Starting phenix.real_space_refine on Fri Aug 22 18:17:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg1_29991/08_2025/8gg1_29991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg1_29991/08_2025/8gg1_29991.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gg1_29991/08_2025/8gg1_29991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg1_29991/08_2025/8gg1_29991.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg1_29991/08_2025/8gg1_29991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg1_29991/08_2025/8gg1_29991.cif" } 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 46 5.16 5 C 4317 2.51 5 N 1161 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6755 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1750 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 3 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 14, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2443 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 79 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 347 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 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: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2163 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 73 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: 1.46, per 1000 atoms: 0.22 Number of scatterers: 6755 At special positions: 0 Unit cell: (83.2992, 134.493, 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 46 16.00 P 3 15.00 O 1228 8.00 N 1161 7.00 C 4317 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: 0.51 Conformation dependent library (CDL) restraints added in 347.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 48.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.647A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.643A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.667A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.535A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.974A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.775A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.532A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.619A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.529A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.704A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.551A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.636A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 86 removed outlier: 4.284A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 101 through 137 removed outlier: 4.376A pdb=" N TRP R 105 " --> pdb=" O PHE R 101 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.890A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.571A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 209 Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.533A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.757A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.000A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.851A 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: 4.625A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.601A 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: 6.671A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.585A 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: 4.001A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.583A 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: 7.100A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.083A 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: 6.843A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.864A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.618A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.759A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1017 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: 0.77 Time building geometry restraints manager: 0.70 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: 1702 1.33 - 1.45: 1398 1.45 - 1.58: 3725 1.58 - 1.70: 5 1.70 - 1.82: 64 Bond restraints: 6894 Sorted by residual: bond pdb=" CA GLN R 299 " pdb=" C GLN R 299 " ideal model delta sigma weight residual 1.521 1.487 0.034 1.17e-02 7.31e+03 8.57e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.41e+00 ... (remaining 6889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9263 1.73 - 3.47: 111 3.47 - 5.20: 22 5.20 - 6.94: 8 6.94 - 8.67: 2 Bond angle restraints: 9406 Sorted by residual: angle pdb=" N SER R 207 " pdb=" CA SER R 207 " pdb=" C SER R 207 " ideal model delta sigma weight residual 111.36 118.66 -7.30 1.09e+00 8.42e-01 4.49e+01 angle pdb=" N PHE R 208 " pdb=" CA PHE R 208 " pdb=" C PHE R 208 " ideal model delta sigma weight residual 114.39 123.06 -8.67 1.45e+00 4.76e-01 3.57e+01 angle pdb=" N ILE R 205 " pdb=" CA ILE R 205 " pdb=" C ILE R 205 " ideal model delta sigma weight residual 110.62 116.39 -5.77 1.02e+00 9.61e-01 3.20e+01 angle pdb=" C PRO R 211 " pdb=" N LEU R 212 " pdb=" CA LEU R 212 " ideal model delta sigma weight residual 120.44 126.57 -6.13 1.36e+00 5.41e-01 2.03e+01 angle pdb=" N VAL R 295 " pdb=" CA VAL R 295 " pdb=" C VAL R 295 " ideal model delta sigma weight residual 110.62 115.06 -4.44 1.02e+00 9.61e-01 1.89e+01 ... (remaining 9401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 3780 21.12 - 42.25: 208 42.25 - 63.37: 23 63.37 - 84.50: 6 84.50 - 105.62: 2 Dihedral angle restraints: 4019 sinusoidal: 1406 harmonic: 2613 Sorted by residual: 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 -56.21 -161.83 105.62 1 2.00e+01 2.50e-03 3.05e+01 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 0.07 104.53 1 2.00e+01 2.50e-03 3.00e+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 69.27 147.70 -78.43 1 2.00e+01 2.50e-03 1.92e+01 ... (remaining 4016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 854 0.046 - 0.092: 204 0.092 - 0.138: 46 0.138 - 0.184: 4 0.184 - 0.230: 1 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA PHE R 208 " pdb=" N PHE R 208 " pdb=" C PHE R 208 " pdb=" CB PHE R 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA TYR R 209 " pdb=" N TYR R 209 " pdb=" C TYR R 209 " pdb=" CB TYR R 209 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 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 5.96e-01 ... (remaining 1106 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 203 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C SER R 203 " 0.038 2.00e-02 2.50e+03 pdb=" O SER R 203 " -0.014 2.00e-02 2.50e+03 pdb=" N SER R 204 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO R 211 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 208 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C PHE R 208 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE R 208 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR R 209 " 0.011 2.00e-02 2.50e+03 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 399 2.74 - 3.28: 6342 3.28 - 3.82: 10618 3.82 - 4.36: 12280 4.36 - 4.90: 22905 Nonbonded interactions: 52544 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.195 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 55 " pdb=" O1A GTP A 401 " model vdw 2.287 3.040 nonbonded pdb=" O SER R 137 " pdb=" OG SER R 137 " model vdw 2.298 3.040 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.300 3.040 ... (remaining 52539 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.910 Find NCS groups from input model: 0.030 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 0.050 6895 Z= 0.167 Angle : 0.544 8.669 9408 Z= 0.320 Chirality : 0.041 0.230 1109 Planarity : 0.003 0.049 1179 Dihedral : 13.129 105.622 2318 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.28), residues: 878 helix: 1.35 (0.26), residues: 399 sheet: 0.41 (0.40), residues: 171 loop : -0.76 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 314 TYR 0.012 0.001 TYR A 339 PHE 0.011 0.001 PHE R 208 TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6894) covalent geometry : angle 0.54412 ( 9406) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.99221 ( 2) hydrogen bonds : bond 0.20950 ( 348) hydrogen bonds : angle 6.33847 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.208 Fit side-chains REVERT: A 29 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8090 (mm-40) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.5634 time to fit residues: 60.2385 Evaluate side-chains 79 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 17 GLN B 32 GLN B 75 GLN B 237 ASN R 51 ASN R 312 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102914 restraints weight = 8586.743| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.02 r_work: 0.3045 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6895 Z= 0.139 Angle : 0.518 6.620 9408 Z= 0.279 Chirality : 0.042 0.138 1109 Planarity : 0.003 0.030 1179 Dihedral : 6.827 107.541 985 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.66 % Allowed : 7.09 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.28), residues: 878 helix: 1.84 (0.26), residues: 400 sheet: 0.47 (0.41), residues: 164 loop : -0.73 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.015 0.001 TYR A 339 PHE 0.012 0.001 PHE B 292 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6894) covalent geometry : angle 0.51781 ( 9406) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.90950 ( 2) hydrogen bonds : bond 0.05560 ( 348) hydrogen bonds : angle 4.30706 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.252 Fit side-chains REVERT: B 314 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.6327 (ttm170) REVERT: R 231 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7660 (tm-30) outliers start: 11 outliers final: 8 residues processed: 89 average time/residue: 0.5593 time to fit residues: 52.4247 Evaluate side-chains 89 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 51 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104587 restraints weight = 8461.112| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.00 r_work: 0.3070 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6895 Z= 0.104 Angle : 0.463 6.535 9408 Z= 0.249 Chirality : 0.040 0.136 1109 Planarity : 0.003 0.028 1179 Dihedral : 6.594 107.617 985 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.96 % Allowed : 10.71 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.29), residues: 878 helix: 2.10 (0.27), residues: 400 sheet: 0.70 (0.41), residues: 164 loop : -0.72 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE B 241 TRP 0.007 0.001 TRP B 339 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6894) covalent geometry : angle 0.46297 ( 9406) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.79219 ( 2) hydrogen bonds : bond 0.04572 ( 348) hydrogen bonds : angle 4.01861 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.230 Fit side-chains REVERT: B 36 ASN cc_start: 0.8320 (m-40) cc_final: 0.7299 (p0) REVERT: B 219 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6929 (mtt90) REVERT: B 314 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6366 (ttm170) outliers start: 13 outliers final: 5 residues processed: 94 average time/residue: 0.5664 time to fit residues: 55.9053 Evaluate side-chains 85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 183 HIS B 237 ASN R 51 ASN R 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105829 restraints weight = 8727.302| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.03 r_work: 0.3068 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6895 Z= 0.106 Angle : 0.463 6.579 9408 Z= 0.249 Chirality : 0.041 0.153 1109 Planarity : 0.003 0.028 1179 Dihedral : 6.467 107.891 985 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.26 % Allowed : 13.12 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.29), residues: 878 helix: 2.23 (0.27), residues: 399 sheet: 0.75 (0.41), residues: 164 loop : -0.74 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 228 TYR 0.012 0.001 TYR A 339 PHE 0.011 0.001 PHE B 241 TRP 0.007 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6894) covalent geometry : angle 0.46333 ( 9406) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.76574 ( 2) hydrogen bonds : bond 0.04327 ( 348) hydrogen bonds : angle 3.90211 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.248 Fit side-chains REVERT: B 36 ASN cc_start: 0.8320 (m-40) cc_final: 0.7275 (p0) REVERT: B 219 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.6932 (mtt90) REVERT: B 314 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6393 (ttm170) outliers start: 15 outliers final: 6 residues processed: 92 average time/residue: 0.5184 time to fit residues: 50.4354 Evaluate side-chains 92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.0010 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 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 = 0.3538 r_free = 0.3538 target = 0.133199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105550 restraints weight = 8633.787| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.02 r_work: 0.3069 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6895 Z= 0.106 Angle : 0.464 6.586 9408 Z= 0.249 Chirality : 0.041 0.158 1109 Planarity : 0.003 0.028 1179 Dihedral : 6.398 108.198 985 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.26 % Allowed : 14.03 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.29), residues: 878 helix: 2.30 (0.27), residues: 400 sheet: 0.76 (0.41), residues: 164 loop : -0.73 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 228 TYR 0.012 0.001 TYR A 339 PHE 0.011 0.001 PHE A 212 TRP 0.007 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6894) covalent geometry : angle 0.46419 ( 9406) SS BOND : bond 0.00272 ( 1) SS BOND : angle 0.74153 ( 2) hydrogen bonds : bond 0.04288 ( 348) hydrogen bonds : angle 3.84413 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.311 Fit side-chains REVERT: B 36 ASN cc_start: 0.8342 (m-40) cc_final: 0.7288 (p0) REVERT: B 156 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: B 219 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6900 (mtt90) REVERT: B 314 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.6303 (ttm170) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.5651 time to fit residues: 57.3020 Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN R 51 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102224 restraints weight = 8614.962| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.03 r_work: 0.3039 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6895 Z= 0.132 Angle : 0.497 6.574 9408 Z= 0.268 Chirality : 0.041 0.161 1109 Planarity : 0.003 0.031 1179 Dihedral : 6.463 108.723 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.87 % Allowed : 13.88 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.29), residues: 878 helix: 2.25 (0.27), residues: 400 sheet: 0.76 (0.41), residues: 164 loop : -0.73 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 228 TYR 0.014 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6894) covalent geometry : angle 0.49684 ( 9406) SS BOND : bond 0.00333 ( 1) SS BOND : angle 0.81389 ( 2) hydrogen bonds : bond 0.04859 ( 348) hydrogen bonds : angle 3.90927 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.275 Fit side-chains REVERT: B 36 ASN cc_start: 0.8385 (m-40) cc_final: 0.7280 (p0) REVERT: B 59 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: B 156 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: B 217 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8004 (pmm) REVERT: B 219 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6990 (mtt90) REVERT: B 314 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6385 (ttm170) outliers start: 19 outliers final: 10 residues processed: 94 average time/residue: 0.5852 time to fit residues: 57.9999 Evaluate side-chains 94 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 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 = 0.3510 r_free = 0.3510 target = 0.130745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102932 restraints weight = 8472.997| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.01 r_work: 0.3052 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6895 Z= 0.120 Angle : 0.484 6.532 9408 Z= 0.261 Chirality : 0.041 0.166 1109 Planarity : 0.003 0.028 1179 Dihedral : 6.416 109.170 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.87 % Allowed : 15.08 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.29), residues: 878 helix: 2.32 (0.27), residues: 400 sheet: 0.67 (0.40), residues: 170 loop : -0.70 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.013 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6894) covalent geometry : angle 0.48425 ( 9406) SS BOND : bond 0.00296 ( 1) SS BOND : angle 0.79580 ( 2) hydrogen bonds : bond 0.04581 ( 348) hydrogen bonds : angle 3.86938 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.276 Fit side-chains REVERT: A 211 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7397 (mmtt) REVERT: B 36 ASN cc_start: 0.8421 (m-40) cc_final: 0.7272 (p0) REVERT: B 59 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: B 156 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: B 217 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7910 (pmm) REVERT: B 219 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.6925 (mtt90) REVERT: B 314 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6373 (ttm170) REVERT: R 231 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7292 (tt0) REVERT: R 297 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7616 (p) outliers start: 19 outliers final: 11 residues processed: 94 average time/residue: 0.5618 time to fit residues: 55.6432 Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102990 restraints weight = 8596.085| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.03 r_work: 0.3052 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6895 Z= 0.119 Angle : 0.483 6.516 9408 Z= 0.261 Chirality : 0.041 0.156 1109 Planarity : 0.003 0.029 1179 Dihedral : 6.409 109.339 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.87 % Allowed : 14.93 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.29), residues: 878 helix: 2.34 (0.27), residues: 400 sheet: 0.72 (0.40), residues: 170 loop : -0.72 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 228 TYR 0.013 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6894) covalent geometry : angle 0.48289 ( 9406) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.80938 ( 2) hydrogen bonds : bond 0.04558 ( 348) hydrogen bonds : angle 3.86276 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.214 Fit side-chains REVERT: A 211 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7411 (mmtt) REVERT: B 59 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: B 156 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: B 219 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7327 (mpt90) REVERT: B 314 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6420 (ttm170) REVERT: R 40 MET cc_start: 0.7488 (mtt) cc_final: 0.7167 (mtt) REVERT: R 297 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7666 (p) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.5685 time to fit residues: 57.0050 Evaluate side-chains 97 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102517 restraints weight = 8576.055| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.86 r_work: 0.3038 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 0.037 6895 Z= 0.130 Angle : 0.503 7.165 9408 Z= 0.271 Chirality : 0.042 0.170 1109 Planarity : 0.003 0.030 1179 Dihedral : 6.407 109.427 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.87 % Allowed : 15.54 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.29), residues: 878 helix: 2.30 (0.27), residues: 400 sheet: 0.73 (0.40), residues: 170 loop : -0.72 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.014 0.001 TYR A 339 PHE 0.013 0.001 PHE B 241 TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6894) covalent geometry : angle 0.50252 ( 9406) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.96490 ( 2) hydrogen bonds : bond 0.04787 ( 348) hydrogen bonds : angle 3.89675 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.271 Fit side-chains REVERT: A 211 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7519 (mmtt) REVERT: B 59 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: B 156 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: B 219 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7069 (mtt90) REVERT: B 314 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.6524 (ttm170) REVERT: R 231 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7414 (tt0) REVERT: R 297 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7846 (p) outliers start: 19 outliers final: 11 residues processed: 94 average time/residue: 0.6147 time to fit residues: 60.7583 Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099533 restraints weight = 8535.632| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.84 r_work: 0.2991 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6895 Z= 0.200 Angle : 0.573 6.652 9408 Z= 0.308 Chirality : 0.044 0.172 1109 Planarity : 0.003 0.035 1179 Dihedral : 6.645 111.041 985 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.71 % Allowed : 15.69 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.28), residues: 878 helix: 2.23 (0.26), residues: 392 sheet: 0.73 (0.40), residues: 168 loop : -0.80 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 228 TYR 0.018 0.002 TYR A 339 PHE 0.013 0.002 PHE R 282 TRP 0.010 0.001 TRP B 339 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 6894) covalent geometry : angle 0.57238 ( 9406) SS BOND : bond 0.00484 ( 1) SS BOND : angle 1.06338 ( 2) hydrogen bonds : bond 0.06114 ( 348) hydrogen bonds : angle 4.08513 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.291 Fit side-chains REVERT: B 156 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: B 219 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6977 (mtt90) REVERT: B 314 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.6521 (ttm170) REVERT: R 231 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7526 (tt0) outliers start: 18 outliers final: 13 residues processed: 99 average time/residue: 0.6219 time to fit residues: 64.5099 Evaluate side-chains 99 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102872 restraints weight = 8577.502| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.84 r_work: 0.3040 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6895 Z= 0.116 Angle : 0.495 6.441 9408 Z= 0.268 Chirality : 0.041 0.175 1109 Planarity : 0.003 0.027 1179 Dihedral : 6.430 110.502 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.26 % Allowed : 16.59 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.29), residues: 878 helix: 2.30 (0.27), residues: 399 sheet: 0.76 (0.40), residues: 168 loop : -0.76 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 228 TYR 0.013 0.001 TYR A 339 PHE 0.013 0.001 PHE B 241 TRP 0.008 0.001 TRP A 277 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6894) covalent geometry : angle 0.49441 ( 9406) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.87905 ( 2) hydrogen bonds : bond 0.04572 ( 348) hydrogen bonds : angle 3.91487 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.84 seconds wall clock time: 40 minutes 52.76 seconds (2452.76 seconds total)