Starting phenix.real_space_refine on Tue Mar 3 23:03:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7euo_31323/03_2026/7euo_31323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7euo_31323/03_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_31323/03_2026/7euo_31323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7euo_31323/03_2026/7euo_31323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7euo_31323/03_2026/7euo_31323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7euo_31323/03_2026/7euo_31323.map" } 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-5986/lib/python3.9/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: 2.14, 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: 0.74 Conformation dependent library (CDL) restraints added in 348.7 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: 0.23 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: 1.39 Time building geometry restraints manager: 0.97 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: 4983 17.93 - 35.87: 430 35.87 - 53.80: 70 53.80 - 71.74: 11 71.74 - 89.67: 7 Dihedral angle restraints: 5501 sinusoidal: 2219 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 5498 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 13.715 89.671 3374 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 covalent geometry : bond 0.00388 ( 9144) covalent geometry : angle 0.64839 (12395) SS BOND : bond 0.00674 ( 3) SS BOND : angle 1.59056 ( 6) hydrogen bonds : bond 0.11985 ( 444) hydrogen bonds : angle 5.76031 ( 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 : 0.207 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: 0.5415 time to fit residues: 96.9691 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 : 0.362 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.132577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088505 restraints weight = 11741.314| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.15 r_work: 0.2996 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1132 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 : 0.567 6.663 12401 Z= 0.298 Chirality : 0.042 0.149 1419 Planarity : 0.004 0.037 1550 Dihedral : 5.612 78.342 1356 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.06 % Allowed : 10.32 % Favored : 87.62 % 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: 0.10 (0.25), residues: 1119 helix: 2.11 (0.27), residues: 389 sheet: -0.36 (0.30), residues: 287 loop : -1.53 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 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 0.009 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9144) covalent geometry : angle 0.56619 (12395) SS BOND : bond 0.00496 ( 3) SS BOND : angle 1.41338 ( 6) hydrogen bonds : bond 0.04801 ( 444) hydrogen bonds : angle 4.68997 ( 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 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8636 (m170) cc_final: 0.8342 (m-70) REVERT: A 193 ASP cc_start: 0.8856 (m-30) cc_final: 0.8600 (m-30) REVERT: A 242 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7315 (mmt90) REVERT: A 309 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: B 32 GLN cc_start: 0.7996 (mp10) cc_final: 0.7361 (mp10) REVERT: B 217 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6759 (ptp) REVERT: G 46 LYS cc_start: 0.9028 (mppt) cc_final: 0.8635 (mtmm) REVERT: G 47 GLU cc_start: 0.8209 (mp0) cc_final: 0.7847 (mp0) REVERT: G 58 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8284 (mp0) REVERT: S 160 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7310 (ttm110) REVERT: S 234 GLU cc_start: 0.8300 (pt0) cc_final: 0.7315 (pp20) outliers start: 20 outliers final: 7 residues processed: 135 average time/residue: 0.5867 time to fit residues: 84.3143 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 107 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.091512 restraints weight = 11665.192| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.11 r_work: 0.3002 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9147 Z= 0.111 Angle : 0.524 6.527 12401 Z= 0.275 Chirality : 0.041 0.144 1419 Planarity : 0.003 0.038 1550 Dihedral : 5.378 74.584 1356 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.17 % Allowed : 14.65 % Favored : 83.18 % 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: 0.28 (0.25), residues: 1119 helix: 2.17 (0.27), residues: 389 sheet: -0.11 (0.30), residues: 285 loop : -1.45 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.015 0.001 TYR S 190 PHE 0.012 0.001 PHE R 24 TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9144) covalent geometry : angle 0.52300 (12395) SS BOND : bond 0.00478 ( 3) SS BOND : angle 1.20740 ( 6) hydrogen bonds : bond 0.04342 ( 444) hydrogen bonds : angle 4.44524 ( 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 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8566 (m170) cc_final: 0.8283 (m-70) REVERT: R 306 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7257 (mm-40) REVERT: A 193 ASP cc_start: 0.8851 (m-30) cc_final: 0.8607 (m-30) REVERT: A 309 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: B 59 TYR cc_start: 0.8544 (m-80) cc_final: 0.8029 (m-80) REVERT: B 130 GLU cc_start: 0.8867 (mp0) cc_final: 0.8271 (mp0) REVERT: G 46 LYS cc_start: 0.8954 (mppt) cc_final: 0.8575 (mtmm) REVERT: G 47 GLU cc_start: 0.8069 (mp0) cc_final: 0.7685 (mp0) REVERT: G 58 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8288 (mp0) REVERT: S 160 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7245 (ttm110) REVERT: S 234 GLU cc_start: 0.8284 (pt0) cc_final: 0.7272 (pp20) outliers start: 21 outliers final: 9 residues processed: 138 average time/residue: 0.6016 time to fit residues: 88.4760 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 : 0.384 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR 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: 7.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.089069 restraints weight = 11873.517| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.34 r_work: 0.2984 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9147 Z= 0.130 Angle : 0.540 8.256 12401 Z= 0.282 Chirality : 0.041 0.139 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.334 70.889 1356 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.68 % Allowed : 16.31 % Favored : 81.01 % 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: 0.35 (0.25), residues: 1119 helix: 2.16 (0.27), residues: 392 sheet: -0.09 (0.30), residues: 287 loop : -1.35 (0.28), residues: 440 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 0.012 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9144) covalent geometry : angle 0.53892 (12395) SS BOND : bond 0.00576 ( 3) SS BOND : angle 1.42254 ( 6) hydrogen bonds : bond 0.04521 ( 444) hydrogen bonds : angle 4.41818 ( 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 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8596 (m170) cc_final: 0.8318 (m-70) REVERT: R 306 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7326 (mm-40) REVERT: A 193 ASP cc_start: 0.8861 (m-30) cc_final: 0.8618 (m-30) REVERT: A 309 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: B 59 TYR cc_start: 0.8633 (m-80) cc_final: 0.8185 (m-80) REVERT: B 130 GLU cc_start: 0.8880 (mp0) cc_final: 0.8367 (mp0) REVERT: B 215 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: B 217 MET cc_start: 0.8130 (ptt) cc_final: 0.7265 (pp-130) REVERT: G 46 LYS cc_start: 0.8891 (mppt) cc_final: 0.8563 (mtmm) REVERT: G 47 GLU cc_start: 0.8069 (mp0) cc_final: 0.7731 (mp0) REVERT: G 58 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8292 (mp0) REVERT: S 160 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7277 (ttm110) REVERT: S 234 GLU cc_start: 0.8329 (pt0) cc_final: 0.7319 (pp20) outliers start: 26 outliers final: 12 residues processed: 131 average time/residue: 0.5829 time to fit residues: 81.0378 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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 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 G residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.5980 chunk 16 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 241 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 = 0.3699 r_free = 0.3699 target = 0.134803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088762 restraints weight = 11720.824| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.31 r_work: 0.2962 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9147 Z= 0.121 Angle : 0.536 7.009 12401 Z= 0.281 Chirality : 0.041 0.139 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.231 65.972 1356 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.58 % Allowed : 17.03 % Favored : 80.39 % 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: 0.41 (0.25), residues: 1119 helix: 2.17 (0.27), residues: 392 sheet: 0.02 (0.30), residues: 286 loop : -1.32 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.011 0.001 TYR S 190 PHE 0.012 0.001 PHE A 189 TRP 0.010 0.001 TRP B 169 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9144) covalent geometry : angle 0.53554 (12395) SS BOND : bond 0.00557 ( 3) SS BOND : angle 1.38635 ( 6) hydrogen bonds : bond 0.04408 ( 444) hydrogen bonds : angle 4.38074 ( 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 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8569 (m170) cc_final: 0.8310 (m-70) REVERT: R 306 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7255 (mm-40) REVERT: A 193 ASP cc_start: 0.8857 (m-30) cc_final: 0.8619 (m-30) REVERT: A 240 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.5188 (ppp) REVERT: A 309 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: B 130 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: B 215 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: B 217 MET cc_start: 0.8102 (ptt) cc_final: 0.7695 (ptm) REVERT: B 234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8010 (t80) REVERT: G 46 LYS cc_start: 0.8849 (mppt) cc_final: 0.8522 (mtmm) REVERT: G 47 GLU cc_start: 0.7964 (mp0) cc_final: 0.7585 (mp0) REVERT: G 58 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8228 (mp0) REVERT: S 160 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7219 (ttm110) REVERT: S 234 GLU cc_start: 0.8335 (pt0) cc_final: 0.7314 (pp20) outliers start: 25 outliers final: 13 residues processed: 133 average time/residue: 0.5601 time to fit residues: 79.2013 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 240 MET 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 130 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE 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: 5.9990 chunk 72 optimal weight: 0.0060 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 0.0980 chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3739 r_free = 0.3739 target = 0.138354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092230 restraints weight = 11676.161| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.32 r_work: 0.3020 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2005 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= 0.099 Angle : 0.515 7.334 12401 Z= 0.267 Chirality : 0.040 0.144 1419 Planarity : 0.003 0.040 1550 Dihedral : 5.143 74.933 1356 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.17 % Allowed : 18.68 % 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: 0.56 (0.26), residues: 1119 helix: 2.22 (0.27), residues: 397 sheet: 0.19 (0.31), residues: 285 loop : -1.27 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 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 covalent geometry : bond 0.00207 ( 9144) covalent geometry : angle 0.51436 (12395) SS BOND : bond 0.00435 ( 3) SS BOND : angle 1.20988 ( 6) hydrogen bonds : bond 0.03755 ( 444) hydrogen bonds : angle 4.20154 ( 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 159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8519 (m170) cc_final: 0.8250 (m-70) REVERT: R 306 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7207 (mm-40) REVERT: A 193 ASP cc_start: 0.8803 (m-30) cc_final: 0.8571 (m-30) REVERT: A 309 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: B 130 GLU cc_start: 0.8804 (mp0) cc_final: 0.8304 (mp0) REVERT: B 215 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7602 (pp20) REVERT: B 217 MET cc_start: 0.7998 (ptt) cc_final: 0.7595 (ptm) REVERT: B 234 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8029 (t80) REVERT: G 46 LYS cc_start: 0.8624 (mppt) cc_final: 0.8337 (mtmm) REVERT: G 47 GLU cc_start: 0.7751 (mp0) cc_final: 0.7385 (mp0) REVERT: S 160 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7144 (ttm110) REVERT: S 234 GLU cc_start: 0.8276 (pt0) cc_final: 0.7267 (pp20) outliers start: 21 outliers final: 7 residues processed: 149 average time/residue: 0.5154 time to fit residues: 82.2155 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain R residue 310 GLU 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 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: 0.9990 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 109 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090980 restraints weight = 11735.306| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.32 r_work: 0.2996 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2090 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= 0.112 Angle : 0.542 6.935 12401 Z= 0.281 Chirality : 0.040 0.150 1419 Planarity : 0.003 0.040 1550 Dihedral : 5.113 72.041 1356 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.37 % Allowed : 19.61 % Favored : 78.02 % 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: 0.56 (0.26), residues: 1119 helix: 2.23 (0.27), residues: 398 sheet: 0.18 (0.31), residues: 281 loop : -1.27 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.017 0.001 TYR S 95 PHE 0.026 0.001 PHE R 74 TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9144) covalent geometry : angle 0.54093 (12395) SS BOND : bond 0.00483 ( 3) SS BOND : angle 1.36686 ( 6) hydrogen bonds : bond 0.04071 ( 444) hydrogen bonds : angle 4.25074 ( 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 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8599 (m170) cc_final: 0.8354 (m-70) REVERT: R 306 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7341 (mm-40) REVERT: A 193 ASP cc_start: 0.8814 (m-30) cc_final: 0.8581 (m-30) REVERT: A 240 MET cc_start: 0.5487 (pmt) cc_final: 0.5247 (pmt) REVERT: A 242 ARG cc_start: 0.7465 (mmt90) cc_final: 0.6964 (mmm-85) REVERT: A 309 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: B 59 TYR cc_start: 0.8587 (m-80) cc_final: 0.8293 (m-80) REVERT: B 130 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: B 215 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: B 217 MET cc_start: 0.8090 (ptt) cc_final: 0.7655 (ptm) REVERT: B 234 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8059 (t80) REVERT: B 298 ASP cc_start: 0.8841 (t70) cc_final: 0.8483 (OUTLIER) REVERT: B 301 LYS cc_start: 0.8320 (mtpt) cc_final: 0.8083 (mtpt) REVERT: G 46 LYS cc_start: 0.8643 (mppt) cc_final: 0.8349 (mtmm) REVERT: G 47 GLU cc_start: 0.7754 (mp0) cc_final: 0.7383 (mp0) REVERT: S 160 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7215 (ttm110) REVERT: S 234 GLU cc_start: 0.8323 (pt0) cc_final: 0.7332 (pp20) outliers start: 23 outliers final: 15 residues processed: 135 average time/residue: 0.6225 time to fit residues: 89.3608 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 295 CYS 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 130 GLU Chi-restraints excluded: chain B residue 189 SER 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: 0.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3674 r_free = 0.3674 target = 0.132574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086470 restraints weight = 11846.520| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.31 r_work: 0.2947 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9147 Z= 0.180 Angle : 0.595 7.161 12401 Z= 0.310 Chirality : 0.042 0.139 1419 Planarity : 0.003 0.040 1550 Dihedral : 5.406 76.478 1356 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.58 % Allowed : 20.23 % Favored : 77.19 % 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: 2.17 (0.26), residues: 398 sheet: 0.08 (0.31), residues: 280 loop : -1.39 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.017 0.001 TYR S 95 PHE 0.019 0.001 PHE R 74 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9144) covalent geometry : angle 0.59365 (12395) SS BOND : bond 0.00733 ( 3) SS BOND : angle 1.85613 ( 6) hydrogen bonds : bond 0.05053 ( 444) hydrogen bonds : angle 4.50677 ( 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 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7351 (mm-40) REVERT: A 193 ASP cc_start: 0.8842 (m-30) cc_final: 0.8592 (m-30) REVERT: A 240 MET cc_start: 0.5529 (pmt) cc_final: 0.5282 (pmt) REVERT: A 242 ARG cc_start: 0.7399 (mmt90) cc_final: 0.6960 (mmm-85) REVERT: A 309 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: B 215 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7717 (pp20) REVERT: B 217 MET cc_start: 0.8105 (ptt) cc_final: 0.7653 (ptm) REVERT: G 46 LYS cc_start: 0.8806 (mppt) cc_final: 0.8457 (mtmm) REVERT: G 47 GLU cc_start: 0.7938 (mp0) cc_final: 0.7431 (mp0) REVERT: S 160 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7289 (ttm110) REVERT: S 230 MET cc_start: 0.8607 (ttt) cc_final: 0.8173 (ttm) REVERT: S 234 GLU cc_start: 0.8389 (pt0) cc_final: 0.7404 (pp20) outliers start: 25 outliers final: 17 residues processed: 132 average time/residue: 0.6518 time to fit residues: 91.3608 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 295 CYS 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 42 ARG 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 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.134257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088089 restraints weight = 11719.521| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.31 r_work: 0.2978 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9147 Z= 0.131 Angle : 0.572 7.538 12401 Z= 0.297 Chirality : 0.041 0.143 1419 Planarity : 0.003 0.041 1550 Dihedral : 5.315 74.290 1356 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.06 % Allowed : 21.16 % Favored : 76.78 % 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: 0.51 (0.25), residues: 1119 helix: 2.34 (0.26), residues: 389 sheet: 0.13 (0.31), residues: 279 loop : -1.36 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.017 0.001 TYR S 95 PHE 0.019 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 covalent geometry : bond 0.00299 ( 9144) covalent geometry : angle 0.57139 (12395) SS BOND : bond 0.00604 ( 3) SS BOND : angle 1.61483 ( 6) hydrogen bonds : bond 0.04547 ( 444) hydrogen bonds : angle 4.43145 ( 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 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7363 (mm-40) REVERT: A 193 ASP cc_start: 0.8831 (m-30) cc_final: 0.8592 (m-30) REVERT: A 298 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 309 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: B 130 GLU cc_start: 0.8829 (mp0) cc_final: 0.8272 (mp0) REVERT: B 215 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7698 (pp20) REVERT: B 217 MET cc_start: 0.8089 (ptt) cc_final: 0.7686 (ptm) REVERT: B 298 ASP cc_start: 0.8894 (t70) cc_final: 0.8561 (OUTLIER) REVERT: G 46 LYS cc_start: 0.8754 (mppt) cc_final: 0.8463 (mtmm) REVERT: G 47 GLU cc_start: 0.7845 (mp0) cc_final: 0.7465 (mp0) REVERT: S 160 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7239 (ttm110) REVERT: S 234 GLU cc_start: 0.8358 (pt0) cc_final: 0.7374 (pp20) outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.6171 time to fit residues: 88.1188 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 : 0.335 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 295 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 37 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 268 ASN 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 = 0.133573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090629 restraints weight = 12118.639| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.20 r_work: 0.2987 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9147 Z= 0.109 Angle : 0.555 7.884 12401 Z= 0.285 Chirality : 0.040 0.147 1419 Planarity : 0.003 0.042 1550 Dihedral : 5.202 76.225 1356 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.34 % Allowed : 21.67 % 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: 0.58 (0.25), residues: 1119 helix: 2.34 (0.26), residues: 392 sheet: 0.18 (0.31), residues: 281 loop : -1.30 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.014 0.001 TYR S 95 PHE 0.020 0.001 PHE R 74 TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9144) covalent geometry : angle 0.55400 (12395) SS BOND : bond 0.00518 ( 3) SS BOND : angle 1.45301 ( 6) hydrogen bonds : bond 0.03910 ( 444) hydrogen bonds : angle 4.28352 ( 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 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.8381 (tpp) cc_final: 0.8062 (ttm) REVERT: R 306 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7262 (mm-40) REVERT: A 193 ASP cc_start: 0.8801 (m-30) cc_final: 0.8564 (m-30) REVERT: A 253 ILE cc_start: 0.8256 (tp) cc_final: 0.8033 (tp) REVERT: A 298 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 309 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: B 130 GLU cc_start: 0.8820 (mp0) cc_final: 0.8277 (mp0) REVERT: B 215 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: B 217 MET cc_start: 0.8081 (ptt) cc_final: 0.7671 (ptm) REVERT: B 234 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8102 (t80) REVERT: B 298 ASP cc_start: 0.8901 (t70) cc_final: 0.8589 (OUTLIER) REVERT: G 46 LYS cc_start: 0.8715 (mppt) cc_final: 0.8444 (mtmm) REVERT: G 47 GLU cc_start: 0.7729 (mp0) cc_final: 0.7458 (mp0) REVERT: S 43 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7900 (mptp) REVERT: S 160 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7122 (ttm110) REVERT: S 192 MET cc_start: 0.8463 (ptt) cc_final: 0.8137 (ptp) REVERT: S 234 GLU cc_start: 0.8350 (pt0) cc_final: 0.7391 (pp20) outliers start: 13 outliers final: 11 residues processed: 137 average time/residue: 0.5870 time to fit residues: 85.7590 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain R residue 295 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3676 r_free = 0.3676 target = 0.133667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.090539 restraints weight = 12020.409| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.20 r_work: 0.2988 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9147 Z= 0.111 Angle : 0.560 7.807 12401 Z= 0.287 Chirality : 0.040 0.150 1419 Planarity : 0.003 0.042 1550 Dihedral : 5.168 75.258 1356 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.75 % Allowed : 21.47 % Favored : 76.78 % 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: 0.64 (0.25), residues: 1119 helix: 2.43 (0.26), residues: 391 sheet: 0.21 (0.32), residues: 278 loop : -1.28 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.013 0.001 TYR S 95 PHE 0.020 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 covalent geometry : bond 0.00244 ( 9144) covalent geometry : angle 0.55898 (12395) SS BOND : bond 0.00472 ( 3) SS BOND : angle 1.49656 ( 6) hydrogen bonds : bond 0.03949 ( 444) hydrogen bonds : angle 4.26658 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.95 seconds wall clock time: 54 minutes 3.74 seconds (3243.74 seconds total)