Starting phenix.real_space_refine on Fri Aug 22 17:47:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5h_39774/08_2025/8z5h_39774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5h_39774/08_2025/8z5h_39774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z5h_39774/08_2025/8z5h_39774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5h_39774/08_2025/8z5h_39774.map" model { file = "/net/cci-nas-00/data/ceres_data/8z5h_39774/08_2025/8z5h_39774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5h_39774/08_2025/8z5h_39774.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4265 2.51 5 N 1153 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6645 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1748 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 15, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 7, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 154 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2450 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 317 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2130 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 8, 'TRANS': 277} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 6, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 124 Time building chain proxies: 1.83, per 1000 atoms: 0.28 Number of scatterers: 6645 At special positions: 0 Unit cell: (74, 100.64, 133.2, 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 40 16.00 O 1187 8.00 N 1153 7.00 C 4265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 13 " - pdb=" SG CYS R 258 " distance=2.23 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: 0.54 Conformation dependent library (CDL) restraints added in 405.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 44.9% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.779A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 4.138A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.655A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.787A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.878A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.258A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.536A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.785A pdb=" N LYS A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.852A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.677A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 18 through 22 Processing helix chain 'R' and resid 23 through 52 Proline residue: R 37 - end of helix removed outlier: 3.712A pdb=" N ALA R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 83 removed outlier: 4.228A pdb=" N TYR R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 93 through 103 removed outlier: 4.399A pdb=" N ILE R 99 " --> pdb=" O GLN R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 124 removed outlier: 4.347A pdb=" N SER R 108 " --> pdb=" O ASN R 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 Processing helix chain 'R' and resid 179 through 195 removed outlier: 3.658A pdb=" N ARG R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE R 185 " --> pdb=" O TRP R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 214 removed outlier: 3.888A pdb=" N GLY R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 255 removed outlier: 3.719A pdb=" N LYS R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP R 224 " --> pdb=" O LYS R 220 " (cutoff:3.500A) Proline residue: R 243 - end of helix removed outlier: 4.016A pdb=" N TRP R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 264 Processing helix chain 'R' and resid 264 through 275 Processing helix chain 'R' and resid 277 through 288 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 295 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.716A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.685A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.358A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.739A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.709A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.750A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.545A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.084A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 966 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: 1.00 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1060 1.31 - 1.44: 1957 1.44 - 1.56: 3733 1.56 - 1.69: 0 1.69 - 1.82: 49 Bond restraints: 6799 Sorted by residual: bond pdb=" CA HIS R 17 " pdb=" C HIS R 17 " ideal model delta sigma weight residual 1.528 1.471 0.058 1.07e-02 8.73e+03 2.91e+01 bond pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 1.528 1.465 0.063 1.25e-02 6.40e+03 2.56e+01 bond pdb=" CA HIS R 17 " pdb=" CB HIS R 17 " ideal model delta sigma weight residual 1.527 1.490 0.038 7.60e-03 1.73e+04 2.46e+01 bond pdb=" CA THR R 14 " pdb=" C THR R 14 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.12e+01 bond pdb=" C ASP A 225 " pdb=" O ASP A 225 " ideal model delta sigma weight residual 1.233 1.183 0.050 1.22e-02 6.72e+03 1.67e+01 ... (remaining 6794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9093 2.14 - 4.27: 170 4.27 - 6.41: 23 6.41 - 8.55: 7 8.55 - 10.68: 7 Bond angle restraints: 9300 Sorted by residual: angle pdb=" N GLY R 263 " pdb=" CA GLY R 263 " pdb=" C GLY R 263 " ideal model delta sigma weight residual 112.50 121.93 -9.43 1.16e+00 7.43e-01 6.61e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 111.52 120.45 -8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" N HIS R 175 " pdb=" CA HIS R 175 " pdb=" C HIS R 175 " ideal model delta sigma weight residual 108.69 98.01 10.68 1.77e+00 3.19e-01 3.64e+01 angle pdb=" C TYR R 176 " pdb=" N PRO R 177 " pdb=" CA PRO R 177 " ideal model delta sigma weight residual 119.84 112.30 7.54 1.25e+00 6.40e-01 3.63e+01 angle pdb=" N ILE R 178 " pdb=" CA ILE R 178 " pdb=" C ILE R 178 " ideal model delta sigma weight residual 109.30 116.16 -6.86 1.31e+00 5.83e-01 2.74e+01 ... (remaining 9295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 3556 15.05 - 30.09: 277 30.09 - 45.14: 72 45.14 - 60.19: 14 60.19 - 75.23: 9 Dihedral angle restraints: 3928 sinusoidal: 1259 harmonic: 2669 Sorted by residual: dihedral pdb=" CB CYS R 13 " pdb=" SG CYS R 13 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual -86.00 -142.56 56.56 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CA HIS R 89 " pdb=" C HIS R 89 " pdb=" N GLY R 90 " pdb=" CA GLY R 90 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLN A 59 " pdb=" C GLN A 59 " pdb=" N MET A 60 " pdb=" CA MET A 60 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 3925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1078 0.124 - 0.249: 19 0.249 - 0.373: 1 0.373 - 0.497: 1 0.497 - 0.622: 1 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" CA ILE R 178 " pdb=" N ILE R 178 " pdb=" C ILE R 178 " pdb=" CB ILE R 178 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA ASP A 225 " pdb=" N ASP A 225 " pdb=" C ASP A 225 " pdb=" CB ASP A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1097 not shown) Planarity restraints: 1182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU R 174 " 0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C GLU R 174 " -0.092 2.00e-02 2.50e+03 pdb=" O GLU R 174 " 0.035 2.00e-02 2.50e+03 pdb=" N HIS R 175 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 262 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LYS R 262 " -0.057 2.00e-02 2.50e+03 pdb=" O LYS R 262 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY R 263 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 17 " -0.028 2.00e-02 2.50e+03 2.35e-02 8.29e+00 pdb=" CG HIS R 17 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS R 17 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS R 17 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS R 17 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS R 17 " -0.023 2.00e-02 2.50e+03 ... (remaining 1179 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2335 2.85 - 3.36: 6014 3.36 - 3.87: 10260 3.87 - 4.39: 10849 4.39 - 4.90: 19812 Nonbonded interactions: 49270 Sorted by model distance: nonbonded pdb=" OD1 ASP B 290 " pdb=" NH1 ARG B 314 " model vdw 2.336 3.120 nonbonded pdb=" OG SER B 84 " pdb=" CE1 PHE G 61 " model vdw 2.359 3.340 nonbonded pdb=" O THR B 274 " pdb=" OG SER B 275 " model vdw 2.363 3.040 nonbonded pdb=" OE2 GLU A 344 " pdb=" NH2 ARG A 347 " model vdw 2.373 3.120 nonbonded pdb=" O THR B 164 " pdb=" OG1 THR B 164 " model vdw 2.375 3.040 ... (remaining 49265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.006 0.197 6800 Z= 0.328 Angle : 0.765 10.682 9302 Z= 0.450 Chirality : 0.054 0.622 1100 Planarity : 0.004 0.053 1182 Dihedral : 12.978 75.233 2195 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Cbeta Deviations : 0.12 % 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: -0.46 (0.29), residues: 901 helix: 1.13 (0.28), residues: 386 sheet: 0.05 (0.43), residues: 159 loop : -2.14 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 128 TYR 0.016 0.001 TYR R 80 PHE 0.022 0.002 PHE R 173 TRP 0.010 0.001 TRP A 244 HIS 0.016 0.002 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 6799) covalent geometry : angle 0.76412 ( 9300) SS BOND : bond 0.19744 ( 1) SS BOND : angle 2.75052 ( 2) hydrogen bonds : bond 0.17531 ( 332) hydrogen bonds : angle 6.37917 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.247 Fit side-chains REVERT: A 272 ASP cc_start: 0.8247 (t0) cc_final: 0.7976 (t0) REVERT: A 346 LEU cc_start: 0.8415 (mt) cc_final: 0.8091 (mp) REVERT: B 58 ILE cc_start: 0.7712 (pt) cc_final: 0.7455 (mt) REVERT: B 247 ASP cc_start: 0.6704 (t70) cc_final: 0.6420 (t0) REVERT: B 291 ASP cc_start: 0.7199 (p0) cc_final: 0.6977 (p0) REVERT: R 32 LEU cc_start: 0.8056 (tp) cc_final: 0.7684 (tp) REVERT: R 204 SER cc_start: 0.8547 (p) cc_final: 0.8305 (p) REVERT: R 242 LEU cc_start: 0.8652 (tt) cc_final: 0.8342 (tp) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.0943 time to fit residues: 25.7524 Evaluate side-chains 194 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.0040 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 340 ASN R 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102699 restraints weight = 10560.331| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.32 r_work: 0.3163 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6800 Z= 0.115 Angle : 0.535 5.795 9302 Z= 0.288 Chirality : 0.041 0.145 1100 Planarity : 0.004 0.049 1182 Dihedral : 4.529 23.318 976 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.73 % Allowed : 12.38 % Favored : 84.89 % 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: 0.09 (0.29), residues: 901 helix: 1.49 (0.28), residues: 392 sheet: 0.66 (0.45), residues: 149 loop : -1.91 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 128 TYR 0.009 0.001 TYR A 360 PHE 0.015 0.001 PHE A 222 TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6799) covalent geometry : angle 0.53480 ( 9300) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.67071 ( 2) hydrogen bonds : bond 0.04083 ( 332) hydrogen bonds : angle 4.31681 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.260 Fit side-chains REVERT: A 346 LEU cc_start: 0.8402 (mt) cc_final: 0.8174 (mm) REVERT: B 161 SER cc_start: 0.7984 (t) cc_final: 0.7744 (t) REVERT: B 237 ASN cc_start: 0.8699 (t0) cc_final: 0.8426 (t0) REVERT: B 247 ASP cc_start: 0.7309 (t70) cc_final: 0.7013 (t0) REVERT: R 85 ASP cc_start: 0.5071 (OUTLIER) cc_final: 0.4851 (m-30) REVERT: R 204 SER cc_start: 0.8430 (p) cc_final: 0.8201 (p) REVERT: R 242 LEU cc_start: 0.8608 (tt) cc_final: 0.8315 (tp) outliers start: 17 outliers final: 10 residues processed: 195 average time/residue: 0.1012 time to fit residues: 25.0365 Evaluate side-chains 195 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 240 CYS Chi-restraints excluded: chain R residue 279 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 0.0060 chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 88 optimal weight: 0.0170 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 GLN ** R 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101374 restraints weight = 10335.713| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.26 r_work: 0.3142 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6800 Z= 0.100 Angle : 0.498 5.854 9302 Z= 0.266 Chirality : 0.041 0.131 1100 Planarity : 0.003 0.046 1182 Dihedral : 4.309 28.740 976 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.89 % Allowed : 15.27 % Favored : 81.83 % 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: 0.42 (0.29), residues: 901 helix: 1.77 (0.28), residues: 392 sheet: 0.97 (0.45), residues: 148 loop : -1.81 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.015 0.001 TYR R 268 PHE 0.017 0.001 PHE A 222 TRP 0.009 0.001 TRP A 244 HIS 0.005 0.001 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 6799) covalent geometry : angle 0.49821 ( 9300) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.50273 ( 2) hydrogen bonds : bond 0.03524 ( 332) hydrogen bonds : angle 3.87105 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.146 Fit side-chains REVERT: A 346 LEU cc_start: 0.8361 (mt) cc_final: 0.8135 (mm) REVERT: B 58 ILE cc_start: 0.8277 (pt) cc_final: 0.8037 (mt) REVERT: B 125 ASN cc_start: 0.8323 (t0) cc_final: 0.8075 (t0) REVERT: B 161 SER cc_start: 0.8075 (t) cc_final: 0.7867 (t) REVERT: B 212 ASP cc_start: 0.7863 (t0) cc_final: 0.7653 (t0) REVERT: B 219 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7717 (mmt90) REVERT: B 237 ASN cc_start: 0.8732 (t0) cc_final: 0.8503 (t0) REVERT: B 247 ASP cc_start: 0.7288 (t70) cc_final: 0.6991 (t0) REVERT: B 258 ASP cc_start: 0.7748 (t0) cc_final: 0.7459 (t0) REVERT: B 338 ILE cc_start: 0.8512 (mm) cc_final: 0.8296 (mm) REVERT: R 204 SER cc_start: 0.8446 (p) cc_final: 0.8210 (p) REVERT: R 242 LEU cc_start: 0.8673 (tt) cc_final: 0.8426 (tp) outliers start: 18 outliers final: 11 residues processed: 211 average time/residue: 0.0967 time to fit residues: 26.0116 Evaluate side-chains 204 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 279 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096849 restraints weight = 10551.975| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.26 r_work: 0.3059 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6800 Z= 0.150 Angle : 0.530 6.016 9302 Z= 0.285 Chirality : 0.042 0.136 1100 Planarity : 0.003 0.047 1182 Dihedral : 4.556 32.573 976 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.54 % Allowed : 18.97 % Favored : 77.49 % 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: 0.51 (0.29), residues: 901 helix: 1.82 (0.28), residues: 392 sheet: 0.92 (0.42), residues: 161 loop : -1.78 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 251 TYR 0.020 0.001 TYR R 268 PHE 0.020 0.002 PHE A 222 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6799) covalent geometry : angle 0.52970 ( 9300) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.40019 ( 2) hydrogen bonds : bond 0.04387 ( 332) hydrogen bonds : angle 3.92207 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.194 Fit side-chains REVERT: B 125 ASN cc_start: 0.8447 (t0) cc_final: 0.8189 (t0) REVERT: B 161 SER cc_start: 0.8448 (t) cc_final: 0.8216 (t) REVERT: B 219 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7882 (mtt-85) REVERT: B 228 ASP cc_start: 0.7930 (p0) cc_final: 0.7497 (p0) REVERT: B 237 ASN cc_start: 0.8724 (t0) cc_final: 0.8422 (t0) REVERT: B 258 ASP cc_start: 0.8008 (t0) cc_final: 0.7615 (t0) REVERT: R 204 SER cc_start: 0.8496 (p) cc_final: 0.8263 (p) REVERT: R 242 LEU cc_start: 0.8707 (tt) cc_final: 0.8446 (tp) outliers start: 22 outliers final: 17 residues processed: 211 average time/residue: 0.0833 time to fit residues: 22.6816 Evaluate side-chains 209 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 240 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097907 restraints weight = 10535.024| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.25 r_work: 0.3078 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6800 Z= 0.111 Angle : 0.511 8.857 9302 Z= 0.268 Chirality : 0.041 0.142 1100 Planarity : 0.003 0.046 1182 Dihedral : 4.343 30.050 976 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.38 % Allowed : 20.10 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.29), residues: 901 helix: 1.93 (0.28), residues: 393 sheet: 0.92 (0.41), residues: 178 loop : -1.62 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.021 0.001 TYR R 268 PHE 0.018 0.001 PHE A 222 TRP 0.011 0.001 TRP A 244 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6799) covalent geometry : angle 0.51073 ( 9300) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.24348 ( 2) hydrogen bonds : bond 0.03593 ( 332) hydrogen bonds : angle 3.76855 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.190 Fit side-chains REVERT: B 125 ASN cc_start: 0.8357 (t0) cc_final: 0.8147 (t0) REVERT: B 161 SER cc_start: 0.8414 (t) cc_final: 0.8014 (p) REVERT: B 187 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8375 (m) REVERT: B 219 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7853 (mtt-85) REVERT: B 230 ASN cc_start: 0.8396 (m-40) cc_final: 0.7980 (m-40) REVERT: B 237 ASN cc_start: 0.8702 (t0) cc_final: 0.8483 (t0) REVERT: B 258 ASP cc_start: 0.8042 (t0) cc_final: 0.7668 (t0) REVERT: R 204 SER cc_start: 0.8483 (p) cc_final: 0.8272 (p) REVERT: R 242 LEU cc_start: 0.8685 (tt) cc_final: 0.8438 (tp) outliers start: 21 outliers final: 17 residues processed: 195 average time/residue: 0.0838 time to fit residues: 21.0590 Evaluate side-chains 198 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 240 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 39 ASN R 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097123 restraints weight = 10517.706| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.27 r_work: 0.3037 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6800 Z= 0.131 Angle : 0.514 6.101 9302 Z= 0.273 Chirality : 0.041 0.138 1100 Planarity : 0.003 0.045 1182 Dihedral : 4.389 31.249 976 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.70 % Allowed : 21.54 % Favored : 74.76 % 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 aren not related in a simple way. whole: 0.76 (0.29), residues: 901 helix: 1.96 (0.28), residues: 393 sheet: 1.03 (0.41), residues: 167 loop : -1.59 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.022 0.001 TYR R 268 PHE 0.022 0.001 PHE A 222 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6799) covalent geometry : angle 0.51377 ( 9300) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.24316 ( 2) hydrogen bonds : bond 0.03934 ( 332) hydrogen bonds : angle 3.78622 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.210 Fit side-chains REVERT: B 125 ASN cc_start: 0.8365 (t0) cc_final: 0.8092 (t0) REVERT: B 161 SER cc_start: 0.8491 (t) cc_final: 0.8123 (p) REVERT: B 187 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8364 (m) REVERT: B 212 ASP cc_start: 0.7930 (t0) cc_final: 0.7676 (t0) REVERT: B 219 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7923 (mtt-85) REVERT: B 230 ASN cc_start: 0.8351 (m-40) cc_final: 0.7974 (m-40) REVERT: B 237 ASN cc_start: 0.8667 (t0) cc_final: 0.8323 (t0) REVERT: B 258 ASP cc_start: 0.8056 (t0) cc_final: 0.7719 (t0) REVERT: R 204 SER cc_start: 0.8507 (p) cc_final: 0.8294 (p) REVERT: R 242 LEU cc_start: 0.8702 (tt) cc_final: 0.8431 (tp) outliers start: 23 outliers final: 16 residues processed: 199 average time/residue: 0.1020 time to fit residues: 25.6601 Evaluate side-chains 203 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 240 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 39 ASN R 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096050 restraints weight = 10201.566| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.30 r_work: 0.3030 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6800 Z= 0.136 Angle : 0.520 7.422 9302 Z= 0.275 Chirality : 0.041 0.133 1100 Planarity : 0.003 0.045 1182 Dihedral : 4.443 31.531 976 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.54 % Allowed : 22.67 % Favored : 73.79 % 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: 0.79 (0.29), residues: 901 helix: 1.95 (0.28), residues: 393 sheet: 1.00 (0.40), residues: 173 loop : -1.55 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.022 0.001 TYR R 268 PHE 0.018 0.001 PHE A 222 TRP 0.011 0.001 TRP A 244 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6799) covalent geometry : angle 0.51964 ( 9300) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.19902 ( 2) hydrogen bonds : bond 0.03957 ( 332) hydrogen bonds : angle 3.82552 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.288 Fit side-chains REVERT: B 67 SER cc_start: 0.8754 (m) cc_final: 0.8211 (t) REVERT: B 71 VAL cc_start: 0.8623 (t) cc_final: 0.8325 (p) REVERT: B 125 ASN cc_start: 0.8401 (t0) cc_final: 0.8136 (t0) REVERT: B 161 SER cc_start: 0.8547 (t) cc_final: 0.8152 (p) REVERT: B 212 ASP cc_start: 0.7932 (t0) cc_final: 0.7710 (t0) REVERT: B 219 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7958 (mtt-85) REVERT: B 237 ASN cc_start: 0.8682 (t0) cc_final: 0.8327 (t0) REVERT: B 258 ASP cc_start: 0.8064 (t0) cc_final: 0.7709 (t0) REVERT: R 204 SER cc_start: 0.8541 (p) cc_final: 0.8328 (p) REVERT: R 242 LEU cc_start: 0.8701 (tt) cc_final: 0.8425 (tp) outliers start: 22 outliers final: 19 residues processed: 198 average time/residue: 0.0898 time to fit residues: 22.3894 Evaluate side-chains 203 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 240 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN R 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.093084 restraints weight = 10508.317| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.45 r_work: 0.3045 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6800 Z= 0.128 Angle : 0.516 7.351 9302 Z= 0.272 Chirality : 0.041 0.134 1100 Planarity : 0.003 0.046 1182 Dihedral : 4.387 30.458 976 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.86 % Allowed : 23.47 % Favored : 72.67 % 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: 0.79 (0.29), residues: 901 helix: 1.97 (0.28), residues: 393 sheet: 1.01 (0.41), residues: 166 loop : -1.54 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.022 0.001 TYR R 268 PHE 0.021 0.001 PHE A 222 TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6799) covalent geometry : angle 0.51633 ( 9300) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.22826 ( 2) hydrogen bonds : bond 0.03839 ( 332) hydrogen bonds : angle 3.79935 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.153 Fit side-chains REVERT: B 67 SER cc_start: 0.8694 (m) cc_final: 0.8182 (t) REVERT: B 119 ASN cc_start: 0.8059 (m-40) cc_final: 0.7843 (m110) REVERT: B 125 ASN cc_start: 0.8394 (t0) cc_final: 0.8114 (t0) REVERT: B 160 SER cc_start: 0.8332 (m) cc_final: 0.7998 (p) REVERT: B 161 SER cc_start: 0.8442 (t) cc_final: 0.8204 (p) REVERT: B 187 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8490 (m) REVERT: B 212 ASP cc_start: 0.7968 (t0) cc_final: 0.7721 (t0) REVERT: B 219 ARG cc_start: 0.8209 (mtt-85) cc_final: 0.7989 (mtt-85) REVERT: B 230 ASN cc_start: 0.8376 (m-40) cc_final: 0.8009 (m-40) REVERT: B 237 ASN cc_start: 0.8674 (t0) cc_final: 0.8419 (t0) REVERT: B 258 ASP cc_start: 0.8055 (t0) cc_final: 0.7701 (t0) REVERT: R 204 SER cc_start: 0.8512 (p) cc_final: 0.8303 (p) REVERT: R 242 LEU cc_start: 0.8670 (tt) cc_final: 0.8390 (tp) outliers start: 24 outliers final: 20 residues processed: 201 average time/residue: 0.0841 time to fit residues: 21.4889 Evaluate side-chains 212 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 240 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 42 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.113381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098228 restraints weight = 10480.212| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.29 r_work: 0.3051 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6800 Z= 0.104 Angle : 0.500 7.184 9302 Z= 0.263 Chirality : 0.040 0.130 1100 Planarity : 0.003 0.045 1182 Dihedral : 4.202 27.848 976 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.89 % Allowed : 23.95 % Favored : 73.15 % 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 aren not related in a simple way. whole: 0.88 (0.29), residues: 901 helix: 2.09 (0.28), residues: 387 sheet: 1.01 (0.41), residues: 164 loop : -1.45 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.022 0.001 TYR R 268 PHE 0.020 0.001 PHE R 190 TRP 0.012 0.001 TRP A 244 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6799) covalent geometry : angle 0.49972 ( 9300) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.23986 ( 2) hydrogen bonds : bond 0.03369 ( 332) hydrogen bonds : angle 3.70497 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.231 Fit side-chains REVERT: A 344 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 350 THR cc_start: 0.8439 (t) cc_final: 0.8134 (p) REVERT: B 67 SER cc_start: 0.8694 (m) cc_final: 0.8206 (t) REVERT: B 119 ASN cc_start: 0.8165 (m-40) cc_final: 0.7963 (m110) REVERT: B 125 ASN cc_start: 0.8365 (t0) cc_final: 0.8125 (t0) REVERT: B 212 ASP cc_start: 0.7894 (t0) cc_final: 0.7681 (t0) REVERT: B 219 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7935 (mtt-85) REVERT: B 230 ASN cc_start: 0.8349 (m-40) cc_final: 0.7995 (m-40) REVERT: B 237 ASN cc_start: 0.8670 (t0) cc_final: 0.8322 (t0) REVERT: B 258 ASP cc_start: 0.8012 (t0) cc_final: 0.7668 (t0) REVERT: R 204 SER cc_start: 0.8516 (p) cc_final: 0.8313 (p) REVERT: R 242 LEU cc_start: 0.8671 (tt) cc_final: 0.8396 (tp) outliers start: 18 outliers final: 17 residues processed: 188 average time/residue: 0.0779 time to fit residues: 18.8188 Evaluate side-chains 199 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 240 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 82 optimal weight: 0.9980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096477 restraints weight = 10498.150| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.26 r_work: 0.3072 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6800 Z= 0.114 Angle : 0.507 7.325 9302 Z= 0.266 Chirality : 0.040 0.130 1100 Planarity : 0.003 0.044 1182 Dihedral : 4.054 18.928 974 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.73 % Allowed : 24.12 % Favored : 73.15 % 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 aren not related in a simple way. whole: 0.89 (0.29), residues: 901 helix: 2.09 (0.28), residues: 387 sheet: 1.04 (0.41), residues: 166 loop : -1.46 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.022 0.001 TYR R 268 PHE 0.021 0.001 PHE R 190 TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6799) covalent geometry : angle 0.50681 ( 9300) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.24587 ( 2) hydrogen bonds : bond 0.03585 ( 332) hydrogen bonds : angle 3.71288 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.220 Fit side-chains REVERT: A 350 THR cc_start: 0.8462 (t) cc_final: 0.8138 (p) REVERT: B 67 SER cc_start: 0.8749 (m) cc_final: 0.8272 (t) REVERT: B 125 ASN cc_start: 0.8427 (t0) cc_final: 0.8154 (t0) REVERT: B 160 SER cc_start: 0.8098 (m) cc_final: 0.7729 (p) REVERT: B 230 ASN cc_start: 0.8334 (m-40) cc_final: 0.7998 (m-40) REVERT: B 237 ASN cc_start: 0.8721 (t0) cc_final: 0.8498 (t0) REVERT: B 258 ASP cc_start: 0.8031 (t0) cc_final: 0.7628 (t0) REVERT: B 291 ASP cc_start: 0.7774 (m-30) cc_final: 0.7525 (m-30) REVERT: R 204 SER cc_start: 0.8502 (p) cc_final: 0.8278 (p) REVERT: R 242 LEU cc_start: 0.8698 (tt) cc_final: 0.8426 (tp) outliers start: 17 outliers final: 15 residues processed: 198 average time/residue: 0.1033 time to fit residues: 25.9130 Evaluate side-chains 206 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 240 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.112579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097737 restraints weight = 10420.460| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.22 r_work: 0.3078 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6800 Z= 0.108 Angle : 0.509 7.104 9302 Z= 0.267 Chirality : 0.040 0.130 1100 Planarity : 0.003 0.044 1182 Dihedral : 4.046 19.466 974 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.89 % Allowed : 23.63 % Favored : 73.47 % 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: 0.92 (0.29), residues: 901 helix: 2.09 (0.28), residues: 387 sheet: 1.13 (0.41), residues: 163 loop : -1.43 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.022 0.001 TYR R 268 PHE 0.021 0.001 PHE R 190 TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6799) covalent geometry : angle 0.50939 ( 9300) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.24118 ( 2) hydrogen bonds : bond 0.03457 ( 332) hydrogen bonds : angle 3.67811 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.30 seconds wall clock time: 30 minutes 20.91 seconds (1820.91 seconds total)