Starting phenix.real_space_refine on Tue Aug 4 20:51:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfz_29989/08_2026/8gfz_29989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfz_29989/08_2026/8gfz_29989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2026/8gfz_29989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2026/8gfz_29989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2026/8gfz_29989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfz_29989/08_2026/8gfz_29989.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4311 2.51 5 N 1154 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1763 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2433 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 8, 'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 349 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2147 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 20 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 1.25, per 1000 atoms: 0.19 Number of scatterers: 6744 At special positions: 0 Unit cell: (85.0346, 132.758, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1231 8.00 N 1154 7.00 C 4311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 0.46 Conformation dependent library (CDL) restraints added in 326.9 milliseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.570A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.527A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.696A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.604A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.649A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.605A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.528A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.623A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 37 through 61 Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.083A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.598A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.606A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 238 removed outlier: 3.785A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.560A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.705A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.082A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.813A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.519A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.646A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.095A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.798A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.887A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.976A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 1008 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: 0.62 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1737 1.33 - 1.45: 1331 1.45 - 1.57: 3747 1.57 - 1.69: 5 1.69 - 1.81: 62 Bond restraints: 6882 Sorted by residual: bond pdb=" CA GLU R 237 " pdb=" C GLU R 237 " ideal model delta sigma weight residual 1.524 1.486 0.039 1.43e-02 4.89e+03 7.26e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CA GLU R 237 " pdb=" CB GLU R 237 " ideal model delta sigma weight residual 1.531 1.496 0.035 1.34e-02 5.57e+03 6.71e+00 bond pdb=" N LYS R 235 " pdb=" CA LYS R 235 " ideal model delta sigma weight residual 1.459 1.429 0.030 1.21e-02 6.83e+03 6.27e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 6877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 9274 1.84 - 3.68: 88 3.68 - 5.51: 23 5.51 - 7.35: 2 7.35 - 9.19: 1 Bond angle restraints: 9388 Sorted by residual: angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" C SER R 236 " ideal model delta sigma weight residual 111.28 120.47 -9.19 1.09e+00 8.42e-01 7.11e+01 angle pdb=" N ASP R 234 " pdb=" CA ASP R 234 " pdb=" C ASP R 234 " ideal model delta sigma weight residual 111.82 117.66 -5.84 1.16e+00 7.43e-01 2.53e+01 angle pdb=" O ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 121.87 117.29 4.58 9.70e-01 1.06e+00 2.23e+01 angle pdb=" CA ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 117.15 121.88 -4.73 1.14e+00 7.69e-01 1.72e+01 angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" CB SER R 236 " ideal model delta sigma weight residual 110.12 105.99 4.13 1.47e+00 4.63e-01 7.89e+00 ... (remaining 9383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.07: 3895 28.07 - 56.14: 108 56.14 - 84.22: 9 84.22 - 112.29: 0 112.29 - 140.36: 3 Dihedral angle restraints: 4015 sinusoidal: 1417 harmonic: 2598 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -35.77 140.36 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 175.06 128.74 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -57.70 126.97 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 4012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 797 0.041 - 0.082: 244 0.082 - 0.123: 61 0.123 - 0.164: 3 0.164 - 0.205: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA SER R 236 " pdb=" N SER R 236 " pdb=" C SER R 236 " pdb=" CB SER R 236 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1103 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE R 205 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 332 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C THR R 281 " 0.023 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.008 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 510 2.74 - 3.28: 6307 3.28 - 3.82: 10683 3.82 - 4.36: 12368 4.36 - 4.90: 22591 Nonbonded interactions: 52459 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.201 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.309 3.040 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.309 3.040 ... (remaining 52454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.550 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6883 Z= 0.157 Angle : 0.500 9.190 9390 Z= 0.287 Chirality : 0.041 0.205 1106 Planarity : 0.003 0.034 1177 Dihedral : 13.528 140.362 2324 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.28), residues: 873 helix: 1.44 (0.27), residues: 381 sheet: 0.47 (0.41), residues: 165 loop : -0.60 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 239 TYR 0.008 0.001 TYR A 339 PHE 0.014 0.001 PHE B 234 TRP 0.006 0.001 TRP B 99 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 ( 6882) covalent geometry : angle 0.50008 / 0.29 ( 9388) SS BOND : bond 0.00160 / 0.08 ( 1) SS BOND : angle 0.68669 / 0.38 ( 2) hydrogen bonds : bond 0.20994 / 14.29 ( 346) hydrogen bonds : angle 6.23167 / 4.33 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.193 Fit side-chains REVERT: A 386 MET cc_start: 0.8572 (ttm) cc_final: 0.8269 (ttp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.4712 time to fit residues: 48.4759 Evaluate side-chains 81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 74 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094544 restraints weight = 8767.416| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.84 r_work: 0.2878 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6883 Z= 0.117 Angle : 0.488 5.542 9390 Z= 0.262 Chirality : 0.041 0.131 1106 Planarity : 0.003 0.029 1177 Dihedral : 8.595 140.285 979 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.20 % Allowed : 7.36 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.28), residues: 873 helix: 1.77 (0.27), residues: 391 sheet: 0.55 (0.39), residues: 171 loop : -0.56 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.008 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 6882) covalent geometry : angle 0.48735 / 0.26 ( 9388) SS BOND : bond 0.00222 / 0.12 ( 1) SS BOND : angle 1.01635 / 0.58 ( 2) hydrogen bonds : bond 0.05109 / 3.41 ( 346) hydrogen bonds : angle 4.48059 / 3.12 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.255 Fit side-chains REVERT: A 221 MET cc_start: 0.8303 (ttp) cc_final: 0.7996 (ttp) REVERT: R 188 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7310 (mm-30) REVERT: R 231 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8002 (tm-30) REVERT: R 239 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8065 (ptt180) outliers start: 8 outliers final: 0 residues processed: 97 average time/residue: 0.5936 time to fit residues: 60.3210 Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 239 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095384 restraints weight = 8721.803| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.84 r_work: 0.2883 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6883 Z= 0.105 Angle : 0.458 5.431 9390 Z= 0.245 Chirality : 0.040 0.131 1106 Planarity : 0.003 0.029 1177 Dihedral : 8.241 139.128 979 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.60 % Allowed : 10.96 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.29), residues: 873 helix: 2.03 (0.27), residues: 390 sheet: 0.68 (0.40), residues: 171 loop : -0.50 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.008 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.006 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 6882) covalent geometry : angle 0.45809 / 0.25 ( 9388) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 0.91777 / 0.52 ( 2) hydrogen bonds : bond 0.04521 / 3.01 ( 346) hydrogen bonds : angle 4.15814 / 2.89 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.264 Fit side-chains REVERT: B 303 ASP cc_start: 0.8501 (p0) cc_final: 0.8169 (p0) REVERT: R 79 ASP cc_start: 0.8384 (m-30) cc_final: 0.8075 (m-30) REVERT: R 231 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7856 (tm-30) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.5131 time to fit residues: 48.4181 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 52 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.2374 > 50:) chunk 65 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.091568 restraints weight = 8810.102| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.84 r_work: 0.2829 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6883 Z= 0.147 Angle : 0.508 5.574 9390 Z= 0.271 Chirality : 0.042 0.133 1106 Planarity : 0.003 0.036 1177 Dihedral : 8.290 139.735 979 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.65 % Allowed : 12.31 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 873 helix: 1.97 (0.27), residues: 390 sheet: 0.82 (0.41), residues: 164 loop : -0.59 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.010 0.001 TYR A 339 PHE 0.014 0.001 PHE A 212 TRP 0.007 0.001 TRP B 339 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6882) covalent geometry : angle 0.50822 / 0.27 ( 9388) SS BOND : bond 0.00272 / 0.14 ( 1) SS BOND : angle 0.98895 / 0.55 ( 2) hydrogen bonds : bond 0.05400 / 3.59 ( 346) hydrogen bonds : angle 4.23991 / 2.95 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.168 Fit side-chains REVERT: B 226 GLU cc_start: 0.7725 (pt0) cc_final: 0.7489 (pt0) REVERT: B 303 ASP cc_start: 0.8555 (p0) cc_final: 0.8208 (p0) REVERT: R 79 ASP cc_start: 0.8431 (m-30) cc_final: 0.8065 (m-30) REVERT: R 231 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7833 (tm-30) outliers start: 11 outliers final: 3 residues processed: 88 average time/residue: 0.4769 time to fit residues: 44.1000 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN R 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.091786 restraints weight = 8808.311| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.84 r_work: 0.2857 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6883 Z= 0.136 Angle : 0.494 5.612 9390 Z= 0.265 Chirality : 0.042 0.131 1106 Planarity : 0.003 0.035 1177 Dihedral : 8.203 138.378 979 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.25 % Allowed : 12.16 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 873 helix: 1.98 (0.27), residues: 389 sheet: 0.88 (0.41), residues: 164 loop : -0.69 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.009 0.001 TYR A 339 PHE 0.014 0.001 PHE A 212 TRP 0.008 0.001 TRP B 99 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6882) covalent geometry : angle 0.49365 / 0.26 ( 9388) SS BOND : bond 0.00234 / 0.12 ( 1) SS BOND : angle 0.98084 / 0.55 ( 2) hydrogen bonds : bond 0.05123 / 3.40 ( 346) hydrogen bonds : angle 4.18688 / 2.91 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.151 Fit side-chains REVERT: A 221 MET cc_start: 0.8258 (ttp) cc_final: 0.7957 (ttp) REVERT: B 303 ASP cc_start: 0.8575 (p0) cc_final: 0.8232 (p0) REVERT: R 79 ASP cc_start: 0.8502 (m-30) cc_final: 0.8130 (m-30) REVERT: R 156 MET cc_start: 0.8719 (ttt) cc_final: 0.8514 (ttp) REVERT: R 231 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7857 (tm-30) REVERT: R 239 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8062 (ptt180) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 0.5138 time to fit residues: 47.4158 Evaluate side-chains 84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 225 GLU Chi-restraints excluded: chain R residue 239 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN R 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.091266 restraints weight = 8870.423| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.85 r_work: 0.2837 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6883 Z= 0.134 Angle : 0.491 5.567 9390 Z= 0.263 Chirality : 0.042 0.131 1106 Planarity : 0.003 0.035 1177 Dihedral : 8.058 132.529 979 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.55 % Allowed : 12.46 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.29), residues: 873 helix: 2.02 (0.27), residues: 389 sheet: 0.86 (0.41), residues: 164 loop : -0.69 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.009 0.001 TYR A 339 PHE 0.015 0.001 PHE A 212 TRP 0.007 0.001 TRP B 99 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6882) covalent geometry : angle 0.49044 / 0.26 ( 9388) SS BOND : bond 0.00225 / 0.12 ( 1) SS BOND : angle 0.94099 / 0.53 ( 2) hydrogen bonds : bond 0.05067 / 3.37 ( 346) hydrogen bonds : angle 4.15692 / 2.89 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.247 Fit side-chains REVERT: A 25 LYS cc_start: 0.8027 (tttt) cc_final: 0.7759 (ttmm) REVERT: B 303 ASP cc_start: 0.8548 (p0) cc_final: 0.8219 (p0) REVERT: R 79 ASP cc_start: 0.8523 (m-30) cc_final: 0.8150 (m-30) REVERT: R 156 MET cc_start: 0.8728 (ttt) cc_final: 0.8521 (ttp) REVERT: R 231 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7841 (tm-30) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.4813 time to fit residues: 46.0703 Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 225 GLU Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 14 optimal weight: 0.0870 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 0.0170 chunk 82 optimal weight: 0.8980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099042 restraints weight = 8679.985| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.66 r_work: 0.2940 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.002 0.026 6883 Z= 0.084 Angle : 0.432 5.504 9390 Z= 0.232 Chirality : 0.040 0.130 1106 Planarity : 0.003 0.026 1177 Dihedral : 7.636 127.113 979 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.65 % Allowed : 13.51 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.29), residues: 873 helix: 2.29 (0.27), residues: 390 sheet: 0.87 (0.40), residues: 168 loop : -0.53 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.007 0.001 TYR R 209 PHE 0.015 0.001 PHE A 212 TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.08 ( 6882) covalent geometry : angle 0.43163 / 0.23 ( 9388) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 0.90037 / 0.52 ( 2) hydrogen bonds : bond 0.03483 / 2.32 ( 346) hydrogen bonds : angle 3.90884 / 2.71 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.263 Fit side-chains REVERT: A 268 GLU cc_start: 0.7692 (tp30) cc_final: 0.7117 (tt0) REVERT: A 386 MET cc_start: 0.8830 (ttm) cc_final: 0.8431 (ttp) REVERT: R 79 ASP cc_start: 0.8470 (m-30) cc_final: 0.8122 (m-30) REVERT: R 231 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7806 (tm-30) outliers start: 11 outliers final: 7 residues processed: 86 average time/residue: 0.5673 time to fit residues: 51.3279 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.093738 restraints weight = 8805.421| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.84 r_work: 0.2858 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6883 Z= 0.117 Angle : 0.480 5.550 9390 Z= 0.256 Chirality : 0.042 0.275 1106 Planarity : 0.003 0.033 1177 Dihedral : 7.587 124.553 979 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.80 % Allowed : 13.81 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.29), residues: 873 helix: 2.26 (0.27), residues: 391 sheet: 0.88 (0.40), residues: 169 loop : -0.54 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.008 0.001 TYR A 339 PHE 0.015 0.001 PHE A 212 TRP 0.007 0.001 TRP B 99 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6882) covalent geometry : angle 0.47967 / 0.26 ( 9388) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 0.84480 / 0.47 ( 2) hydrogen bonds : bond 0.04547 / 3.04 ( 346) hydrogen bonds : angle 3.98644 / 2.77 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.270 Fit side-chains REVERT: B 303 ASP cc_start: 0.8428 (p0) cc_final: 0.8139 (p0) REVERT: R 79 ASP cc_start: 0.8459 (m-30) cc_final: 0.8092 (m-30) REVERT: R 228 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7434 (ttm110) REVERT: R 231 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7772 (tm-30) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.5354 time to fit residues: 48.0058 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092740 restraints weight = 8784.235| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.84 r_work: 0.2839 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6883 Z= 0.126 Angle : 0.494 5.558 9390 Z= 0.262 Chirality : 0.042 0.144 1106 Planarity : 0.003 0.033 1177 Dihedral : 7.538 121.833 979 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.65 % Allowed : 14.26 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.29), residues: 873 helix: 2.20 (0.27), residues: 390 sheet: 0.88 (0.40), residues: 164 loop : -0.60 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.009 0.001 TYR A 339 PHE 0.016 0.001 PHE A 212 TRP 0.007 0.001 TRP B 99 HIS 0.011 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6882) covalent geometry : angle 0.49342 / 0.26 ( 9388) SS BOND : bond 0.00239 / 0.13 ( 1) SS BOND : angle 0.91140 / 0.51 ( 2) hydrogen bonds : bond 0.04779 / 3.18 ( 346) hydrogen bonds : angle 4.05532 / 2.81 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.182 Fit side-chains REVERT: A 220 HIS cc_start: 0.8083 (t-170) cc_final: 0.7843 (t70) REVERT: B 303 ASP cc_start: 0.8451 (p0) cc_final: 0.8148 (p0) REVERT: R 79 ASP cc_start: 0.8515 (m-30) cc_final: 0.8114 (m-30) REVERT: R 228 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7440 (ttm110) REVERT: R 231 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7770 (tm-30) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.4970 time to fit residues: 46.0622 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.093227 restraints weight = 8795.378| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.83 r_work: 0.2855 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6883 Z= 0.113 Angle : 0.484 5.493 9390 Z= 0.258 Chirality : 0.042 0.259 1106 Planarity : 0.003 0.032 1177 Dihedral : 7.395 117.978 979 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.20 % Allowed : 14.86 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.29), residues: 873 helix: 2.24 (0.27), residues: 391 sheet: 0.82 (0.40), residues: 168 loop : -0.56 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.008 0.001 TYR A 339 PHE 0.017 0.001 PHE A 212 TRP 0.007 0.001 TRP B 99 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6882) covalent geometry : angle 0.48379 / 0.26 ( 9388) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 0.92440 / 0.52 ( 2) hydrogen bonds : bond 0.04488 / 3.00 ( 346) hydrogen bonds : angle 4.00768 / 2.78 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.196 Fit side-chains REVERT: A 220 HIS cc_start: 0.8081 (t-170) cc_final: 0.7793 (t70) REVERT: A 268 GLU cc_start: 0.7667 (tp30) cc_final: 0.6944 (tt0) REVERT: B 303 ASP cc_start: 0.8451 (p0) cc_final: 0.8163 (p0) REVERT: R 79 ASP cc_start: 0.8514 (m-30) cc_final: 0.8041 (m-30) REVERT: R 228 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7419 (ttm110) REVERT: R 231 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7750 (tm-30) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.5568 time to fit residues: 48.5847 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.091873 restraints weight = 8802.515| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.83 r_work: 0.2830 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6883 Z= 0.140 Angle : 0.510 5.515 9390 Z= 0.271 Chirality : 0.042 0.149 1106 Planarity : 0.003 0.035 1177 Dihedral : 7.392 115.495 979 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.65 % Allowed : 14.41 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.29), residues: 873 helix: 2.17 (0.27), residues: 389 sheet: 0.72 (0.40), residues: 170 loop : -0.61 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.009 0.001 TYR A 339 PHE 0.017 0.001 PHE A 212 TRP 0.007 0.001 TRP B 339 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6882) covalent geometry : angle 0.51028 / 0.27 ( 9388) SS BOND : bond 0.00259 / 0.14 ( 1) SS BOND : angle 0.93213 / 0.52 ( 2) hydrogen bonds : bond 0.05072 / 3.38 ( 346) hydrogen bonds : angle 4.09209 / 2.84 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2139.56 seconds wall clock time: 37 minutes 8.63 seconds (2228.63 seconds total)