Starting phenix.real_space_refine on Thu Jul 2 15:41:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7euo_31323/07_2026/7euo_31323.cif" } resolution = 2.9 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= -0.001 sd= 0.072 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 64 5.16 5 C 5732 2.51 5 N 1511 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2323 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Classifications: {'peptide': 3} Modifications used: {'COO': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.16, per 1000 atoms: 0.24 Number of scatterers: 8950 At special positions: 0 Unit cell: (88.4, 124.95, 123.25, 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 64 16.00 O 1643 8.00 N 1511 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.78 Conformation dependent library (CDL) restraints added in 472.5 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 removed outlier: 3.831A pdb=" N ASP R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 27 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 Processing helix chain 'R' and resid 77 through 88 removed outlier: 4.519A pdb=" N PHE R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.735A pdb=" N ASN R 135 " --> pdb=" O VAL R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 163 removed outlier: 4.514A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 274 removed outlier: 3.882A pdb=" N GLN R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 302 removed outlier: 3.821A pdb=" N ASP R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 316 Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.010A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.542A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.106A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.602A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.845A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.711A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.854A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.555A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.768A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.187A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.894A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.804A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.942A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.857A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.659A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.709A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.650A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.980A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.980A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.624A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1266 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: 1.44 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1444 1.32 - 1.44: 2509 1.44 - 1.57: 5095 1.57 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9144 Sorted by residual: bond pdb=" CA SER B 281 " pdb=" C SER B 281 " ideal model delta sigma weight residual 1.522 1.474 0.047 1.31e-02 5.83e+03 1.29e+01 bond pdb=" C ILE R 204 " pdb=" O ILE R 204 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.60e-02 3.91e+03 1.13e+01 bond pdb=" N ILE R 207 " pdb=" CA ILE R 207 " ideal model delta sigma weight residual 1.459 1.418 0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.74e+00 ... (remaining 9139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 12026 1.63 - 3.26: 298 3.26 - 4.89: 56 4.89 - 6.52: 12 6.52 - 8.15: 3 Bond angle restraints: 12395 Sorted by residual: angle pdb=" N ARG R 201 " pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 111.14 107.05 4.09 1.08e+00 8.57e-01 1.44e+01 angle pdb=" O ILE R 203 " pdb=" C ILE R 203 " pdb=" N ILE R 204 " ideal model delta sigma weight residual 121.83 118.40 3.43 1.03e+00 9.43e-01 1.11e+01 angle pdb=" N LEU R 78 " pdb=" CA LEU R 78 " pdb=" C LEU R 78 " ideal model delta sigma weight residual 109.81 116.69 -6.88 2.21e+00 2.05e-01 9.68e+00 angle pdb=" CA PRO A 282 " pdb=" N PRO A 282 " pdb=" CD PRO A 282 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.83e+00 angle pdb=" C ILE R 207 " pdb=" N ILE R 208 " pdb=" CA ILE R 208 " ideal model delta sigma weight residual 122.35 118.85 3.50 1.18e+00 7.18e-01 8.78e+00 ... (remaining 12390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4885 17.93 - 35.87: 420 35.87 - 53.80: 66 53.80 - 71.74: 11 71.74 - 89.67: 7 Dihedral angle restraints: 5389 sinusoidal: 2107 harmonic: 3282 Sorted by residual: dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1346 0.097 - 0.195: 66 0.195 - 0.292: 3 0.292 - 0.389: 2 0.389 - 0.486: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C10 CLR R 402 " pdb=" C1 CLR R 402 " pdb=" C5 CLR R 402 " pdb=" C9 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1416 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 203 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ILE R 203 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE R 203 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE R 204 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 280 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LYS B 280 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS B 280 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 281 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.040 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 282 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.032 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 706 2.74 - 3.28: 8682 3.28 - 3.82: 13883 3.82 - 4.36: 16034 4.36 - 4.90: 29453 Nonbonded interactions: 68758 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.198 3.040 nonbonded pdb=" NH1 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.270 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP R 186 " pdb=" NZ LYS R 188 " model vdw 2.282 3.120 ... (remaining 68753 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: 1.210 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.870 Find NCS groups from input model: 0.040 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:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.004 0.090 9147 Z= 0.201 Angle : 0.649 8.155 12401 Z= 0.355 Chirality : 0.051 0.486 1419 Planarity : 0.004 0.059 1550 Dihedral : 13.747 89.671 3262 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.25), residues: 1119 helix: 1.83 (0.27), residues: 387 sheet: -0.53 (0.29), residues: 286 loop : -1.65 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 160 TYR 0.013 0.001 TYR S 190 PHE 0.010 0.001 PHE A 189 TRP 0.020 0.002 TRP B 211 HIS 0.013 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 ( 9144) covalent geometry : angle 0.64839 / 0.35 (12395) SS BOND : bond 0.00674 / 0.33 ( 3) SS BOND : angle 1.59056 / 0.96 ( 6) hydrogen bonds : bond 0.11985 / 8.64 ( 444) hydrogen bonds : angle 5.76031 / 4.21 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8604 (m170) cc_final: 0.8366 (m-70) REVERT: A 193 ASP cc_start: 0.8488 (m-30) cc_final: 0.8255 (m-30) REVERT: A 242 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7757 (mmt90) REVERT: G 58 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8320 (mp0) REVERT: S 160 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7360 (ttm110) REVERT: S 234 GLU cc_start: 0.7924 (pt0) cc_final: 0.7262 (pp20) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.5583 time to fit residues: 100.4334 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 268 ASN S 142 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.088543 restraints weight = 11744.844| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.15 r_work: 0.2997 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9147 Z= 0.129 Angle : 0.566 6.610 12401 Z= 0.297 Chirality : 0.042 0.151 1419 Planarity : 0.004 0.037 1550 Dihedral : 4.810 78.147 1244 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.06 % Allowed : 10.42 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1119 helix: 2.09 (0.27), residues: 390 sheet: -0.34 (0.30), residues: 287 loop : -1.52 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.020 0.001 TYR S 190 PHE 0.015 0.001 PHE R 24 TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9144) covalent geometry : angle 0.56517 / 0.30 (12395) SS BOND : bond 0.00496 / 0.24 ( 3) SS BOND : angle 1.39399 / 0.85 ( 6) hydrogen bonds : bond 0.04756 / 3.17 ( 444) hydrogen bonds : angle 4.65919 / 3.39 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8578 (m170) cc_final: 0.8292 (m-70) REVERT: A 193 ASP cc_start: 0.8853 (m-30) cc_final: 0.8598 (m-30) REVERT: A 309 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: B 32 GLN cc_start: 0.7998 (mp10) cc_final: 0.7360 (mp10) REVERT: B 59 TYR cc_start: 0.8737 (m-80) cc_final: 0.8531 (m-80) REVERT: B 217 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6733 (ptp) REVERT: G 46 LYS cc_start: 0.9023 (mppt) cc_final: 0.8633 (mtmm) REVERT: G 47 GLU cc_start: 0.8212 (mp0) cc_final: 0.7868 (mp0) REVERT: G 58 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8286 (mp0) REVERT: S 160 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7344 (ttm110) REVERT: S 234 GLU cc_start: 0.8303 (pt0) cc_final: 0.7317 (pp20) outliers start: 20 outliers final: 8 residues processed: 136 average time/residue: 0.5926 time to fit residues: 86.0460 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.0970 chunk 107 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 259 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085686 restraints weight = 11785.015| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.16 r_work: 0.2942 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9147 Z= 0.186 Angle : 0.585 6.832 12401 Z= 0.309 Chirality : 0.043 0.136 1419 Planarity : 0.004 0.037 1550 Dihedral : 4.852 78.175 1244 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.58 % Allowed : 14.86 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1119 helix: 2.13 (0.27), residues: 389 sheet: -0.31 (0.30), residues: 289 loop : -1.50 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.014 0.001 TYR S 190 PHE 0.014 0.001 PHE B 235 TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 9144) covalent geometry : angle 0.58362 / 0.31 (12395) SS BOND : bond 0.00718 / 0.35 ( 3) SS BOND : angle 1.72440 / 1.08 ( 6) hydrogen bonds : bond 0.05396 / 3.62 ( 444) hydrogen bonds : angle 4.68228 / 3.39 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7371 (mm-40) REVERT: A 193 ASP cc_start: 0.8865 (m-30) cc_final: 0.8607 (m-30) REVERT: A 309 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: B 130 GLU cc_start: 0.8901 (mp0) cc_final: 0.8281 (mp0) REVERT: G 46 LYS cc_start: 0.9009 (mppt) cc_final: 0.8641 (mtmm) REVERT: G 47 GLU cc_start: 0.8192 (mp0) cc_final: 0.7828 (mp0) REVERT: G 58 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8257 (mp0) REVERT: S 160 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7335 (ttm110) REVERT: S 234 GLU cc_start: 0.8375 (pt0) cc_final: 0.7384 (pp20) outliers start: 25 outliers final: 12 residues processed: 125 average time/residue: 0.6337 time to fit residues: 84.2638 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 90 HIS ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.087579 restraints weight = 11796.173| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.11 r_work: 0.2955 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9147 Z= 0.167 Angle : 0.567 7.993 12401 Z= 0.299 Chirality : 0.042 0.138 1419 Planarity : 0.003 0.038 1550 Dihedral : 4.792 76.379 1244 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.89 % Allowed : 16.00 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1119 helix: 2.14 (0.27), residues: 389 sheet: -0.23 (0.30), residues: 288 loop : -1.43 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.012 0.001 TYR S 190 PHE 0.013 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9144) covalent geometry : angle 0.56580 / 0.30 (12395) SS BOND : bond 0.00682 / 0.34 ( 3) SS BOND : angle 1.54351 / 0.96 ( 6) hydrogen bonds : bond 0.05150 / 3.44 ( 444) hydrogen bonds : angle 4.59655 / 3.32 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.8619 (tpp) cc_final: 0.8055 (mtt) REVERT: R 306 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7464 (mm-40) REVERT: A 193 ASP cc_start: 0.8868 (m-30) cc_final: 0.8616 (m-30) REVERT: A 309 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: B 215 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7752 (pp20) REVERT: B 217 MET cc_start: 0.8325 (ptt) cc_final: 0.7648 (ppp) REVERT: G 46 LYS cc_start: 0.9042 (mppt) cc_final: 0.8667 (mtmm) REVERT: G 47 GLU cc_start: 0.8247 (mp0) cc_final: 0.7819 (mp0) REVERT: G 58 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8276 (mp0) REVERT: S 160 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7426 (ttm110) REVERT: S 234 GLU cc_start: 0.8435 (pt0) cc_final: 0.7477 (pp20) outliers start: 28 outliers final: 16 residues processed: 132 average time/residue: 0.6469 time to fit residues: 90.8244 Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086448 restraints weight = 11817.361| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.30 r_work: 0.2920 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9147 Z= 0.149 Angle : 0.555 7.264 12401 Z= 0.292 Chirality : 0.041 0.137 1419 Planarity : 0.003 0.039 1550 Dihedral : 4.704 73.795 1244 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.89 % Allowed : 17.96 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1119 helix: 2.20 (0.27), residues: 389 sheet: -0.17 (0.30), residues: 287 loop : -1.38 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 242 TYR 0.012 0.001 TYR S 190 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9144) covalent geometry : angle 0.55460 / 0.29 (12395) SS BOND : bond 0.00689 / 0.34 ( 3) SS BOND : angle 1.47572 / 0.91 ( 6) hydrogen bonds : bond 0.04940 / 3.28 ( 444) hydrogen bonds : angle 4.55065 / 3.29 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7332 (mm-40) REVERT: A 193 ASP cc_start: 0.8859 (m-30) cc_final: 0.8615 (m-30) REVERT: A 309 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: B 215 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: B 217 MET cc_start: 0.8198 (ptt) cc_final: 0.7790 (ptm) REVERT: G 46 LYS cc_start: 0.8900 (mppt) cc_final: 0.8552 (mtmm) REVERT: G 47 GLU cc_start: 0.8113 (mp0) cc_final: 0.7780 (mp0) REVERT: S 160 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7287 (ttm110) REVERT: S 234 GLU cc_start: 0.8369 (pt0) cc_final: 0.7358 (pp20) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 0.5852 time to fit residues: 80.1267 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088670 restraints weight = 11777.691| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.31 r_work: 0.2988 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9147 Z= 0.110 Angle : 0.524 6.954 12401 Z= 0.273 Chirality : 0.040 0.141 1419 Planarity : 0.003 0.040 1550 Dihedral : 4.466 69.089 1244 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.68 % Allowed : 18.99 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1119 helix: 2.21 (0.26), residues: 397 sheet: -0.03 (0.30), residues: 286 loop : -1.35 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 242 TYR 0.012 0.001 TYR S 190 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9144) covalent geometry : angle 0.52281 / 0.27 (12395) SS BOND : bond 0.00569 / 0.28 ( 3) SS BOND : angle 1.36411 / 0.85 ( 6) hydrogen bonds : bond 0.04228 / 2.80 ( 444) hydrogen bonds : angle 4.36268 / 3.16 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8595 (m170) cc_final: 0.8339 (m-70) REVERT: R 87 MET cc_start: 0.8455 (tpp) cc_final: 0.7916 (mtt) REVERT: R 306 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7220 (mm-40) REVERT: A 193 ASP cc_start: 0.8850 (m-30) cc_final: 0.8612 (m-30) REVERT: A 240 MET cc_start: 0.5636 (pmt) cc_final: 0.5251 (pmt) REVERT: A 242 ARG cc_start: 0.7282 (mmt90) cc_final: 0.6567 (mmm-85) REVERT: A 309 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: B 130 GLU cc_start: 0.8832 (mp0) cc_final: 0.8274 (mp0) REVERT: B 215 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7640 (pp20) REVERT: B 217 MET cc_start: 0.8140 (ptt) cc_final: 0.7735 (ptm) REVERT: G 46 LYS cc_start: 0.8791 (mppt) cc_final: 0.8474 (mtmm) REVERT: G 47 GLU cc_start: 0.7953 (mp0) cc_final: 0.7594 (mp0) REVERT: S 160 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7253 (ttm110) REVERT: S 234 GLU cc_start: 0.8326 (pt0) cc_final: 0.7319 (pp20) outliers start: 26 outliers final: 13 residues processed: 140 average time/residue: 0.5856 time to fit residues: 87.4283 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 21 optimal weight: 8.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090251 restraints weight = 11763.667| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.31 r_work: 0.3000 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9147 Z= 0.107 Angle : 0.530 6.934 12401 Z= 0.279 Chirality : 0.040 0.144 1419 Planarity : 0.003 0.043 1550 Dihedral : 4.321 64.107 1244 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.17 % Allowed : 19.71 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1119 helix: 2.18 (0.26), residues: 396 sheet: 0.09 (0.31), residues: 279 loop : -1.36 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 242 TYR 0.012 0.001 TYR S 190 PHE 0.010 0.001 PHE A 189 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 9144) covalent geometry : angle 0.52967 / 0.28 (12395) SS BOND : bond 0.00518 / 0.25 ( 3) SS BOND : angle 1.31297 / 0.82 ( 6) hydrogen bonds : bond 0.04053 / 2.67 ( 444) hydrogen bonds : angle 4.32518 / 3.13 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8590 (m170) cc_final: 0.8331 (m-70) REVERT: R 87 MET cc_start: 0.8283 (tpp) cc_final: 0.7797 (mtt) REVERT: R 306 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7286 (mm-40) REVERT: A 193 ASP cc_start: 0.8822 (m-30) cc_final: 0.8586 (m-30) REVERT: A 309 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: B 130 GLU cc_start: 0.8769 (mp0) cc_final: 0.8230 (mp0) REVERT: B 215 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7668 (pp20) REVERT: B 217 MET cc_start: 0.8051 (ptt) cc_final: 0.7620 (ptm) REVERT: B 234 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7972 (t80) REVERT: G 46 LYS cc_start: 0.8692 (mppt) cc_final: 0.8382 (mtmm) REVERT: G 47 GLU cc_start: 0.7777 (mp0) cc_final: 0.7391 (mp0) REVERT: S 160 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7145 (ttm110) REVERT: S 234 GLU cc_start: 0.8293 (pt0) cc_final: 0.7280 (pp20) outliers start: 21 outliers final: 13 residues processed: 137 average time/residue: 0.5910 time to fit residues: 86.5971 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086570 restraints weight = 11819.181| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.31 r_work: 0.2956 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9147 Z= 0.154 Angle : 0.582 7.889 12401 Z= 0.303 Chirality : 0.041 0.147 1419 Planarity : 0.003 0.043 1550 Dihedral : 4.626 77.789 1244 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.99 % Allowed : 20.02 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1119 helix: 2.14 (0.26), residues: 397 sheet: -0.00 (0.31), residues: 280 loop : -1.38 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.011 0.001 TYR S 190 PHE 0.023 0.001 PHE R 74 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9144) covalent geometry : angle 0.58062 / 0.30 (12395) SS BOND : bond 0.00680 / 0.33 ( 3) SS BOND : angle 1.71586 / 1.09 ( 6) hydrogen bonds : bond 0.04763 / 3.18 ( 444) hydrogen bonds : angle 4.43976 / 3.21 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7277 (mm-40) REVERT: A 193 ASP cc_start: 0.8845 (m-30) cc_final: 0.8602 (m-30) REVERT: A 309 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: B 215 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7595 (pp20) REVERT: B 217 MET cc_start: 0.8134 (ptt) cc_final: 0.7608 (ptm) REVERT: G 46 LYS cc_start: 0.8790 (mppt) cc_final: 0.8469 (mtmm) REVERT: G 47 GLU cc_start: 0.7877 (mp0) cc_final: 0.7466 (mp0) REVERT: S 43 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7809 (mttp) REVERT: S 160 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7229 (ttm110) REVERT: S 234 GLU cc_start: 0.8346 (pt0) cc_final: 0.7371 (pp20) outliers start: 29 outliers final: 17 residues processed: 136 average time/residue: 0.6195 time to fit residues: 89.7582 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087971 restraints weight = 11723.886| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.31 r_work: 0.2975 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9147 Z= 0.131 Angle : 0.572 7.835 12401 Z= 0.297 Chirality : 0.041 0.146 1419 Planarity : 0.003 0.044 1550 Dihedral : 4.580 76.352 1244 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.48 % Allowed : 20.95 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.25), residues: 1119 helix: 2.17 (0.26), residues: 395 sheet: 0.04 (0.31), residues: 279 loop : -1.39 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.011 0.001 TYR S 190 PHE 0.023 0.001 PHE R 74 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9144) covalent geometry : angle 0.57097 / 0.30 (12395) SS BOND : bond 0.00622 / 0.30 ( 3) SS BOND : angle 1.64212 / 1.04 ( 6) hydrogen bonds : bond 0.04507 / 3.00 ( 444) hydrogen bonds : angle 4.40913 / 3.19 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7258 (mm-40) REVERT: A 193 ASP cc_start: 0.8841 (m-30) cc_final: 0.8599 (m-30) REVERT: A 253 ILE cc_start: 0.8240 (tp) cc_final: 0.8027 (tp) REVERT: A 309 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: B 130 GLU cc_start: 0.8792 (mp0) cc_final: 0.8255 (mp0) REVERT: B 215 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7639 (pp20) REVERT: B 217 MET cc_start: 0.8131 (ptt) cc_final: 0.7771 (ptm) REVERT: G 46 LYS cc_start: 0.8772 (mppt) cc_final: 0.8457 (mtmm) REVERT: G 47 GLU cc_start: 0.7846 (mp0) cc_final: 0.7436 (mp0) REVERT: S 43 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7756 (mttp) REVERT: S 160 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7222 (ttm110) REVERT: S 234 GLU cc_start: 0.8339 (pt0) cc_final: 0.7351 (pp20) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.5361 time to fit residues: 75.7250 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 53 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091444 restraints weight = 11739.681| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.30 r_work: 0.3015 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9147 Z= 0.107 Angle : 0.555 8.113 12401 Z= 0.285 Chirality : 0.040 0.148 1419 Planarity : 0.003 0.046 1550 Dihedral : 4.528 81.978 1244 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.96 % Allowed : 21.36 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.25), residues: 1119 helix: 2.18 (0.26), residues: 398 sheet: 0.05 (0.31), residues: 283 loop : -1.27 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.012 0.001 TYR S 190 PHE 0.023 0.001 PHE R 74 TRP 0.012 0.001 TRP R 95 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9144) covalent geometry : angle 0.55404 / 0.29 (12395) SS BOND : bond 0.00500 / 0.24 ( 3) SS BOND : angle 1.50193 / 0.95 ( 6) hydrogen bonds : bond 0.03892 / 2.57 ( 444) hydrogen bonds : angle 4.26359 / 3.09 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8699 (m170) cc_final: 0.8480 (m-70) REVERT: R 306 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7205 (mm-40) REVERT: A 193 ASP cc_start: 0.8809 (m-30) cc_final: 0.8577 (m-30) REVERT: A 309 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: B 130 GLU cc_start: 0.8700 (mp0) cc_final: 0.8164 (mp0) REVERT: B 215 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7436 (pp20) REVERT: B 217 MET cc_start: 0.8035 (ptt) cc_final: 0.7525 (ptm) REVERT: B 234 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 298 ASP cc_start: 0.8819 (t70) cc_final: 0.8540 (OUTLIER) REVERT: G 46 LYS cc_start: 0.8618 (mppt) cc_final: 0.8370 (mtmm) REVERT: G 47 GLU cc_start: 0.7594 (mp0) cc_final: 0.7249 (mp0) REVERT: S 43 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7626 (mttp) REVERT: S 160 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7020 (ttm110) REVERT: S 192 MET cc_start: 0.8361 (ptt) cc_final: 0.8043 (ptp) REVERT: S 234 GLU cc_start: 0.8261 (pt0) cc_final: 0.7492 (pp20) outliers start: 19 outliers final: 14 residues processed: 140 average time/residue: 0.5177 time to fit residues: 77.3234 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088196 restraints weight = 11687.768| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.29 r_work: 0.2980 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9147 Z= 0.140 Angle : 0.598 13.087 12401 Z= 0.306 Chirality : 0.041 0.145 1419 Planarity : 0.004 0.044 1550 Dihedral : 4.625 84.594 1244 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.48 % Allowed : 21.05 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1119 helix: 2.25 (0.26), residues: 396 sheet: 0.06 (0.31), residues: 282 loop : -1.31 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.011 0.001 TYR S 190 PHE 0.021 0.001 PHE R 74 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9144) covalent geometry : angle 0.59661 / 0.31 (12395) SS BOND : bond 0.00619 / 0.30 ( 3) SS BOND : angle 1.73646 / 1.10 ( 6) hydrogen bonds : bond 0.04466 / 2.97 ( 444) hydrogen bonds : angle 4.35047 / 3.15 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.08 seconds wall clock time: 55 minutes 34.23 seconds (3334.23 seconds total)