), residues: 58 loop : -0.42 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 232 TYR 0.008 0.001 TYR B 13 PHE 0.020 0.001 PHE C 307 TRP 0.010 0.001 TRP C 220 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 8423) covalent geometry : angle 0.47861 / 0.24 (11366) hydrogen bonds : bond 0.05544 / 3.73 ( 389) hydrogen bonds : angle 3.78194 / 2.70 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.300 Fit side-chains REVERT: B 83 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7966 (mmp) REVERT: E 51 ASP cc_start: 0.8724 (p0) cc_final: 0.8440 (p0) REVERT: E 67 MET cc_start: 0.9081 (ttm) cc_final: 0.8669 (ttm) REVERT: E 68 GLU cc_start: 0.9367 (tm-30) cc_final: 0.8850 (tm-30) outliers start: 5 outliers final: 1 residues processed: 50 average time/residue: 0.5878 time to fit residues: 31.2801 Evaluate side-chains 50 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 239 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.040780 restraints weight = 28789.069| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.53 r_work: 0.2527 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8423 Z= 0.129 Angle : 0.463 8.901 11366 Z= 0.234 Chirality : 0.039 0.139 1267 Planarity : 0.003 0.045 1451 Dihedral : 4.119 47.096 1112 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.22 % Allowed : 5.69 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.28), residues: 1002 helix: 1.58 (0.23), residues: 581 sheet: 1.06 (0.73), residues: 60 loop : -0.35 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 295 TYR 0.007 0.001 TYR B 13 PHE 0.020 0.001 PHE C 307 TRP 0.010 0.001 TRP C 220 HIS 0.002 0.000 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8423) covalent geometry : angle 0.46349 / 0.23 (11366) hydrogen bonds : bond 0.05044 / 3.39 ( 389) hydrogen bonds : angle 3.60837 / 2.58 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.326 Fit side-chains REVERT: B 83 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8350 (mmp) REVERT: E 62 LYS cc_start: 0.8882 (ttpp) cc_final: 0.8679 (ttpp) REVERT: E 67 MET cc_start: 0.8997 (ttm) cc_final: 0.8622 (ttm) REVERT: E 68 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8816 (tm-30) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.6135 time to fit residues: 31.9386 Evaluate side-chains 49 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.055810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041152 restraints weight = 28185.854| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.80 r_work: 0.2494 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8423 Z= 0.096 Angle : 0.445 9.140 11366 Z= 0.222 Chirality : 0.038 0.140 1267 Planarity : 0.003 0.045 1451 Dihedral : 3.955 45.707 1112 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.33 % Allowed : 5.80 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.28), residues: 1002 helix: 1.73 (0.23), residues: 581 sheet: 1.13 (0.74), residues: 60 loop : -0.27 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 232 TYR 0.007 0.001 TYR D 376 PHE 0.020 0.001 PHE C 307 TRP 0.009 0.001 TRP C 220 HIS 0.002 0.000 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 8423) covalent geometry : angle 0.44487 / 0.22 (11366) hydrogen bonds : bond 0.04166 / 2.81 ( 389) hydrogen bonds : angle 3.41310 / 2.44 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.341 Fit side-chains REVERT: B 83 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8240 (mmt) REVERT: D 260 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8865 (mtm) REVERT: E 67 MET cc_start: 0.8921 (ttm) cc_final: 0.8646 (ttm) REVERT: E 68 GLU cc_start: 0.9378 (tm-30) cc_final: 0.8919 (tm-30) outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.6168 time to fit residues: 32.7077 Evaluate side-chains 51 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 50 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 88 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.040980 restraints weight = 28180.474| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.52 r_work: 0.2533 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8423 Z= 0.132 Angle : 0.464 9.364 11366 Z= 0.231 Chirality : 0.039 0.139 1267 Planarity : 0.003 0.044 1451 Dihedral : 3.969 45.273 1112 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.78 % Allowed : 6.02 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.28), residues: 1002 helix: 1.73 (0.23), residues: 581 sheet: 1.00 (0.74), residues: 60 loop : -0.31 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 295 TYR 0.006 0.001 TYR B 13 PHE 0.020 0.001 PHE B 99 TRP 0.009 0.001 TRP C 220 HIS 0.002 0.000 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 8423) covalent geometry : angle 0.46449 / 0.23 (11366) hydrogen bonds : bond 0.04730 / 3.17 ( 389) hydrogen bonds : angle 3.46332 / 2.48 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.221 Fit side-chains REVERT: B 83 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8548 (mmt) REVERT: D 250 MET cc_start: 0.8897 (ttm) cc_final: 0.8694 (mtm) REVERT: E 18 GLU cc_start: 0.6904 (pm20) cc_final: 0.6669 (pm20) REVERT: E 51 ASP cc_start: 0.8626 (p0) cc_final: 0.8402 (p0) REVERT: E 66 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8653 (mmmm) REVERT: E 68 GLU cc_start: 0.9349 (tm-30) cc_final: 0.8922 (tm-30) outliers start: 7 outliers final: 1 residues processed: 50 average time/residue: 0.6282 time to fit residues: 33.2731 Evaluate side-chains 50 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 239 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.042356 restraints weight = 28408.337| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.54 r_work: 0.2571 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8423 Z= 0.086 Angle : 0.440 9.656 11366 Z= 0.217 Chirality : 0.037 0.140 1267 Planarity : 0.003 0.044 1451 Dihedral : 3.819 44.466 1112 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.56 % Allowed : 6.47 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.28), residues: 1002 helix: 1.87 (0.23), residues: 581 sheet: 1.02 (0.74), residues: 60 loop : -0.25 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 295 TYR 0.007 0.001 TYR D 376 PHE 0.019 0.001 PHE C 307 TRP 0.009 0.001 TRP C 220 HIS 0.002 0.000 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 ( 8423) covalent geometry : angle 0.44046 / 0.22 (11366) hydrogen bonds : bond 0.03704 / 2.51 ( 389) hydrogen bonds : angle 3.27980 / 2.34 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.347 Fit side-chains REVERT: B 83 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8517 (mmt) REVERT: E 18 GLU cc_start: 0.6958 (pm20) cc_final: 0.6748 (pm20) REVERT: E 51 ASP cc_start: 0.8663 (p0) cc_final: 0.8419 (p0) REVERT: E 66 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8619 (mmmm) REVERT: E 68 GLU cc_start: 0.9349 (tm-30) cc_final: 0.8897 (pp20) outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 0.5974 time to fit residues: 30.4260 Evaluate side-chains 50 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain D residue 370 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.039324 restraints weight = 28696.039| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 3.53 r_work: 0.2476 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 8423 Z= 0.225 Angle : 0.539 9.694 11366 Z= 0.273 Chirality : 0.042 0.138 1267 Planarity : 0.004 0.044 1451 Dihedral : 4.278 47.247 1112 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.56 % Allowed : 6.80 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.28), residues: 1002 helix: 1.54 (0.23), residues: 586 sheet: 0.87 (0.74), residues: 58 loop : -0.41 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 323 TYR 0.008 0.001 TYR D 330 PHE 0.027 0.002 PHE B 99 TRP 0.008 0.001 TRP C 220 HIS 0.003 0.001 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 ( 8423) covalent geometry : angle 0.53945 / 0.27 (11366) hydrogen bonds : bond 0.06477 / 4.30 ( 389) hydrogen bonds : angle 3.73320 / 2.66 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.260 Fit side-chains REVERT: B 83 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8269 (mmp) REVERT: E 51 ASP cc_start: 0.8734 (p0) cc_final: 0.8491 (p0) REVERT: E 68 GLU cc_start: 0.9355 (tm-30) cc_final: 0.8875 (pp20) outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 0.6370 time to fit residues: 32.9817 Evaluate side-chains 49 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 239 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042987 restraints weight = 28781.728| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.82 r_work: 0.2599 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8423 Z= 0.108 Angle : 0.469 10.119 11366 Z= 0.234 Chirality : 0.038 0.140 1267 Planarity : 0.003 0.044 1451 Dihedral : 4.066 46.364 1112 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.33 % Allowed : 7.13 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.28), residues: 1002 helix: 1.75 (0.23), residues: 588 sheet: 0.89 (0.73), residues: 60 loop : -0.30 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 135 TYR 0.007 0.001 TYR D 376 PHE 0.020 0.001 PHE C 307 TRP 0.010 0.001 TRP C 220 HIS 0.003 0.000 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8423) covalent geometry : angle 0.46860 / 0.23 (11366) hydrogen bonds : bond 0.04403 / 2.96 ( 389) hydrogen bonds : angle 3.41553 / 2.43 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.339 Fit side-chains REVERT: B 83 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (mmt) REVERT: E 51 ASP cc_start: 0.8699 (p0) cc_final: 0.8439 (p0) REVERT: E 66 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8207 (mmmm) REVERT: E 68 GLU cc_start: 0.9340 (tm-30) cc_final: 0.8836 (pp20) outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.6747 time to fit residues: 35.0501 Evaluate side-chains 50 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 56 optimal weight: 0.3980 chunk 23 optimal weight: 0.0040 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.4930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 244 GLN ** D 33 HIS ** 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 = 0.3156 r_free = 0.3156 target = 0.057490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.043633 restraints weight = 28040.053| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.49 r_work: 0.2627 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8423 Z= 0.082 Angle : 0.444 10.309 11366 Z= 0.217 Chirality : 0.037 0.139 1267 Planarity : 0.003 0.046 1451 Dihedral : 3.680 42.425 1112 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.11 % Allowed : 7.36 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.28), residues: 1002 helix: 1.90 (0.23), residues: 584 sheet: 1.04 (0.74), residues: 60 loop : -0.19 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 295 TYR 0.007 0.001 TYR D 376 PHE 0.019 0.001 PHE C 307 TRP 0.010 0.001 TRP C 220 HIS 0.003 0.000 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.08 ( 8423) covalent geometry : angle 0.44445 / 0.22 (11366) hydrogen bonds : bond 0.03070 / 2.11 ( 389) hydrogen bonds : angle 3.18087 / 2.26 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.215 Fit side-chains REVERT: B 83 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (mmt) REVERT: B 247 MET cc_start: 0.8105 (ttt) cc_final: 0.7888 (ttt) REVERT: E 67 MET cc_start: 0.8648 (ttm) cc_final: 0.8381 (ttm) REVERT: E 68 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8769 (pp20) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.6066 time to fit residues: 31.5428 Evaluate side-chains 49 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 244 GLN ** D 33 HIS ** 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 = 0.3135 r_free = 0.3135 target = 0.056660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.042790 restraints weight = 28214.579| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.48 r_work: 0.2590 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8423 Z= 0.093 Angle : 0.453 10.315 11366 Z= 0.222 Chirality : 0.037 0.139 1267 Planarity : 0.003 0.045 1451 Dihedral : 3.662 42.456 1112 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.22 % Allowed : 6.80 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.28), residues: 1002 helix: 1.92 (0.23), residues: 585 sheet: 1.03 (0.73), residues: 60 loop : -0.15 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 227 TYR 0.007 0.001 TYR D 81 PHE 0.018 0.001 PHE C 307 TRP 0.008 0.001 TRP C 220 HIS 0.003 0.000 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 ( 8423) covalent geometry : angle 0.45282 / 0.22 (11366) hydrogen bonds : bond 0.03592 / 2.43 ( 389) hydrogen bonds : angle 3.19448 / 2.27 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.03 seconds wall clock time: 32 minutes 14.56 seconds (1934.56 seconds total)