Starting phenix.real_space_refine on Thu Jun 4 03:01:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x20_66468/06_2026/9x20_66468.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x20_66468/06_2026/9x20_66468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x20_66468/06_2026/9x20_66468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x20_66468/06_2026/9x20_66468.map" model { file = "/net/cci-nas-00/data/ceres_data/9x20_66468/06_2026/9x20_66468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x20_66468/06_2026/9x20_66468.cif" } resolution = 3.18 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= 0.028 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 65 5.16 5 C 6373 2.51 5 N 1688 2.21 5 O 1855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9981 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "R" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3135 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 436 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.26 Number of scatterers: 9981 At special positions: 0 Unit cell: (101.352, 119.48, 168.096, 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 65 16.00 O 1855 8.00 N 1688 7.00 C 6373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " 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: 0.88 Conformation dependent library (CDL) restraints added in 372.6 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 16 sheets defined 40.2% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'P' and resid 8 through 35 Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 112 through 116 removed outlier: 3.616A pdb=" N ASN R 115 " --> pdb=" O GLN R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 169 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.959A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 215 Processing helix chain 'R' and resid 219 through 223 removed outlier: 3.619A pdb=" N ASP R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 256 removed outlier: 4.136A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 274 Processing helix chain 'R' and resid 275 through 291 removed outlier: 3.550A pdb=" N LEU R 279 " --> pdb=" O GLY R 275 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.599A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.888A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 357 Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.383A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 376 removed outlier: 3.767A pdb=" N ALA R 375 " --> pdb=" O ASP R 372 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG R 376 " --> pdb=" O GLU R 373 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 404 removed outlier: 3.964A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.740A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.619A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.057A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.557A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.529A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.927A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.574A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.687A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.536A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.691A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.773A 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 62 through 65 removed outlier: 3.520A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.644A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 221 through 225 Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.054A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.655A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.960A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.769A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 148 through 153 removed outlier: 5.726A pdb=" N CYS B 149 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER B 160 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE B 151 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 158 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.135A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.831A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.512A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.534A pdb=" N ARG E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.735A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR E 94 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.735A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR E 94 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB6, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.729A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 195 " --> pdb=" O TYR E 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 156 through 158 removed outlier: 3.675A pdb=" N SER E 207 " --> pdb=" O THR E 214 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1365 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: 1.68 Time building geometry restraints manager: 1.18 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: 3209 1.34 - 1.46: 2552 1.46 - 1.58: 4356 1.58 - 1.70: 1 1.70 - 1.81: 91 Bond restraints: 10209 Sorted by residual: bond pdb=" CB PRO C 60 " pdb=" CG PRO C 60 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.54e+00 bond pdb=" N PRO C 60 " pdb=" CA PRO C 60 " ideal model delta sigma weight residual 1.474 1.462 0.012 7.40e-03 1.83e+04 2.70e+00 bond pdb=" N GLY E 66 " pdb=" CA GLY E 66 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.05e+00 bond pdb=" CA VAL R 276 " pdb=" C VAL R 276 " ideal model delta sigma weight residual 1.520 1.528 -0.008 8.80e-03 1.29e+04 9.02e-01 bond pdb=" CG PRO C 60 " pdb=" CD PRO C 60 " ideal model delta sigma weight residual 1.503 1.534 -0.031 3.40e-02 8.65e+02 8.44e-01 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 13619 1.57 - 3.15: 181 3.15 - 4.72: 27 4.72 - 6.30: 8 6.30 - 7.87: 3 Bond angle restraints: 13838 Sorted by residual: angle pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" CD PRO C 60 " ideal model delta sigma weight residual 112.00 107.31 4.69 1.40e+00 5.10e-01 1.12e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 122.33 -2.09 6.30e-01 2.52e+00 1.10e+01 angle pdb=" C VAL R 276 " pdb=" CA VAL R 276 " pdb=" CB VAL R 276 " ideal model delta sigma weight residual 114.35 111.19 3.16 1.06e+00 8.90e-01 8.89e+00 angle pdb=" CA GLU P 27 " pdb=" CB GLU P 27 " pdb=" CG GLU P 27 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.67e+00 angle pdb=" CB MET E 83 " pdb=" CG MET E 83 " pdb=" SD MET E 83 " ideal model delta sigma weight residual 112.70 120.57 -7.87 3.00e+00 1.11e-01 6.88e+00 ... (remaining 13833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5243 17.64 - 35.29: 592 35.29 - 52.93: 156 52.93 - 70.58: 18 70.58 - 88.22: 8 Dihedral angle restraints: 6017 sinusoidal: 2349 harmonic: 3668 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 61.51 31.49 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" CA TRP R 214 " pdb=" C TRP R 214 " pdb=" N ASP R 215 " pdb=" CA ASP R 215 " ideal model delta harmonic sigma weight residual -180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual -86.00 -114.62 28.62 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 6014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1019 0.030 - 0.061: 353 0.061 - 0.091: 96 0.091 - 0.121: 65 0.121 - 0.152: 5 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 1535 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO C 53 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.18e+00 pdb=" N PRO R 277 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 39 " -0.009 2.00e-02 2.50e+03 1.11e-02 3.11e+00 pdb=" CG TRP R 39 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP R 39 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP R 39 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 39 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 39 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 39 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 39 " 0.000 2.00e-02 2.50e+03 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 378 2.72 - 3.26: 9737 3.26 - 3.81: 16427 3.81 - 4.35: 19613 4.35 - 4.90: 34227 Nonbonded interactions: 80382 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.181 3.040 nonbonded pdb=" OE2 GLU P 9 " pdb=" OH TYR R 152 " model vdw 2.204 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.206 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.235 3.040 ... (remaining 80377 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: 1.430 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.140 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 0.107 10213 Z= 0.109 Angle : 0.484 7.871 13846 Z= 0.268 Chirality : 0.038 0.152 1538 Planarity : 0.003 0.072 1749 Dihedral : 15.806 88.221 3639 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 0.19 % Allowed : 22.51 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.26 (0.25), residues: 1242 helix: 2.62 (0.25), residues: 432 sheet: 0.29 (0.31), residues: 277 loop : -0.34 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.016 0.001 TYR R 148 PHE 0.021 0.001 PHE B 241 TRP 0.030 0.001 TRP R 39 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10209) covalent geometry : angle 0.48429 / 0.27 (13838) SS BOND : bond 0.00245 / 0.12 ( 4) SS BOND : angle 0.61428 / 0.59 ( 8) hydrogen bonds : bond 0.21200 / 14.37 ( 486) hydrogen bonds : angle 6.34803 / 4.28 ( 1365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 240 MET cc_start: 0.4972 (tpp) cc_final: 0.4516 (mmp) REVERT: E 231 MET cc_start: 0.5213 (mmm) cc_final: 0.4521 (tpp) outliers start: 2 outliers final: 1 residues processed: 132 average time/residue: 0.1067 time to fit residues: 20.0898 Evaluate side-chains 127 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.0370 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 50.0000 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 331 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.224320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153845 restraints weight = 10698.034| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.59 r_work: 0.3570 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10213 Z= 0.162 Angle : 0.528 6.338 13846 Z= 0.285 Chirality : 0.041 0.150 1538 Planarity : 0.004 0.058 1749 Dihedral : 3.705 19.587 1372 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 3.53 % Allowed : 19.91 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.24), residues: 1242 helix: 2.57 (0.25), residues: 438 sheet: 0.47 (0.32), residues: 270 loop : -0.53 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.020 0.001 TYR R 148 PHE 0.019 0.001 PHE A 189 TRP 0.018 0.002 TRP R 39 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10209) covalent geometry : angle 0.52788 / 0.28 (13838) SS BOND : bond 0.00321 / 0.16 ( 4) SS BOND : angle 0.87581 / 0.77 ( 8) hydrogen bonds : bond 0.04751 / 3.21 ( 486) hydrogen bonds : angle 4.69077 / 3.23 ( 1365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.381 Fit side-chains REVERT: A 240 MET cc_start: 0.5302 (tpp) cc_final: 0.4789 (mmp) REVERT: A 304 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7795 (tt0) REVERT: E 83 MET cc_start: 0.8281 (mmm) cc_final: 0.8009 (mmm) REVERT: E 98 ARG cc_start: 0.6969 (ptt90) cc_final: 0.6515 (ptt90) REVERT: E 231 MET cc_start: 0.5445 (mmm) cc_final: 0.5083 (tpp) outliers start: 38 outliers final: 27 residues processed: 168 average time/residue: 0.1023 time to fit residues: 24.6046 Evaluate side-chains 158 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 190 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 331 ASN A 333 GLN B 75 GLN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.225886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.156339 restraints weight = 10771.436| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.66 r_work: 0.3584 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10213 Z= 0.112 Angle : 0.477 6.378 13846 Z= 0.256 Chirality : 0.039 0.149 1538 Planarity : 0.003 0.053 1749 Dihedral : 3.664 24.291 1371 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 3.63 % Allowed : 20.84 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.29 (0.24), residues: 1242 helix: 2.65 (0.25), residues: 447 sheet: 0.46 (0.31), residues: 267 loop : -0.50 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.016 0.001 TYR R 148 PHE 0.017 0.001 PHE A 189 TRP 0.017 0.001 TRP R 39 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10209) covalent geometry : angle 0.47711 / 0.26 (13838) SS BOND : bond 0.00273 / 0.14 ( 4) SS BOND : angle 0.82365 / 0.75 ( 8) hydrogen bonds : bond 0.03756 / 2.54 ( 486) hydrogen bonds : angle 4.18234 / 2.91 ( 1365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.391 Fit side-chains REVERT: A 240 MET cc_start: 0.5505 (tpp) cc_final: 0.4968 (mmp) REVERT: A 345 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6711 (mttp) REVERT: B 52 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7657 (ptp-110) REVERT: B 75 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6328 (tt0) REVERT: E 98 ARG cc_start: 0.6900 (ptt90) cc_final: 0.6608 (ptt90) REVERT: E 161 ARG cc_start: 0.5810 (tpt170) cc_final: 0.5474 (tpt170) outliers start: 39 outliers final: 23 residues processed: 172 average time/residue: 0.0987 time to fit residues: 24.6139 Evaluate side-chains 159 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.222925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146049 restraints weight = 10896.505| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.40 r_work: 0.3474 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10213 Z= 0.168 Angle : 0.521 6.423 13846 Z= 0.277 Chirality : 0.041 0.146 1538 Planarity : 0.004 0.051 1749 Dihedral : 3.813 25.058 1371 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 5.12 % Allowed : 20.37 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.24 (0.24), residues: 1242 helix: 2.62 (0.24), residues: 438 sheet: 0.43 (0.32), residues: 267 loop : -0.48 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 161 TYR 0.021 0.002 TYR R 148 PHE 0.017 0.002 PHE A 189 TRP 0.020 0.001 TRP R 39 HIS 0.004 0.001 HIS P 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (10209) covalent geometry : angle 0.52105 / 0.28 (13838) SS BOND : bond 0.00355 / 0.18 ( 4) SS BOND : angle 0.90325 / 0.81 ( 8) hydrogen bonds : bond 0.03823 / 2.59 ( 486) hydrogen bonds : angle 4.16406 / 2.90 ( 1365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.410 Fit side-chains REVERT: P 27 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: R 418 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6763 (mm-30) REVERT: A 240 MET cc_start: 0.5511 (tpp) cc_final: 0.4980 (mmp) REVERT: A 309 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: A 345 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6939 (mttp) REVERT: B 75 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6743 (tt0) REVERT: E 98 ARG cc_start: 0.7061 (ptt90) cc_final: 0.6660 (ptt90) outliers start: 55 outliers final: 37 residues processed: 177 average time/residue: 0.0980 time to fit residues: 25.0528 Evaluate side-chains 171 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.225325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.155763 restraints weight = 10757.676| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.59 r_work: 0.3590 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10213 Z= 0.113 Angle : 0.486 6.552 13846 Z= 0.258 Chirality : 0.040 0.153 1538 Planarity : 0.003 0.049 1749 Dihedral : 3.716 24.614 1371 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 4.65 % Allowed : 21.21 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.37 (0.25), residues: 1242 helix: 2.77 (0.24), residues: 441 sheet: 0.47 (0.32), residues: 263 loop : -0.45 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.023 0.001 TYR R 402 PHE 0.017 0.001 PHE A 189 TRP 0.020 0.001 TRP R 39 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10209) covalent geometry : angle 0.48541 / 0.26 (13838) SS BOND : bond 0.00276 / 0.14 ( 4) SS BOND : angle 0.81028 / 0.74 ( 8) hydrogen bonds : bond 0.03466 / 2.34 ( 486) hydrogen bonds : angle 4.00585 / 2.80 ( 1365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: P 27 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: R 418 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 240 MET cc_start: 0.5488 (tpp) cc_final: 0.5132 (mmp) REVERT: A 345 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6910 (mttp) REVERT: B 52 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7789 (ptp-110) REVERT: B 75 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6812 (tt0) REVERT: B 266 HIS cc_start: 0.5591 (OUTLIER) cc_final: 0.4209 (t-90) REVERT: E 98 ARG cc_start: 0.7090 (ptt90) cc_final: 0.6747 (ptt90) REVERT: E 238 LEU cc_start: 0.3211 (OUTLIER) cc_final: 0.3000 (mt) outliers start: 50 outliers final: 37 residues processed: 169 average time/residue: 0.1018 time to fit residues: 24.5901 Evaluate side-chains 172 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 123 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.221083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140977 restraints weight = 10857.142| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.38 r_work: 0.3469 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10213 Z= 0.194 Angle : 0.543 7.711 13846 Z= 0.287 Chirality : 0.042 0.150 1538 Planarity : 0.004 0.052 1749 Dihedral : 3.935 24.984 1371 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 5.21 % Allowed : 21.58 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.14 (0.24), residues: 1242 helix: 2.51 (0.24), residues: 439 sheet: 0.36 (0.32), residues: 263 loop : -0.50 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.022 0.002 TYR R 148 PHE 0.017 0.002 PHE A 189 TRP 0.024 0.002 TRP R 39 HIS 0.005 0.001 HIS P 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (10209) covalent geometry : angle 0.54242 / 0.29 (13838) SS BOND : bond 0.00394 / 0.20 ( 4) SS BOND : angle 0.91090 / 0.82 ( 8) hydrogen bonds : bond 0.03829 / 2.61 ( 486) hydrogen bonds : angle 4.12441 / 2.88 ( 1365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 0.398 Fit side-chains REVERT: P 27 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: R 418 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 240 MET cc_start: 0.5592 (tpp) cc_final: 0.5245 (mmp) REVERT: A 345 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6883 (mttp) REVERT: B 49 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7179 (tpp-160) REVERT: B 75 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: B 266 HIS cc_start: 0.5648 (OUTLIER) cc_final: 0.4257 (t-90) REVERT: E 98 ARG cc_start: 0.7091 (ptt90) cc_final: 0.6707 (ptt90) REVERT: E 238 LEU cc_start: 0.3261 (OUTLIER) cc_final: 0.3017 (mt) outliers start: 56 outliers final: 42 residues processed: 175 average time/residue: 0.1008 time to fit residues: 25.4500 Evaluate side-chains 179 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 121 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 50.0000 chunk 101 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.219104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144178 restraints weight = 10943.627| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.30 r_work: 0.3461 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10213 Z= 0.239 Angle : 0.584 8.874 13846 Z= 0.309 Chirality : 0.043 0.158 1538 Planarity : 0.004 0.054 1749 Dihedral : 4.140 25.009 1371 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 6.60 % Allowed : 20.93 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.90 (0.24), residues: 1242 helix: 2.23 (0.24), residues: 439 sheet: 0.17 (0.32), residues: 263 loop : -0.53 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.025 0.002 TYR R 148 PHE 0.019 0.002 PHE B 241 TRP 0.025 0.002 TRP R 39 HIS 0.006 0.001 HIS P 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (10209) covalent geometry : angle 0.58373 / 0.31 (13838) SS BOND : bond 0.00434 / 0.22 ( 4) SS BOND : angle 0.95198 / 0.85 ( 8) hydrogen bonds : bond 0.04070 / 2.77 ( 486) hydrogen bonds : angle 4.25815 / 2.98 ( 1365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 132 time to evaluate : 0.396 Fit side-chains REVERT: P 27 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: R 418 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 240 MET cc_start: 0.5681 (tpp) cc_final: 0.5344 (mmp) REVERT: A 345 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7000 (mttp) REVERT: B 42 ARG cc_start: 0.7876 (tpt90) cc_final: 0.7670 (tmt-80) REVERT: B 49 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7196 (tpp-160) REVERT: B 75 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: B 266 HIS cc_start: 0.5689 (OUTLIER) cc_final: 0.4346 (t-90) REVERT: E 29 PHE cc_start: 0.7892 (t80) cc_final: 0.7674 (t80) REVERT: E 98 ARG cc_start: 0.7184 (ptt90) cc_final: 0.6743 (ptt90) REVERT: E 238 LEU cc_start: 0.3470 (OUTLIER) cc_final: 0.3232 (mt) outliers start: 71 outliers final: 50 residues processed: 186 average time/residue: 0.0929 time to fit residues: 25.1742 Evaluate side-chains 185 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 129 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 30.0000 chunk 14 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 50.0000 chunk 73 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.223632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154461 restraints weight = 10800.504| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.68 r_work: 0.3563 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10213 Z= 0.116 Angle : 0.504 7.616 13846 Z= 0.266 Chirality : 0.040 0.157 1538 Planarity : 0.004 0.052 1749 Dihedral : 3.903 23.300 1371 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 4.65 % Allowed : 23.07 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1242 helix: 2.66 (0.25), residues: 439 sheet: 0.19 (0.32), residues: 276 loop : -0.48 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.026 0.001 TYR A 230 PHE 0.021 0.001 PHE B 241 TRP 0.026 0.001 TRP R 39 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10209) covalent geometry : angle 0.50361 / 0.27 (13838) SS BOND : bond 0.00284 / 0.14 ( 4) SS BOND : angle 0.84532 / 0.79 ( 8) hydrogen bonds : bond 0.03455 / 2.33 ( 486) hydrogen bonds : angle 4.00572 / 2.81 ( 1365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.392 Fit side-chains REVERT: P 27 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: R 213 GLN cc_start: 0.7513 (mt0) cc_final: 0.7005 (mt0) REVERT: R 418 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 240 MET cc_start: 0.5622 (tpp) cc_final: 0.5332 (mmp) REVERT: A 345 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6822 (mttp) REVERT: B 49 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7147 (tpp-160) REVERT: B 52 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7582 (ptp-110) REVERT: B 266 HIS cc_start: 0.5653 (OUTLIER) cc_final: 0.4309 (t-90) REVERT: B 303 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: E 98 ARG cc_start: 0.7172 (ptt90) cc_final: 0.6818 (ptt90) REVERT: E 238 LEU cc_start: 0.3282 (OUTLIER) cc_final: 0.3023 (mt) outliers start: 50 outliers final: 33 residues processed: 168 average time/residue: 0.0955 time to fit residues: 23.2606 Evaluate side-chains 170 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.223942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.146074 restraints weight = 10783.469| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.16 r_work: 0.3547 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10213 Z= 0.114 Angle : 0.498 8.644 13846 Z= 0.260 Chirality : 0.040 0.160 1538 Planarity : 0.004 0.052 1749 Dihedral : 3.812 22.240 1371 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 3.91 % Allowed : 23.91 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.35 (0.25), residues: 1242 helix: 2.77 (0.25), residues: 442 sheet: 0.28 (0.32), residues: 278 loop : -0.39 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.024 0.001 TYR A 230 PHE 0.021 0.001 PHE E 29 TRP 0.027 0.001 TRP R 39 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10209) covalent geometry : angle 0.49774 / 0.26 (13838) SS BOND : bond 0.00275 / 0.14 ( 4) SS BOND : angle 0.78245 / 0.72 ( 8) hydrogen bonds : bond 0.03320 / 2.25 ( 486) hydrogen bonds : angle 3.91691 / 2.76 ( 1365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.416 Fit side-chains REVERT: P 27 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: R 213 GLN cc_start: 0.7478 (mt0) cc_final: 0.6923 (mt0) REVERT: R 413 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: R 418 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 240 MET cc_start: 0.5692 (tpp) cc_final: 0.5423 (mmp) REVERT: A 345 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6847 (mttp) REVERT: B 49 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7151 (tpp-160) REVERT: B 266 HIS cc_start: 0.5741 (OUTLIER) cc_final: 0.4383 (t-90) REVERT: B 303 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: E 98 ARG cc_start: 0.7143 (ptt90) cc_final: 0.6886 (ptt90) outliers start: 42 outliers final: 31 residues processed: 175 average time/residue: 0.0985 time to fit residues: 24.9957 Evaluate side-chains 178 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 193 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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 = 0.4543 r_free = 0.4543 target = 0.221892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142655 restraints weight = 10809.110| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.25 r_work: 0.3488 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10213 Z= 0.155 Angle : 0.533 8.827 13846 Z= 0.278 Chirality : 0.041 0.153 1538 Planarity : 0.004 0.052 1749 Dihedral : 3.933 22.708 1371 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 3.81 % Allowed : 24.19 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.28 (0.25), residues: 1242 helix: 2.67 (0.24), residues: 441 sheet: 0.27 (0.32), residues: 276 loop : -0.38 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.025 0.002 TYR A 230 PHE 0.021 0.002 PHE E 29 TRP 0.026 0.001 TRP R 39 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (10209) covalent geometry : angle 0.53224 / 0.28 (13838) SS BOND : bond 0.00423 / 0.21 ( 4) SS BOND : angle 0.95204 / 0.79 ( 8) hydrogen bonds : bond 0.03518 / 2.39 ( 486) hydrogen bonds : angle 4.02707 / 2.82 ( 1365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.331 Fit side-chains REVERT: P 27 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: R 213 GLN cc_start: 0.7425 (mt0) cc_final: 0.6861 (mt0) REVERT: R 418 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6995 (mm-30) REVERT: A 240 MET cc_start: 0.5788 (tpp) cc_final: 0.5450 (mmp) REVERT: A 345 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6858 (mttp) REVERT: B 49 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7190 (tpp-160) REVERT: B 266 HIS cc_start: 0.5671 (OUTLIER) cc_final: 0.4384 (t-90) REVERT: B 303 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: E 98 ARG cc_start: 0.7195 (ptt90) cc_final: 0.6910 (ptt90) outliers start: 41 outliers final: 35 residues processed: 171 average time/residue: 0.0912 time to fit residues: 22.6537 Evaluate side-chains 180 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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 = 0.4555 r_free = 0.4555 target = 0.223668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143302 restraints weight = 10851.246| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.07 r_work: 0.3535 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10213 Z= 0.119 Angle : 0.514 11.746 13846 Z= 0.266 Chirality : 0.040 0.154 1538 Planarity : 0.004 0.052 1749 Dihedral : 3.858 21.997 1371 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 3.91 % Allowed : 24.19 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.40 (0.25), residues: 1242 helix: 2.78 (0.24), residues: 442 sheet: 0.34 (0.32), residues: 274 loop : -0.34 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.025 0.001 TYR A 230 PHE 0.021 0.001 PHE E 29 TRP 0.025 0.001 TRP R 39 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10209) covalent geometry : angle 0.51389 / 0.27 (13838) SS BOND : bond 0.00349 / 0.17 ( 4) SS BOND : angle 0.89984 / 0.78 ( 8) hydrogen bonds : bond 0.03325 / 2.25 ( 486) hydrogen bonds : angle 4.01325 / 2.80 ( 1365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4477.93 seconds wall clock time: 77 minutes 2.82 seconds (4622.82 seconds total)