Starting phenix.real_space_refine on Fri Aug 22 20:05:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk5_34846/08_2025/8hk5_34846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk5_34846/08_2025/8hk5_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_34846/08_2025/8hk5_34846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk5_34846/08_2025/8hk5_34846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hk5_34846/08_2025/8hk5_34846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk5_34846/08_2025/8hk5_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-2.0-5787/lib/python3.9/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: 1.79, per 1000 atoms: 0.24 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: 0.58 Conformation dependent library (CDL) restraints added in 371.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.23 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: 1.16 Time building geometry restraints manager: 0.79 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.370 Find NCS groups from input model: 0.020 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 aren 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 covalent geometry : bond 0.00315 ( 7754) covalent geometry : angle 0.50461 (10495) SS BOND : bond 0.02601 ( 3) SS BOND : angle 15.80720 ( 6) hydrogen bonds : bond 0.15119 ( 399) hydrogen bonds : angle 5.85674 ( 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 : 0.306 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: 0.4648 time to fit residues: 115.9860 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 : 0.287 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.138475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122531 restraints weight = 10507.508| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.79 r_work: 0.3523 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1984 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= 0.137 Angle : 0.554 7.591 10501 Z= 0.284 Chirality : 0.041 0.147 1209 Planarity : 0.004 0.042 1319 Dihedral : 4.282 46.367 1069 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.31 % Allowed : 14.74 % Favored : 82.95 % 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 aren not related in a simple way. whole: 0.85 (0.27), residues: 955 helix: 1.70 (0.24), residues: 431 sheet: 0.30 (0.38), residues: 183 loop : -0.71 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.014 0.001 TYR A 300 PHE 0.016 0.002 PHE A 93 TRP 0.019 0.002 TRP D 169 HIS 0.010 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7754) covalent geometry : angle 0.55305 (10495) SS BOND : bond 0.00293 ( 3) SS BOND : angle 1.65708 ( 6) hydrogen bonds : bond 0.04359 ( 399) hydrogen bonds : angle 4.67845 ( 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 218 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.220 Fit side-chains REVERT: A 131 SER cc_start: 0.8138 (t) cc_final: 0.7919 (p) REVERT: A 134 ARG cc_start: 0.8260 (mtt180) cc_final: 0.8049 (mtt180) REVERT: A 228 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8338 (tpp80) REVERT: A 265 MET cc_start: 0.8389 (mtt) cc_final: 0.8166 (mtt) REVERT: C 29 LYS cc_start: 0.8310 (tppp) cc_final: 0.7964 (mtpp) REVERT: C 197 LYS cc_start: 0.8241 (tttt) cc_final: 0.7925 (tttm) REVERT: C 209 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7857 (ttpt) REVERT: C 216 GLU cc_start: 0.7799 (tt0) cc_final: 0.7593 (tt0) REVERT: C 251 ASP cc_start: 0.8110 (t0) cc_final: 0.7872 (t0) REVERT: C 268 LEU cc_start: 0.7829 (mt) cc_final: 0.7581 (mm) REVERT: C 271 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8115 (ttpp) REVERT: D 197 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7708 (mtp180) REVERT: D 246 ASP cc_start: 0.8187 (m-30) cc_final: 0.7976 (m-30) REVERT: D 303 ASP cc_start: 0.7478 (m-30) cc_final: 0.7136 (m-30) outliers start: 19 outliers final: 6 residues processed: 207 average time/residue: 0.4673 time to fit residues: 103.0104 Evaluate side-chains 195 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 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 = 0.3813 r_free = 0.3813 target = 0.136824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120614 restraints weight = 10537.879| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.80 r_work: 0.3507 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7757 Z= 0.125 Angle : 0.531 7.575 10501 Z= 0.270 Chirality : 0.041 0.149 1209 Planarity : 0.004 0.059 1319 Dihedral : 4.236 44.288 1069 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.56 % Allowed : 17.42 % Favored : 80.02 % 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 aren not related in a simple way. whole: 1.06 (0.27), residues: 955 helix: 1.96 (0.24), residues: 433 sheet: 0.37 (0.37), residues: 188 loop : -0.77 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 200 TYR 0.014 0.001 TYR A 290 PHE 0.013 0.002 PHE A 275 TRP 0.013 0.001 TRP A 74 HIS 0.008 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7754) covalent geometry : angle 0.53066 (10495) SS BOND : bond 0.00256 ( 3) SS BOND : angle 1.22870 ( 6) hydrogen bonds : bond 0.04344 ( 399) hydrogen bonds : angle 4.61236 ( 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 205 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.194 Fit side-chains REVERT: A 110 SER cc_start: 0.7706 (m) cc_final: 0.7492 (t) REVERT: A 167 LEU cc_start: 0.7725 (tp) cc_final: 0.7516 (mt) REVERT: A 228 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8355 (tpt-90) REVERT: A 236 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.6686 (ttp80) REVERT: A 265 MET cc_start: 0.8386 (mtt) cc_final: 0.8176 (mtt) REVERT: B 29 ASN cc_start: 0.7613 (t0) cc_final: 0.7237 (t0) REVERT: C 29 LYS cc_start: 0.8319 (tppp) cc_final: 0.8039 (mtpp) REVERT: C 186 GLU cc_start: 0.7606 (pt0) cc_final: 0.7376 (pt0) REVERT: C 188 HIS cc_start: 0.8421 (m90) cc_final: 0.8054 (m170) REVERT: C 197 LYS cc_start: 0.8250 (tttt) cc_final: 0.7951 (tttm) REVERT: C 209 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7849 (ttpt) REVERT: C 216 GLU cc_start: 0.7808 (tt0) cc_final: 0.7596 (tt0) REVERT: C 268 LEU cc_start: 0.7800 (mt) cc_final: 0.7573 (mm) REVERT: C 308 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7446 (mt-10) REVERT: D 246 ASP cc_start: 0.8149 (m-30) cc_final: 0.7922 (m-30) REVERT: D 270 ILE cc_start: 0.8225 (tp) cc_final: 0.8007 (mp) REVERT: D 303 ASP cc_start: 0.7464 (m-30) cc_final: 0.7092 (m-30) outliers start: 21 outliers final: 7 residues processed: 192 average time/residue: 0.4657 time to fit residues: 94.8827 Evaluate side-chains 190 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG 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 134 ARG 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: 4.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 84 optimal weight: 0.0030 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121517 restraints weight = 10619.185| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.85 r_work: 0.3485 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2686 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= 0.126 Angle : 0.515 7.756 10501 Z= 0.265 Chirality : 0.041 0.144 1209 Planarity : 0.004 0.038 1319 Dihedral : 4.229 42.093 1069 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.05 % Allowed : 19.00 % Favored : 77.95 % 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 aren not related in a simple way. whole: 1.27 (0.27), residues: 955 helix: 2.14 (0.24), residues: 433 sheet: 0.39 (0.37), residues: 186 loop : -0.59 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 200 TYR 0.014 0.001 TYR A 258 PHE 0.013 0.001 PHE A 182 TRP 0.016 0.001 TRP A 74 HIS 0.003 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7754) covalent geometry : angle 0.51434 (10495) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.08561 ( 6) hydrogen bonds : bond 0.04299 ( 399) hydrogen bonds : angle 4.55320 ( 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 219 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.314 Fit side-chains REVERT: A 110 SER cc_start: 0.7697 (m) cc_final: 0.7458 (t) REVERT: A 228 ARG cc_start: 0.8599 (tpp80) cc_final: 0.8397 (tpp80) REVERT: A 236 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6723 (ttp80) REVERT: A 265 MET cc_start: 0.8394 (mtt) cc_final: 0.8088 (mtt) REVERT: A 272 SER cc_start: 0.8694 (t) cc_final: 0.8435 (p) REVERT: B 29 ASN cc_start: 0.7565 (t0) cc_final: 0.7245 (t0) REVERT: C 29 LYS cc_start: 0.8363 (tppp) cc_final: 0.8087 (mtpp) REVERT: C 186 GLU cc_start: 0.7625 (pt0) cc_final: 0.7414 (pt0) REVERT: C 188 HIS cc_start: 0.8406 (m90) cc_final: 0.8200 (m170) REVERT: C 197 LYS cc_start: 0.8219 (tttt) cc_final: 0.7924 (tttm) REVERT: C 209 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7834 (ttpt) REVERT: C 216 GLU cc_start: 0.7799 (tt0) cc_final: 0.7586 (tt0) REVERT: C 268 LEU cc_start: 0.7749 (mt) cc_final: 0.7522 (mm) REVERT: C 308 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7505 (mt-10) REVERT: D 163 ASP cc_start: 0.7775 (p0) cc_final: 0.7537 (p0) REVERT: D 210 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8043 (tp) REVERT: D 246 ASP cc_start: 0.8174 (m-30) cc_final: 0.7948 (m-30) REVERT: D 303 ASP cc_start: 0.7518 (m-30) cc_final: 0.7135 (m-30) outliers start: 25 outliers final: 12 residues processed: 207 average time/residue: 0.5368 time to fit residues: 118.2872 Evaluate side-chains 202 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 229 ILE 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: 1.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 28 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.137566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120701 restraints weight = 10535.534| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.85 r_work: 0.3474 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2882 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= 0.126 Angle : 0.520 7.278 10501 Z= 0.267 Chirality : 0.041 0.139 1209 Planarity : 0.003 0.038 1319 Dihedral : 4.219 40.310 1069 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.29 % Allowed : 19.61 % Favored : 77.10 % 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 aren not related in a simple way. whole: 1.29 (0.27), residues: 955 helix: 2.23 (0.24), residues: 430 sheet: 0.38 (0.36), residues: 185 loop : -0.65 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 200 TYR 0.013 0.001 TYR A 258 PHE 0.012 0.001 PHE A 182 TRP 0.016 0.001 TRP A 74 HIS 0.003 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7754) covalent geometry : angle 0.51920 (10495) SS BOND : bond 0.00252 ( 3) SS BOND : angle 1.14834 ( 6) hydrogen bonds : bond 0.04282 ( 399) hydrogen bonds : angle 4.54598 ( 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 215 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.312 Fit side-chains REVERT: A 109 CYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6685 (t) REVERT: A 110 SER cc_start: 0.7727 (m) cc_final: 0.7295 (t) REVERT: A 212 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 228 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8360 (tpt-90) REVERT: A 236 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7454 (ttp80) REVERT: A 265 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8201 (mtt) REVERT: A 272 SER cc_start: 0.8689 (t) cc_final: 0.8421 (p) REVERT: B 29 ASN cc_start: 0.7596 (t0) cc_final: 0.7238 (t0) REVERT: C 29 LYS cc_start: 0.8350 (tppp) cc_final: 0.8088 (mtpp) REVERT: C 188 HIS cc_start: 0.8381 (m90) cc_final: 0.8123 (m170) REVERT: C 197 LYS cc_start: 0.8198 (tttt) cc_final: 0.7910 (tttm) REVERT: C 209 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7843 (ttpt) REVERT: C 216 GLU cc_start: 0.7804 (tt0) cc_final: 0.7597 (tt0) REVERT: C 268 LEU cc_start: 0.7835 (mt) cc_final: 0.7611 (mm) REVERT: C 309 ASP cc_start: 0.7302 (m-30) cc_final: 0.6844 (m-30) REVERT: D 163 ASP cc_start: 0.7735 (p0) cc_final: 0.7484 (p0) REVERT: D 246 ASP cc_start: 0.8156 (m-30) cc_final: 0.7934 (m-30) REVERT: D 303 ASP cc_start: 0.7502 (m-30) cc_final: 0.7129 (m-30) outliers start: 27 outliers final: 14 residues processed: 199 average time/residue: 0.5397 time to fit residues: 113.5715 Evaluate side-chains 204 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 265 MET 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 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 212 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119369 restraints weight = 10495.445| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.88 r_work: 0.3441 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7757 Z= 0.161 Angle : 0.547 7.487 10501 Z= 0.283 Chirality : 0.041 0.141 1209 Planarity : 0.004 0.043 1319 Dihedral : 4.381 38.228 1069 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 aren not related in a simple way. whole: 1.27 (0.27), residues: 955 helix: 2.16 (0.24), residues: 431 sheet: 0.41 (0.35), residues: 186 loop : -0.62 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 200 TYR 0.019 0.002 TYR A 258 PHE 0.022 0.002 PHE C 336 TRP 0.017 0.002 TRP A 74 HIS 0.004 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7754) covalent geometry : angle 0.54690 (10495) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.18537 ( 6) hydrogen bonds : bond 0.04671 ( 399) hydrogen bonds : angle 4.64826 ( 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 226 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.291 Fit side-chains REVERT: A 109 CYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6978 (t) REVERT: A 110 SER cc_start: 0.7889 (m) cc_final: 0.7541 (t) REVERT: A 236 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7483 (ttp80) REVERT: A 265 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8138 (mtt) REVERT: A 272 SER cc_start: 0.8740 (t) cc_final: 0.8468 (p) REVERT: A 302 VAL cc_start: 0.8435 (t) cc_final: 0.8225 (m) REVERT: B 29 ASN cc_start: 0.7694 (t0) cc_final: 0.7356 (t0) REVERT: C 29 LYS cc_start: 0.8400 (tppp) cc_final: 0.8125 (mtpp) REVERT: C 188 HIS cc_start: 0.8406 (m90) cc_final: 0.8135 (m170) REVERT: C 197 LYS cc_start: 0.8193 (tttt) cc_final: 0.7919 (tttm) REVERT: C 209 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7862 (ttpt) REVERT: C 268 LEU cc_start: 0.7906 (mt) cc_final: 0.7599 (mt) REVERT: C 330 LYS cc_start: 0.7988 (mttt) cc_final: 0.7660 (mtmm) REVERT: D 163 ASP cc_start: 0.7743 (p0) cc_final: 0.7474 (p0) REVERT: D 170 ASP cc_start: 0.7815 (m-30) cc_final: 0.7597 (m-30) REVERT: D 210 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8101 (tp) REVERT: D 246 ASP cc_start: 0.8234 (m-30) cc_final: 0.7980 (m-30) REVERT: D 303 ASP cc_start: 0.7565 (m-30) cc_final: 0.7158 (m-30) REVERT: G 46 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7857 (mttp) outliers start: 31 outliers final: 16 residues processed: 211 average time/residue: 0.5391 time to fit residues: 120.9036 Evaluate side-chains 206 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 C residue 18 MET Chi-restraints excluded: chain C residue 207 GLU 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 114 CYS Chi-restraints excluded: chain D residue 134 ARG 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 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN 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 = 0.137949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121154 restraints weight = 10331.811| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.81 r_work: 0.3474 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7757 Z= 0.127 Angle : 0.533 7.490 10501 Z= 0.274 Chirality : 0.040 0.139 1209 Planarity : 0.003 0.042 1319 Dihedral : 4.275 36.264 1069 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.53 % Allowed : 20.34 % Favored : 76.13 % 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 aren not related in a simple way. whole: 1.29 (0.27), residues: 955 helix: 2.21 (0.24), residues: 431 sheet: 0.42 (0.36), residues: 184 loop : -0.67 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 200 TYR 0.013 0.001 TYR C 320 PHE 0.018 0.002 PHE C 336 TRP 0.017 0.001 TRP A 74 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7754) covalent geometry : angle 0.53206 (10495) SS BOND : bond 0.00453 ( 3) SS BOND : angle 1.13563 ( 6) hydrogen bonds : bond 0.04342 ( 399) hydrogen bonds : angle 4.57381 ( 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: 29 poor density : 183 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 CYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6943 (t) REVERT: A 110 SER cc_start: 0.7823 (m) cc_final: 0.7451 (t) REVERT: A 168 THR cc_start: 0.8198 (m) cc_final: 0.7725 (m) REVERT: A 236 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6815 (ttp80) REVERT: A 265 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8115 (mtt) REVERT: A 272 SER cc_start: 0.8713 (t) cc_final: 0.8431 (p) REVERT: B 29 ASN cc_start: 0.7706 (t0) cc_final: 0.7334 (t0) REVERT: C 29 LYS cc_start: 0.8339 (tppp) cc_final: 0.8066 (mtpp) REVERT: C 188 HIS cc_start: 0.8403 (m90) cc_final: 0.8157 (m170) REVERT: C 197 LYS cc_start: 0.8221 (tttt) cc_final: 0.7955 (tttm) REVERT: C 209 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7808 (ttpt) REVERT: D 163 ASP cc_start: 0.7697 (p0) cc_final: 0.7431 (p0) REVERT: D 170 ASP cc_start: 0.7730 (m-30) cc_final: 0.7490 (m-30) REVERT: D 210 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8068 (tp) REVERT: D 234 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7597 (t80) REVERT: D 246 ASP cc_start: 0.8169 (m-30) cc_final: 0.7924 (m-30) REVERT: D 303 ASP cc_start: 0.7448 (m-30) cc_final: 0.7026 (m-30) REVERT: G 46 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7895 (mttp) outliers start: 29 outliers final: 13 residues processed: 198 average time/residue: 0.5229 time to fit residues: 110.1465 Evaluate side-chains 194 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 C residue 18 MET 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 114 CYS Chi-restraints excluded: chain D residue 134 ARG 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 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 78 optimal weight: 0.0020 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121405 restraints weight = 10322.788| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.81 r_work: 0.3474 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3264 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= 0.124 Angle : 0.541 7.669 10501 Z= 0.275 Chirality : 0.041 0.142 1209 Planarity : 0.003 0.042 1319 Dihedral : 4.206 34.087 1069 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.41 % Allowed : 20.95 % 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 aren not related in a simple way. whole: 1.30 (0.27), residues: 955 helix: 2.23 (0.24), residues: 432 sheet: 0.40 (0.36), residues: 184 loop : -0.65 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 304 TYR 0.012 0.001 TYR A 258 PHE 0.017 0.002 PHE C 336 TRP 0.016 0.001 TRP A 74 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7754) covalent geometry : angle 0.54059 (10495) SS BOND : bond 0.00316 ( 3) SS BOND : angle 1.15132 ( 6) hydrogen bonds : bond 0.04260 ( 399) hydrogen bonds : angle 4.55848 ( 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 202 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6890 (t) REVERT: A 110 SER cc_start: 0.7805 (m) cc_final: 0.7429 (t) REVERT: A 168 THR cc_start: 0.8155 (m) cc_final: 0.7690 (m) REVERT: A 236 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6810 (ttp80) REVERT: A 265 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8121 (mtt) REVERT: A 272 SER cc_start: 0.8686 (t) cc_final: 0.8402 (p) REVERT: A 302 VAL cc_start: 0.8437 (t) cc_final: 0.8233 (m) REVERT: B 29 ASN cc_start: 0.7680 (t0) cc_final: 0.7316 (t0) REVERT: C 29 LYS cc_start: 0.8339 (tppp) cc_final: 0.8049 (mtpp) REVERT: C 197 LYS cc_start: 0.8228 (tttt) cc_final: 0.7994 (mtpp) REVERT: C 209 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7835 (ttpt) REVERT: C 309 ASP cc_start: 0.7291 (m-30) cc_final: 0.6794 (m-30) REVERT: D 170 ASP cc_start: 0.7743 (m-30) cc_final: 0.7388 (p0) REVERT: D 210 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7941 (tp) REVERT: D 234 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7541 (t80) REVERT: D 290 ASP cc_start: 0.6838 (m-30) cc_final: 0.6520 (m-30) REVERT: D 303 ASP cc_start: 0.7447 (m-30) cc_final: 0.7029 (m-30) REVERT: G 46 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7881 (mttp) outliers start: 28 outliers final: 12 residues processed: 188 average time/residue: 0.5175 time to fit residues: 103.4796 Evaluate side-chains 189 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 C residue 18 MET 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 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU 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 G residue 46 LYS 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: 0.0770 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN 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 = 0.3779 r_free = 0.3779 target = 0.135897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118963 restraints weight = 10223.110| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.80 r_work: 0.3441 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7757 Z= 0.188 Angle : 0.586 9.876 10501 Z= 0.299 Chirality : 0.042 0.140 1209 Planarity : 0.004 0.049 1319 Dihedral : 4.432 32.130 1069 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.53 % Allowed : 20.22 % Favored : 76.25 % 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 aren not related in a simple way. whole: 1.18 (0.27), residues: 955 helix: 2.08 (0.24), residues: 433 sheet: 0.34 (0.37), residues: 178 loop : -0.64 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 200 TYR 0.019 0.002 TYR A 258 PHE 0.016 0.002 PHE C 336 TRP 0.015 0.002 TRP A 74 HIS 0.003 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 7754) covalent geometry : angle 0.58565 (10495) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.28157 ( 6) hydrogen bonds : bond 0.04817 ( 399) hydrogen bonds : angle 4.71022 ( 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 205 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.7933 (m) cc_final: 0.7626 (t) REVERT: A 134 ARG cc_start: 0.8330 (mtt180) cc_final: 0.8129 (mtt180) REVERT: A 236 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7510 (ttp80) REVERT: A 265 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8144 (mtt) REVERT: C 29 LYS cc_start: 0.8373 (tppp) cc_final: 0.8092 (mtpp) REVERT: C 197 LYS cc_start: 0.8245 (tttt) cc_final: 0.8043 (mtpp) REVERT: C 209 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7835 (ttpt) REVERT: C 247 MET cc_start: 0.8296 (mtp) cc_final: 0.8014 (mtt) REVERT: C 271 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8247 (pttt) REVERT: C 308 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7665 (mt-10) REVERT: C 309 ASP cc_start: 0.7299 (m-30) cc_final: 0.6813 (m-30) REVERT: C 330 LYS cc_start: 0.7947 (mttt) cc_final: 0.7660 (mttp) REVERT: D 61 MET cc_start: 0.8374 (pp-130) cc_final: 0.7793 (pp-130) REVERT: D 170 ASP cc_start: 0.7757 (m-30) cc_final: 0.7410 (p0) REVERT: D 210 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8006 (tp) REVERT: D 270 ILE cc_start: 0.8270 (tp) cc_final: 0.8042 (mm) REVERT: D 290 ASP cc_start: 0.6875 (m-30) cc_final: 0.6574 (m-30) REVERT: D 303 ASP cc_start: 0.7466 (m-30) cc_final: 0.7069 (m-30) REVERT: G 46 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7833 (mttp) outliers start: 29 outliers final: 17 residues processed: 192 average time/residue: 0.5095 time to fit residues: 103.7878 Evaluate side-chains 189 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE 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 C residue 18 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 249 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 114 CYS Chi-restraints excluded: chain D residue 134 ARG 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 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN ** 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 = 0.3795 r_free = 0.3795 target = 0.136936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120163 restraints weight = 10246.978| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.80 r_work: 0.3461 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3461 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= 0.143 Angle : 0.570 12.153 10501 Z= 0.292 Chirality : 0.042 0.139 1209 Planarity : 0.004 0.049 1319 Dihedral : 4.330 29.680 1069 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.80 % Allowed : 21.68 % Favored : 75.52 % 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 aren not related in a simple way. whole: 1.23 (0.27), residues: 955 helix: 2.12 (0.25), residues: 433 sheet: 0.32 (0.37), residues: 180 loop : -0.58 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 200 TYR 0.022 0.002 TYR D 59 PHE 0.017 0.002 PHE C 336 TRP 0.017 0.002 TRP A 74 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7754) covalent geometry : angle 0.56980 (10495) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.21803 ( 6) hydrogen bonds : bond 0.04496 ( 399) hydrogen bonds : angle 4.65429 ( 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 196 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8206 (mp) cc_final: 0.7988 (mt) REVERT: A 168 THR cc_start: 0.8247 (m) cc_final: 0.7790 (m) REVERT: A 236 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6864 (ttp80) REVERT: A 265 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8145 (mtt) REVERT: C 29 LYS cc_start: 0.8389 (tppp) cc_final: 0.8098 (mtpp) REVERT: C 209 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7821 (ttpt) REVERT: C 247 MET cc_start: 0.8305 (mtp) cc_final: 0.8018 (mtt) REVERT: C 271 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8262 (pttt) REVERT: C 308 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 309 ASP cc_start: 0.7318 (m-30) cc_final: 0.6808 (m-30) REVERT: C 318 GLU cc_start: 0.7104 (pm20) cc_final: 0.6808 (pm20) REVERT: C 330 LYS cc_start: 0.7901 (mttt) cc_final: 0.7606 (mttm) REVERT: D 137 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7625 (ptp90) REVERT: D 170 ASP cc_start: 0.7754 (m-30) cc_final: 0.7411 (p0) REVERT: D 210 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (tp) REVERT: D 212 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: D 234 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7599 (t80) REVERT: D 290 ASP cc_start: 0.6859 (m-30) cc_final: 0.6553 (m-30) REVERT: D 303 ASP cc_start: 0.7435 (m-30) cc_final: 0.7034 (m-30) REVERT: G 46 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7834 (mttp) outliers start: 23 outliers final: 13 residues processed: 184 average time/residue: 0.5486 time to fit residues: 107.3656 Evaluate side-chains 187 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 265 MET Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 207 GLU 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 114 CYS Chi-restraints excluded: chain D residue 134 ARG 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 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121205 restraints weight = 10282.523| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.81 r_work: 0.3477 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3493 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= 0.122 Angle : 0.560 10.572 10501 Z= 0.283 Chirality : 0.041 0.156 1209 Planarity : 0.004 0.049 1319 Dihedral : 4.212 26.524 1069 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.68 % Allowed : 22.41 % Favored : 74.91 % 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 aren not related in a simple way. whole: 1.30 (0.27), residues: 955 helix: 2.22 (0.25), residues: 432 sheet: 0.23 (0.37), residues: 180 loop : -0.52 (0.32), residues: 343 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 336 TRP 0.016 0.001 TRP A 74 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7754) covalent geometry : angle 0.55936 (10495) SS BOND : bond 0.00376 ( 3) SS BOND : angle 1.16188 ( 6) hydrogen bonds : bond 0.04238 ( 399) hydrogen bonds : angle 4.56421 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.95 seconds wall clock time: 52 minutes 1.57 seconds (3121.57 seconds total)