Starting phenix.real_space_refine on Thu Jul 2 07:22:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk5_34846/07_2026/8hk5_34846.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 57 5.16 5 C 4861 2.51 5 N 1303 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7604 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain: "B" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 573 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1809 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2509 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 356 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.23 Number of scatterers: 7604 At special positions: 0 Unit cell: (84.048, 99.704, 147.496, 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 57 16.00 O 1383 8.00 N 1303 7.00 C 4861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 47 " distance=1.99 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 54 " distance=2.02 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 55 " distance=2.05 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: 0.67 Conformation dependent library (CDL) restraints added in 462.4 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 47.6% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 34 through 66 Processing helix chain 'A' and resid 70 through 88 removed outlier: 4.331A pdb=" N TRP A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.606A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 140 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 149 through 174 removed outlier: 3.591A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 211 through 231 Processing helix chain 'A' and resid 237 through 266 removed outlier: 4.393A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.697A pdb=" N LEU A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.938A pdb=" N CYS A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.706A pdb=" N ARG A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.605A pdb=" N ILE B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 27 Processing helix chain 'B' and resid 33 through 40 removed outlier: 4.399A pdb=" N ARG B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 Processing helix chain 'C' and resid 6 through 33 removed outlier: 4.135A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.248A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.714A pdb=" N LEU C 232 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.644A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.665A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 14 through 26 Processing helix chain 'D' and resid 29 through 34 removed outlier: 3.962A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.548A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 180 Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.976A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 4.012A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.632A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 7.193A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 134 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.927A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.795A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.421A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 6.420A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE D 278 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU D 284 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1152 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: 1.06 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1239 1.31 - 1.44: 2067 1.44 - 1.57: 4372 1.57 - 1.70: 0 1.70 - 1.83: 76 Bond restraints: 7754 Sorted by residual: bond pdb=" CA TYR B 23 " pdb=" C TYR B 23 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" C CYS B 34 " pdb=" O CYS B 34 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.16e-02 7.43e+03 1.86e+01 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.459 1.407 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" N ASP D 291 " pdb=" CA ASP D 291 " ideal model delta sigma weight residual 1.462 1.417 0.045 1.15e-02 7.56e+03 1.53e+01 bond pdb=" N ARG B 37 " pdb=" CA ARG B 37 " ideal model delta sigma weight residual 1.459 1.414 0.046 1.20e-02 6.94e+03 1.44e+01 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 10306 1.47 - 2.95: 135 2.95 - 4.42: 46 4.42 - 5.89: 3 5.89 - 7.37: 5 Bond angle restraints: 10495 Sorted by residual: angle pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" C GLU A 180 " ideal model delta sigma weight residual 109.24 101.90 7.34 1.63e+00 3.76e-01 2.03e+01 angle pdb=" N TYR B 23 " pdb=" CA TYR B 23 " pdb=" C TYR B 23 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" O GLU B 32 " pdb=" C GLU B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 123.19 118.62 4.57 1.30e+00 5.92e-01 1.24e+01 angle pdb=" CA GLU B 32 " pdb=" C GLU B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 115.63 120.52 -4.89 1.51e+00 4.39e-01 1.05e+01 angle pdb=" CA CYS B 55 " pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " ideal model delta sigma weight residual 114.40 121.77 -7.37 2.30e+00 1.89e-01 1.03e+01 ... (remaining 10490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 4293 16.04 - 32.08: 278 32.08 - 48.12: 51 48.12 - 64.17: 13 64.17 - 80.21: 7 Dihedral angle restraints: 4642 sinusoidal: 1826 harmonic: 2816 Sorted by residual: dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -112.86 26.86 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CG ARG B 37 " pdb=" CD ARG B 37 " pdb=" NE ARG B 37 " pdb=" CZ ARG B 37 " ideal model delta sinusoidal sigma weight residual 180.00 137.02 42.98 2 1.50e+01 4.44e-03 9.92e+00 ... (remaining 4639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1075 0.064 - 0.128: 128 0.128 - 0.192: 4 0.192 - 0.256: 0 0.256 - 0.320: 2 Chirality restraints: 1209 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA CYS B 22 " pdb=" N CYS B 22 " pdb=" C CYS B 22 " pdb=" CB CYS B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB THR C 329 " pdb=" CA THR C 329 " pdb=" OG1 THR C 329 " pdb=" CG2 THR C 329 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1206 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 310 " -0.192 9.50e-02 1.11e+02 8.61e-02 4.55e+00 pdb=" NE ARG A 310 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 310 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 310 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 21 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C CYS B 21 " 0.025 2.00e-02 2.50e+03 pdb=" O CYS B 21 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS B 22 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 32 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C GLU B 32 " -0.020 2.00e-02 2.50e+03 pdb=" O GLU B 32 " 0.007 2.00e-02 2.50e+03 pdb=" N THR B 33 " 0.007 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 91 2.64 - 3.20: 7100 3.20 - 3.77: 11623 3.77 - 4.33: 16324 4.33 - 4.90: 26972 Nonbonded interactions: 62110 Sorted by model distance: nonbonded pdb=" OG SER D 281 " pdb=" OD2 ASP G 48 " model vdw 2.073 3.040 nonbonded pdb=" OG SER D 147 " pdb=" O MET D 188 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR D 274 " pdb=" OD1 ASP D 290 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP C 251 " pdb=" ND2 ASN C 255 " model vdw 2.243 3.120 nonbonded pdb=" OH TYR A 300 " pdb=" NH1 ARG A 310 " model vdw 2.249 3.120 ... (remaining 62105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7757 Z= 0.219 Angle : 0.630 33.924 10501 Z= 0.356 Chirality : 0.040 0.320 1209 Planarity : 0.003 0.086 1319 Dihedral : 11.846 80.207 2803 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.26), residues: 955 helix: 0.58 (0.24), residues: 436 sheet: -0.04 (0.38), residues: 189 loop : -1.36 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.005 0.000 TYR C 296 PHE 0.015 0.001 PHE D 234 TRP 0.004 0.000 TRP A 74 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.22 ( 7754) covalent geometry : angle 0.50461 / 0.31 (10495) SS BOND : bond 0.02601 / 1.35 ( 3) SS BOND : angle 15.80720 / 9.04 ( 6) hydrogen bonds : bond 0.15119 / 10.80 ( 399) hydrogen bonds : angle 5.85674 / 4.17 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7915 (tpp80) REVERT: A 298 ILE cc_start: 0.8483 (mt) cc_final: 0.8230 (mp) REVERT: C 209 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7553 (ttpt) REVERT: D 82 TRP cc_start: 0.8506 (m100) cc_final: 0.8273 (m100) REVERT: D 86 THR cc_start: 0.8091 (p) cc_final: 0.7834 (p) REVERT: D 217 MET cc_start: 0.5944 (ttm) cc_final: 0.5647 (ttm) REVERT: D 273 ILE cc_start: 0.7134 (mt) cc_final: 0.6924 (mt) REVERT: D 303 ASP cc_start: 0.6706 (m-30) cc_final: 0.6455 (m-30) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.4222 time to fit residues: 105.7576 Evaluate side-chains 179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 194 HIS B 67 HIS D 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122487 restraints weight = 10497.298| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.79 r_work: 0.3522 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7757 Z= 0.139 Angle : 0.552 7.610 10501 Z= 0.283 Chirality : 0.041 0.139 1209 Planarity : 0.004 0.040 1319 Dihedral : 4.260 46.961 1069 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.95 % Allowed : 15.35 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.27), residues: 955 helix: 1.58 (0.24), residues: 437 sheet: 0.29 (0.38), residues: 183 loop : -0.80 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 200 TYR 0.012 0.002 TYR A 300 PHE 0.015 0.002 PHE A 93 TRP 0.018 0.002 TRP D 169 HIS 0.010 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7754) covalent geometry : angle 0.55054 / 0.28 (10495) SS BOND : bond 0.00770 / 0.40 ( 3) SS BOND : angle 1.67370 / 0.77 ( 6) hydrogen bonds : bond 0.04457 / 3.07 ( 399) hydrogen bonds : angle 4.71529 / 3.42 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.275 Fit side-chains REVERT: A 131 SER cc_start: 0.8142 (t) cc_final: 0.7918 (p) REVERT: A 134 ARG cc_start: 0.8254 (mtt180) cc_final: 0.8047 (mtt180) REVERT: A 228 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8334 (tpp80) REVERT: A 265 MET cc_start: 0.8399 (mtt) cc_final: 0.8187 (mtt) REVERT: C 29 LYS cc_start: 0.8306 (tppp) cc_final: 0.7948 (mtpp) REVERT: C 197 LYS cc_start: 0.8261 (tttt) cc_final: 0.7950 (tttm) REVERT: C 209 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7878 (ttpt) REVERT: C 216 GLU cc_start: 0.7794 (tt0) cc_final: 0.7586 (tt0) REVERT: C 251 ASP cc_start: 0.8107 (t0) cc_final: 0.7865 (t0) REVERT: C 268 LEU cc_start: 0.7832 (mt) cc_final: 0.7589 (mm) REVERT: C 271 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8098 (ttpp) REVERT: D 197 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7681 (mtp180) REVERT: D 246 ASP cc_start: 0.8150 (m-30) cc_final: 0.7936 (m-30) REVERT: D 273 ILE cc_start: 0.7761 (mt) cc_final: 0.7512 (mt) REVERT: D 303 ASP cc_start: 0.7487 (m-30) cc_final: 0.7154 (m-30) outliers start: 16 outliers final: 5 residues processed: 205 average time/residue: 0.4125 time to fit residues: 90.2853 Evaluate side-chains 193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 HIS C 269 ASN D 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121535 restraints weight = 10446.237| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.83 r_work: 0.3475 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7757 Z= 0.152 Angle : 0.552 7.437 10501 Z= 0.281 Chirality : 0.042 0.145 1209 Planarity : 0.004 0.062 1319 Dihedral : 4.364 44.367 1069 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.17 % Allowed : 17.05 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 955 helix: 1.88 (0.24), residues: 431 sheet: 0.40 (0.37), residues: 193 loop : -0.70 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 62 TYR 0.016 0.002 TYR A 258 PHE 0.014 0.002 PHE C 196 TRP 0.014 0.002 TRP A 74 HIS 0.009 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7754) covalent geometry : angle 0.55135 / 0.28 (10495) SS BOND : bond 0.00505 / 0.26 ( 3) SS BOND : angle 1.37000 / 0.61 ( 6) hydrogen bonds : bond 0.04625 / 3.19 ( 399) hydrogen bonds : angle 4.69680 / 3.41 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.188 Fit side-chains REVERT: A 110 SER cc_start: 0.7801 (m) cc_final: 0.7578 (t) REVERT: A 167 LEU cc_start: 0.7861 (tp) cc_final: 0.7654 (mt) REVERT: A 236 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7431 (ttp80) REVERT: A 298 ILE cc_start: 0.8576 (mt) cc_final: 0.8312 (mp) REVERT: B 29 ASN cc_start: 0.7675 (t0) cc_final: 0.7300 (t0) REVERT: C 29 LYS cc_start: 0.8324 (tppp) cc_final: 0.8043 (mtpp) REVERT: C 197 LYS cc_start: 0.8254 (tttt) cc_final: 0.7988 (tttm) REVERT: C 209 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7879 (ttpt) REVERT: C 268 LEU cc_start: 0.7861 (mt) cc_final: 0.7613 (mm) REVERT: D 136 SER cc_start: 0.8676 (t) cc_final: 0.8466 (p) REVERT: D 163 ASP cc_start: 0.7773 (p0) cc_final: 0.7541 (p0) REVERT: D 197 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7750 (mtp180) REVERT: D 246 ASP cc_start: 0.8170 (m-30) cc_final: 0.7895 (m-30) REVERT: D 270 ILE cc_start: 0.8245 (tp) cc_final: 0.8026 (mp) REVERT: D 303 ASP cc_start: 0.7502 (m-30) cc_final: 0.7151 (m-30) outliers start: 26 outliers final: 11 residues processed: 201 average time/residue: 0.3980 time to fit residues: 85.0810 Evaluate side-chains 195 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 84 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.0670 chunk 71 optimal weight: 0.3980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.138115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121277 restraints weight = 10633.124| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.87 r_work: 0.3480 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7757 Z= 0.118 Angle : 0.518 7.009 10501 Z= 0.265 Chirality : 0.041 0.142 1209 Planarity : 0.004 0.043 1319 Dihedral : 4.245 42.181 1069 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.17 % Allowed : 19.12 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.27), residues: 955 helix: 2.07 (0.24), residues: 432 sheet: 0.41 (0.36), residues: 190 loop : -0.62 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 200 TYR 0.011 0.001 TYR A 258 PHE 0.014 0.001 PHE A 275 TRP 0.014 0.001 TRP A 74 HIS 0.003 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 7754) covalent geometry : angle 0.51696 / 0.26 (10495) SS BOND : bond 0.00592 / 0.31 ( 3) SS BOND : angle 1.13884 / 0.50 ( 6) hydrogen bonds : bond 0.04245 / 2.92 ( 399) hydrogen bonds : angle 4.57585 / 3.34 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.263 Fit side-chains REVERT: A 110 SER cc_start: 0.7711 (m) cc_final: 0.7461 (t) REVERT: A 236 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7403 (ttp80) REVERT: A 265 MET cc_start: 0.8387 (mtt) cc_final: 0.8000 (mtm) REVERT: A 272 SER cc_start: 0.8689 (t) cc_final: 0.8425 (p) REVERT: A 298 ILE cc_start: 0.8588 (mt) cc_final: 0.8274 (mp) REVERT: B 29 ASN cc_start: 0.7573 (t0) cc_final: 0.7259 (t0) REVERT: C 29 LYS cc_start: 0.8366 (tppp) cc_final: 0.8089 (mtpp) REVERT: C 197 LYS cc_start: 0.8242 (tttt) cc_final: 0.7947 (tttm) REVERT: C 209 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7841 (ttpt) REVERT: C 263 SER cc_start: 0.8162 (p) cc_final: 0.7953 (p) REVERT: C 268 LEU cc_start: 0.7788 (mt) cc_final: 0.7569 (mm) REVERT: D 101 MET cc_start: 0.8390 (ptm) cc_final: 0.8133 (ptp) REVERT: D 163 ASP cc_start: 0.7677 (p0) cc_final: 0.7469 (p0) REVERT: D 197 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7709 (mtp180) REVERT: D 210 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (tp) REVERT: D 246 ASP cc_start: 0.8167 (m-30) cc_final: 0.7966 (m-30) REVERT: D 303 ASP cc_start: 0.7518 (m-30) cc_final: 0.7133 (m-30) outliers start: 26 outliers final: 12 residues processed: 206 average time/residue: 0.3849 time to fit residues: 84.5148 Evaluate side-chains 198 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 234 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118832 restraints weight = 10485.408| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.86 r_work: 0.3445 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7757 Z= 0.165 Angle : 0.554 7.380 10501 Z= 0.285 Chirality : 0.042 0.140 1209 Planarity : 0.004 0.047 1319 Dihedral : 4.438 40.577 1069 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.53 % Allowed : 19.85 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 955 helix: 2.07 (0.24), residues: 431 sheet: 0.43 (0.36), residues: 190 loop : -0.61 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 304 TYR 0.019 0.002 TYR A 258 PHE 0.016 0.002 PHE A 182 TRP 0.017 0.002 TRP A 74 HIS 0.004 0.001 HIS C 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 7754) covalent geometry : angle 0.55289 / 0.28 (10495) SS BOND : bond 0.00359 / 0.18 ( 3) SS BOND : angle 1.29292 / 0.58 ( 6) hydrogen bonds : bond 0.04718 / 3.23 ( 399) hydrogen bonds : angle 4.67126 / 3.41 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6958 (t) REVERT: A 110 SER cc_start: 0.7860 (m) cc_final: 0.7469 (t) REVERT: A 236 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7448 (ttp80) REVERT: A 265 MET cc_start: 0.8426 (mtt) cc_final: 0.8196 (mtt) REVERT: A 272 SER cc_start: 0.8699 (t) cc_final: 0.8420 (p) REVERT: B 29 ASN cc_start: 0.7600 (t0) cc_final: 0.7315 (t0) REVERT: C 29 LYS cc_start: 0.8375 (tppp) cc_final: 0.8100 (mtpp) REVERT: C 186 GLU cc_start: 0.7620 (pt0) cc_final: 0.7375 (pt0) REVERT: C 188 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.8067 (m170) REVERT: C 197 LYS cc_start: 0.8245 (tttt) cc_final: 0.7900 (tttm) REVERT: C 209 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7859 (ttpt) REVERT: C 263 SER cc_start: 0.8198 (p) cc_final: 0.7998 (p) REVERT: C 268 LEU cc_start: 0.7875 (mt) cc_final: 0.7657 (mm) REVERT: C 308 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 330 LYS cc_start: 0.7938 (mttt) cc_final: 0.7614 (mtmm) REVERT: D 136 SER cc_start: 0.8677 (t) cc_final: 0.8461 (p) REVERT: D 170 ASP cc_start: 0.7825 (m-30) cc_final: 0.7384 (p0) REVERT: D 210 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8094 (tp) REVERT: D 270 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7871 (mp) REVERT: D 290 ASP cc_start: 0.6797 (m-30) cc_final: 0.6450 (m-30) REVERT: D 303 ASP cc_start: 0.7539 (m-30) cc_final: 0.7124 (m-30) outliers start: 29 outliers final: 16 residues processed: 200 average time/residue: 0.4297 time to fit residues: 91.3649 Evaluate side-chains 203 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS D 230 ASN D 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119390 restraints weight = 10486.446| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.85 r_work: 0.3455 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7757 Z= 0.136 Angle : 0.534 7.321 10501 Z= 0.275 Chirality : 0.041 0.139 1209 Planarity : 0.004 0.050 1319 Dihedral : 4.363 39.001 1069 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.78 % Allowed : 19.61 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 955 helix: 2.10 (0.25), residues: 431 sheet: 0.32 (0.37), residues: 182 loop : -0.65 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 200 TYR 0.014 0.001 TYR A 258 PHE 0.013 0.002 PHE A 182 TRP 0.018 0.001 TRP A 74 HIS 0.008 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 7754) covalent geometry : angle 0.53290 / 0.27 (10495) SS BOND : bond 0.00349 / 0.18 ( 3) SS BOND : angle 1.25080 / 0.57 ( 6) hydrogen bonds : bond 0.04435 / 3.04 ( 399) hydrogen bonds : angle 4.63453 / 3.39 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6905 (t) REVERT: A 110 SER cc_start: 0.7825 (m) cc_final: 0.7460 (t) REVERT: A 236 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7433 (ttp80) REVERT: A 265 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8206 (mtt) REVERT: A 272 SER cc_start: 0.8713 (t) cc_final: 0.8431 (p) REVERT: C 29 LYS cc_start: 0.8376 (tppp) cc_final: 0.8106 (mtpp) REVERT: C 186 GLU cc_start: 0.7555 (pt0) cc_final: 0.7328 (pt0) REVERT: C 188 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.8034 (m170) REVERT: C 197 LYS cc_start: 0.8228 (tttt) cc_final: 0.7886 (tttm) REVERT: C 209 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7846 (ttpt) REVERT: C 263 SER cc_start: 0.8189 (p) cc_final: 0.7989 (p) REVERT: C 268 LEU cc_start: 0.7871 (mt) cc_final: 0.7659 (mm) REVERT: C 308 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7561 (mt-10) REVERT: C 330 LYS cc_start: 0.7957 (mttt) cc_final: 0.7637 (mtmm) REVERT: D 61 MET cc_start: 0.8311 (pp-130) cc_final: 0.7857 (pp-130) REVERT: D 101 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8186 (ptp) REVERT: D 170 ASP cc_start: 0.7783 (m-30) cc_final: 0.7384 (p0) REVERT: D 210 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 270 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7890 (mp) REVERT: D 290 ASP cc_start: 0.6796 (m-30) cc_final: 0.6428 (m-30) REVERT: D 303 ASP cc_start: 0.7513 (m-30) cc_final: 0.7092 (m-30) outliers start: 31 outliers final: 19 residues processed: 200 average time/residue: 0.4455 time to fit residues: 94.7918 Evaluate side-chains 205 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 ASN C 188 HIS D 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119491 restraints weight = 10458.411| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.84 r_work: 0.3451 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7757 Z= 0.151 Angle : 0.541 7.529 10501 Z= 0.278 Chirality : 0.041 0.142 1209 Planarity : 0.004 0.053 1319 Dihedral : 4.369 37.622 1069 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.63 % Allowed : 19.73 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 955 helix: 2.10 (0.24), residues: 431 sheet: 0.33 (0.37), residues: 183 loop : -0.66 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 200 TYR 0.015 0.002 TYR C 320 PHE 0.014 0.002 PHE C 196 TRP 0.017 0.002 TRP A 74 HIS 0.007 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7754) covalent geometry : angle 0.54034 / 0.28 (10495) SS BOND : bond 0.00398 / 0.21 ( 3) SS BOND : angle 1.26315 / 0.58 ( 6) hydrogen bonds : bond 0.04525 / 3.10 ( 399) hydrogen bonds : angle 4.65227 / 3.40 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.241 Fit side-chains REVERT: A 109 CYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6967 (t) REVERT: A 110 SER cc_start: 0.7861 (m) cc_final: 0.7500 (t) REVERT: A 236 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7447 (ttp80) REVERT: A 265 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8164 (mtt) REVERT: A 272 SER cc_start: 0.8721 (t) cc_final: 0.8429 (p) REVERT: B 29 ASN cc_start: 0.7646 (t0) cc_final: 0.7358 (t0) REVERT: C 29 LYS cc_start: 0.8364 (tppp) cc_final: 0.8086 (mtpp) REVERT: C 186 GLU cc_start: 0.7524 (pt0) cc_final: 0.7292 (pt0) REVERT: C 197 LYS cc_start: 0.8247 (tttt) cc_final: 0.7921 (mtpp) REVERT: C 209 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7833 (ttpt) REVERT: C 308 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7647 (mt-10) REVERT: C 330 LYS cc_start: 0.7963 (mttt) cc_final: 0.7640 (mtmm) REVERT: D 101 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8184 (ptp) REVERT: D 170 ASP cc_start: 0.7783 (m-30) cc_final: 0.7354 (p0) REVERT: D 210 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8060 (tp) REVERT: D 290 ASP cc_start: 0.6800 (m-30) cc_final: 0.6441 (m-30) REVERT: D 303 ASP cc_start: 0.7513 (m-30) cc_final: 0.7089 (m-30) outliers start: 38 outliers final: 22 residues processed: 195 average time/residue: 0.4773 time to fit residues: 98.8494 Evaluate side-chains 196 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119282 restraints weight = 10336.363| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.83 r_work: 0.3451 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7757 Z= 0.151 Angle : 0.555 7.726 10501 Z= 0.283 Chirality : 0.041 0.141 1209 Planarity : 0.004 0.052 1319 Dihedral : 4.381 35.354 1069 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.02 % Allowed : 20.22 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.27), residues: 955 helix: 2.03 (0.24), residues: 433 sheet: 0.42 (0.37), residues: 182 loop : -0.64 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 304 TYR 0.021 0.002 TYR D 59 PHE 0.013 0.002 PHE C 196 TRP 0.017 0.002 TRP A 74 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7754) covalent geometry : angle 0.55432 / 0.28 (10495) SS BOND : bond 0.00450 / 0.24 ( 3) SS BOND : angle 1.24342 / 0.58 ( 6) hydrogen bonds : bond 0.04538 / 3.12 ( 399) hydrogen bonds : angle 4.64830 / 3.41 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8217 (mp) cc_final: 0.7975 (mt) REVERT: A 109 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7112 (t) REVERT: A 110 SER cc_start: 0.7913 (m) cc_final: 0.7568 (t) REVERT: A 236 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: A 265 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8133 (mtt) REVERT: A 272 SER cc_start: 0.8729 (t) cc_final: 0.8440 (p) REVERT: C 29 LYS cc_start: 0.8371 (tppp) cc_final: 0.8095 (mtpp) REVERT: C 197 LYS cc_start: 0.8231 (tttt) cc_final: 0.7998 (mtpp) REVERT: C 209 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7816 (ttpt) REVERT: C 263 SER cc_start: 0.8257 (p) cc_final: 0.8051 (p) REVERT: C 308 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 309 ASP cc_start: 0.7282 (m-30) cc_final: 0.6806 (m-30) REVERT: C 330 LYS cc_start: 0.7927 (mttt) cc_final: 0.7643 (mttp) REVERT: C 336 PHE cc_start: 0.8115 (t80) cc_final: 0.7897 (t80) REVERT: D 59 TYR cc_start: 0.8456 (m-80) cc_final: 0.8105 (m-80) REVERT: D 101 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (ptp) REVERT: D 170 ASP cc_start: 0.7775 (m-30) cc_final: 0.7382 (p0) REVERT: D 210 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8024 (tp) REVERT: D 290 ASP cc_start: 0.6865 (m-30) cc_final: 0.6539 (m-30) REVERT: D 303 ASP cc_start: 0.7466 (m-30) cc_final: 0.7059 (m-30) outliers start: 33 outliers final: 20 residues processed: 202 average time/residue: 0.4639 time to fit residues: 99.6301 Evaluate side-chains 203 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 ASN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120058 restraints weight = 10234.421| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.81 r_work: 0.3464 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7757 Z= 0.135 Angle : 0.552 8.730 10501 Z= 0.282 Chirality : 0.041 0.141 1209 Planarity : 0.004 0.049 1319 Dihedral : 4.314 32.877 1069 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.78 % Allowed : 20.34 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 955 helix: 2.11 (0.24), residues: 433 sheet: 0.43 (0.37), residues: 180 loop : -0.63 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 200 TYR 0.017 0.002 TYR D 59 PHE 0.016 0.002 PHE C 267 TRP 0.018 0.002 TRP A 74 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7754) covalent geometry : angle 0.55090 / 0.28 (10495) SS BOND : bond 0.00379 / 0.20 ( 3) SS BOND : angle 1.25115 / 0.58 ( 6) hydrogen bonds : bond 0.04399 / 3.02 ( 399) hydrogen bonds : angle 4.62476 / 3.39 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8163 (mp) cc_final: 0.7929 (mt) REVERT: A 109 CYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7094 (t) REVERT: A 110 SER cc_start: 0.7891 (m) cc_final: 0.7538 (t) REVERT: A 168 THR cc_start: 0.8177 (m) cc_final: 0.7728 (m) REVERT: A 236 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6817 (ttp80) REVERT: A 265 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8109 (mtt) REVERT: A 272 SER cc_start: 0.8702 (t) cc_final: 0.8407 (p) REVERT: B 29 ASN cc_start: 0.7698 (t0) cc_final: 0.7129 (t0) REVERT: C 29 LYS cc_start: 0.8365 (tppp) cc_final: 0.8073 (mtpp) REVERT: C 197 LYS cc_start: 0.8222 (tttt) cc_final: 0.7928 (mtpp) REVERT: C 209 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7814 (ttpt) REVERT: C 308 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7625 (mt-10) REVERT: C 309 ASP cc_start: 0.7265 (m-30) cc_final: 0.6771 (m-30) REVERT: C 330 LYS cc_start: 0.7892 (mttt) cc_final: 0.7586 (mttm) REVERT: D 61 MET cc_start: 0.8342 (pp-130) cc_final: 0.7655 (pp-130) REVERT: D 101 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8187 (ptp) REVERT: D 170 ASP cc_start: 0.7771 (m-30) cc_final: 0.7362 (p0) REVERT: D 210 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8034 (tp) REVERT: D 234 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7554 (t80) REVERT: D 290 ASP cc_start: 0.6878 (m-30) cc_final: 0.6539 (m-30) REVERT: D 303 ASP cc_start: 0.7466 (m-30) cc_final: 0.7047 (m-30) outliers start: 31 outliers final: 17 residues processed: 190 average time/residue: 0.4546 time to fit residues: 92.0423 Evaluate side-chains 193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120067 restraints weight = 10236.994| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.82 r_work: 0.3459 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7757 Z= 0.144 Angle : 0.564 11.330 10501 Z= 0.287 Chirality : 0.041 0.141 1209 Planarity : 0.004 0.046 1319 Dihedral : 4.332 30.180 1069 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.41 % Allowed : 20.83 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.27), residues: 955 helix: 2.07 (0.24), residues: 433 sheet: 0.34 (0.37), residues: 182 loop : -0.57 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 200 TYR 0.014 0.002 TYR A 258 PHE 0.016 0.002 PHE C 267 TRP 0.016 0.002 TRP A 74 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7754) covalent geometry : angle 0.56382 / 0.29 (10495) SS BOND : bond 0.00413 / 0.22 ( 3) SS BOND : angle 1.25148 / 0.59 ( 6) hydrogen bonds : bond 0.04459 / 3.05 ( 399) hydrogen bonds : angle 4.63383 / 3.41 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8182 (mp) cc_final: 0.7943 (mt) REVERT: A 109 CYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7147 (t) REVERT: A 110 SER cc_start: 0.7952 (m) cc_final: 0.7612 (t) REVERT: A 168 THR cc_start: 0.8206 (m) cc_final: 0.7762 (m) REVERT: A 236 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7419 (ttp80) REVERT: A 265 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8144 (mtt) REVERT: A 272 SER cc_start: 0.8703 (t) cc_final: 0.8419 (p) REVERT: B 29 ASN cc_start: 0.7685 (t0) cc_final: 0.7103 (t0) REVERT: C 29 LYS cc_start: 0.8368 (tppp) cc_final: 0.8075 (mtpp) REVERT: C 197 LYS cc_start: 0.8243 (tttt) cc_final: 0.8027 (mtpp) REVERT: C 209 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7814 (ttpt) REVERT: C 271 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8151 (pttm) REVERT: C 308 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7647 (mt-10) REVERT: C 309 ASP cc_start: 0.7277 (m-30) cc_final: 0.6786 (m-30) REVERT: C 330 LYS cc_start: 0.7908 (mttt) cc_final: 0.7591 (mttm) REVERT: D 61 MET cc_start: 0.8346 (pp-130) cc_final: 0.7620 (pp-130) REVERT: D 101 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8190 (ptp) REVERT: D 170 ASP cc_start: 0.7794 (m-30) cc_final: 0.7372 (p0) REVERT: D 210 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8029 (tp) REVERT: D 234 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7505 (t80) REVERT: D 290 ASP cc_start: 0.6897 (m-30) cc_final: 0.6563 (m-30) REVERT: D 303 ASP cc_start: 0.7432 (m-30) cc_final: 0.7014 (m-30) REVERT: G 21 MET cc_start: 0.6257 (mtp) cc_final: 0.5902 (mtp) outliers start: 28 outliers final: 19 residues processed: 189 average time/residue: 0.4171 time to fit residues: 84.1303 Evaluate side-chains 194 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 67 optimal weight: 0.0470 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121692 restraints weight = 10304.444| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.87 r_work: 0.3479 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7757 Z= 0.114 Angle : 0.551 11.654 10501 Z= 0.277 Chirality : 0.040 0.145 1209 Planarity : 0.004 0.046 1319 Dihedral : 4.165 26.956 1069 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.53 % Allowed : 21.32 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.27), residues: 955 helix: 2.20 (0.24), residues: 433 sheet: 0.40 (0.36), residues: 189 loop : -0.61 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 200 TYR 0.015 0.001 TYR C 320 PHE 0.011 0.001 PHE A 182 TRP 0.017 0.001 TRP A 74 HIS 0.002 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7754) covalent geometry : angle 0.55063 / 0.28 (10495) SS BOND : bond 0.00231 / 0.12 ( 3) SS BOND : angle 1.19057 / 0.55 ( 6) hydrogen bonds : bond 0.04102 / 2.80 ( 399) hydrogen bonds : angle 4.54346 / 3.35 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.52 seconds wall clock time: 46 minutes 4.15 seconds (2764.15 seconds total)