Starting phenix.real_space_refine on Fri Aug 22 17:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo2_42425/08_2025/8uo2_42425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo2_42425/08_2025/8uo2_42425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uo2_42425/08_2025/8uo2_42425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo2_42425/08_2025/8uo2_42425.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uo2_42425/08_2025/8uo2_42425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo2_42425/08_2025/8uo2_42425.map" } resolution = 3.6 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= 0.018 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 32 5.16 5 C 4126 2.51 5 N 1154 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 6504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 1920 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 6, 'TRANS': 276} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 536 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 18, 'GLN:plan1': 9, 'ARG:plan': 14, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 278 Chain: "B" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2396 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 7, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 145 Chain: "G" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 341 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1800 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 629 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'TRP:plan': 3, 'PHE:plan': 9, 'ASN:plan1': 7, 'GLU:plan': 10, 'GLN:plan1': 7, 'TYR:plan': 2, 'ASP:plan': 6, 'ARG:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 252 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.27 Number of scatterers: 6504 At special positions: 0 Unit cell: (84.1669, 135.361, 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 32 16.00 P 3 15.00 O 1189 8.00 N 1154 7.00 C 4126 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: 0.44 Conformation dependent library (CDL) restraints added in 395.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 49.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.698A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.736A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 165' Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.775A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.692A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.591A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.257A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.507A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.760A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.661A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.760A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.661A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 32 through 61 removed outlier: 4.032A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.850A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.084A 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 102 through 137 removed outlier: 3.748A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.281A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.635A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.746A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 4.025A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.858A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.605A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 326 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.505A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.370A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.656A 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 52 removed outlier: 3.810A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.693A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.778A 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 103 removed outlier: 6.951A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.865A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.970A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.848A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 349 hydrogen bonds defined for protein. 1020 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: 0.82 Time building geometry restraints manager: 0.62 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: 1697 1.33 - 1.45: 1252 1.45 - 1.57: 3635 1.57 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 6629 Sorted by residual: bond pdb=" C ALA A 366 " pdb=" N VAL A 367 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.26e-02 6.30e+03 8.45e+01 bond pdb=" CA LYS A 338 " pdb=" C LYS A 338 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.81e+00 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.19e-02 7.06e+03 9.42e+00 bond pdb=" CA SER B 245 " pdb=" CB SER B 245 " ideal model delta sigma weight residual 1.535 1.471 0.064 2.09e-02 2.29e+03 9.32e+00 ... (remaining 6624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8834 2.13 - 4.26: 222 4.26 - 6.39: 35 6.39 - 8.52: 9 8.52 - 10.65: 3 Bond angle restraints: 9103 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 104.51 6.77 1.09e+00 8.42e-01 3.86e+01 angle pdb=" N GLN A 267 " pdb=" CA GLN A 267 " pdb=" C GLN A 267 " ideal model delta sigma weight residual 111.71 105.87 5.84 1.15e+00 7.56e-01 2.57e+01 angle pdb=" N GLU A 268 " pdb=" CA GLU A 268 " pdb=" C GLU A 268 " ideal model delta sigma weight residual 111.28 106.51 4.77 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.23 115.77 -6.54 1.55e+00 4.16e-01 1.78e+01 angle pdb=" C SER R 236 " pdb=" N GLU R 237 " pdb=" CA GLU R 237 " ideal model delta sigma weight residual 123.11 117.24 5.87 1.42e+00 4.96e-01 1.71e+01 ... (remaining 9098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 3757 33.33 - 66.67: 62 66.67 - 100.00: 4 100.00 - 133.33: 1 133.33 - 166.67: 2 Dihedral angle restraints: 3826 sinusoidal: 1036 harmonic: 2790 Sorted by residual: 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 -97.40 166.67 1 2.00e+01 2.50e-03 4.74e+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 -54.17 158.76 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 274.12 159.15 114.97 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 3823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 898 0.055 - 0.110: 165 0.110 - 0.165: 39 0.165 - 0.220: 5 0.220 - 0.275: 1 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE A 257 " pdb=" N ILE A 257 " pdb=" C ILE A 257 " pdb=" CB ILE A 257 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1105 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 366 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ALA A 366 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 366 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 367 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 219 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ARG B 219 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 219 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 220 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 266 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C LEU A 266 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 266 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 267 " -0.013 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1204 2.77 - 3.30: 6111 3.30 - 3.83: 10308 3.83 - 4.37: 10547 4.37 - 4.90: 19304 Nonbonded interactions: 47474 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.237 3.040 nonbonded pdb=" O LEU A 45 " pdb=" CG2 VAL A 224 " model vdw 2.274 3.460 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.309 3.040 nonbonded pdb=" NE2 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.374 3.120 nonbonded pdb=" N SER A 54 " pdb=" O1B GTP A 401 " model vdw 2.377 3.120 ... (remaining 47469 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 group one per residue 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.005 0.116 6630 Z= 0.346 Angle : 0.761 10.646 9105 Z= 0.488 Chirality : 0.047 0.275 1108 Planarity : 0.003 0.035 1167 Dihedral : 13.649 166.667 2005 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.40 % Allowed : 1.20 % Favored : 98.40 % 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: 1.29 (0.28), residues: 936 helix: 2.46 (0.25), residues: 414 sheet: -0.21 (0.42), residues: 168 loop : -0.52 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.011 0.001 TYR R 316 PHE 0.012 0.001 PHE A 246 TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 6629) covalent geometry : angle 0.76084 ( 9103) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.35940 ( 2) hydrogen bonds : bond 0.23383 ( 349) hydrogen bonds : angle 5.86788 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.233 Fit side-chains REVERT: G 48 ASP cc_start: 0.9036 (t70) cc_final: 0.8362 (t0) REVERT: R 217 PHE cc_start: 0.7921 (t80) cc_final: 0.7677 (t80) outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.0473 time to fit residues: 6.8232 Evaluate side-chains 73 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0170 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095798 restraints weight = 13931.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098735 restraints weight = 7468.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100753 restraints weight = 4993.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102033 restraints weight = 3831.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103086 restraints weight = 3207.159| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6630 Z= 0.112 Angle : 0.457 5.869 9105 Z= 0.253 Chirality : 0.041 0.191 1108 Planarity : 0.003 0.034 1167 Dihedral : 8.816 156.910 1031 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.40 % Allowed : 10.42 % Favored : 88.18 % 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: 1.42 (0.27), residues: 936 helix: 2.73 (0.25), residues: 418 sheet: 0.03 (0.42), residues: 165 loop : -0.83 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.023 0.001 TYR R 308 PHE 0.012 0.001 PHE A 246 TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6629) covalent geometry : angle 0.45744 ( 9103) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.56016 ( 2) hydrogen bonds : bond 0.04960 ( 349) hydrogen bonds : angle 4.04277 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.264 Fit side-chains REVERT: G 48 ASP cc_start: 0.8921 (t70) cc_final: 0.8333 (t0) REVERT: R 209 TYR cc_start: 0.7838 (m-80) cc_final: 0.7599 (m-10) outliers start: 7 outliers final: 6 residues processed: 85 average time/residue: 0.0635 time to fit residues: 7.8273 Evaluate side-chains 78 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 88 ASN B 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.095855 restraints weight = 13877.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098747 restraints weight = 7482.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100740 restraints weight = 5042.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102144 restraints weight = 3866.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102831 restraints weight = 3215.154| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6630 Z= 0.090 Angle : 0.413 5.915 9105 Z= 0.225 Chirality : 0.039 0.134 1108 Planarity : 0.003 0.035 1167 Dihedral : 8.335 153.000 1031 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.20 % Allowed : 13.43 % Favored : 85.37 % 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: 1.74 (0.28), residues: 936 helix: 3.08 (0.25), residues: 419 sheet: 0.12 (0.41), residues: 166 loop : -0.77 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 342 TYR 0.020 0.001 TYR R 308 PHE 0.018 0.001 PHE A 345 TRP 0.007 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 6629) covalent geometry : angle 0.41334 ( 9103) SS BOND : bond 0.00344 ( 1) SS BOND : angle 0.39872 ( 2) hydrogen bonds : bond 0.03807 ( 349) hydrogen bonds : angle 3.56077 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.211 Fit side-chains REVERT: A 344 GLU cc_start: 0.7839 (tp30) cc_final: 0.7632 (tp30) REVERT: B 262 MET cc_start: 0.8098 (tpp) cc_final: 0.7862 (tpp) REVERT: G 48 ASP cc_start: 0.8900 (t70) cc_final: 0.8247 (t0) REVERT: R 209 TYR cc_start: 0.7899 (m-80) cc_final: 0.7661 (m-10) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.0639 time to fit residues: 7.4615 Evaluate side-chains 76 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088259 restraints weight = 14336.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090870 restraints weight = 7782.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092710 restraints weight = 5314.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093961 restraints weight = 4129.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094841 restraints weight = 3485.156| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6630 Z= 0.221 Angle : 0.545 6.040 9105 Z= 0.306 Chirality : 0.043 0.161 1108 Planarity : 0.003 0.047 1167 Dihedral : 8.488 156.690 1031 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.00 % Allowed : 15.83 % Favored : 82.16 % 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: 1.41 (0.28), residues: 936 helix: 2.85 (0.25), residues: 417 sheet: -0.28 (0.41), residues: 165 loop : -0.84 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.020 0.002 TYR R 308 PHE 0.021 0.002 PHE B 235 TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 6629) covalent geometry : angle 0.54471 ( 9103) SS BOND : bond 0.00410 ( 1) SS BOND : angle 0.58195 ( 2) hydrogen bonds : bond 0.05439 ( 349) hydrogen bonds : angle 4.01873 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.261 Fit side-chains REVERT: A 344 GLU cc_start: 0.8214 (tp30) cc_final: 0.7990 (tp30) REVERT: B 262 MET cc_start: 0.8279 (tpp) cc_final: 0.7980 (tpp) REVERT: B 298 ASP cc_start: 0.8416 (t0) cc_final: 0.8012 (t0) REVERT: G 48 ASP cc_start: 0.8978 (t70) cc_final: 0.8317 (t0) REVERT: R 312 ASN cc_start: 0.8502 (t0) cc_final: 0.8096 (t0) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.0588 time to fit residues: 6.8873 Evaluate side-chains 80 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089800 restraints weight = 14320.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092442 restraints weight = 7729.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094346 restraints weight = 5250.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095606 restraints weight = 4049.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096538 restraints weight = 3408.181| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6630 Z= 0.143 Angle : 0.454 5.921 9105 Z= 0.254 Chirality : 0.041 0.137 1108 Planarity : 0.003 0.046 1167 Dihedral : 8.282 155.217 1031 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.61 % Allowed : 16.63 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.28), residues: 936 helix: 2.99 (0.26), residues: 418 sheet: -0.35 (0.40), residues: 168 loop : -0.88 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.021 0.001 TYR R 308 PHE 0.017 0.001 PHE R 217 TRP 0.013 0.001 TRP R 313 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6629) covalent geometry : angle 0.45426 ( 9103) SS BOND : bond 0.00390 ( 1) SS BOND : angle 0.36182 ( 2) hydrogen bonds : bond 0.04398 ( 349) hydrogen bonds : angle 3.70098 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.209 Fit side-chains REVERT: A 344 GLU cc_start: 0.8185 (tp30) cc_final: 0.7959 (tp30) REVERT: B 61 MET cc_start: 0.8943 (tmm) cc_final: 0.8711 (tmm) REVERT: B 262 MET cc_start: 0.8220 (tpp) cc_final: 0.7877 (tpp) REVERT: G 48 ASP cc_start: 0.8895 (t70) cc_final: 0.8161 (t0) REVERT: R 312 ASN cc_start: 0.8500 (t0) cc_final: 0.7602 (t0) REVERT: R 316 TYR cc_start: 0.8596 (m-10) cc_final: 0.8194 (m-10) outliers start: 13 outliers final: 11 residues processed: 84 average time/residue: 0.0675 time to fit residues: 8.0458 Evaluate side-chains 83 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 chunk 39 optimal weight: 0.0970 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092690 restraints weight = 14131.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095470 restraints weight = 7638.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097426 restraints weight = 5146.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098700 restraints weight = 3961.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099687 restraints weight = 3327.912| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 6630 Z= 0.083 Angle : 0.408 5.919 9105 Z= 0.223 Chirality : 0.040 0.130 1108 Planarity : 0.003 0.041 1167 Dihedral : 7.969 151.465 1031 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.81 % Allowed : 17.23 % Favored : 79.96 % 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: 1.67 (0.28), residues: 936 helix: 3.18 (0.25), residues: 418 sheet: -0.21 (0.40), residues: 168 loop : -0.84 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 342 TYR 0.024 0.001 TYR R 308 PHE 0.015 0.001 PHE R 217 TRP 0.008 0.001 TRP R 109 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00159 ( 6629) covalent geometry : angle 0.40813 ( 9103) SS BOND : bond 0.00377 ( 1) SS BOND : angle 0.37876 ( 2) hydrogen bonds : bond 0.03397 ( 349) hydrogen bonds : angle 3.39767 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.259 Fit side-chains REVERT: A 344 GLU cc_start: 0.8132 (tp30) cc_final: 0.7906 (tp30) REVERT: B 262 MET cc_start: 0.8186 (tpp) cc_final: 0.7854 (tpp) REVERT: B 298 ASP cc_start: 0.8271 (t0) cc_final: 0.7596 (t0) REVERT: G 48 ASP cc_start: 0.8856 (t70) cc_final: 0.8164 (t0) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.0567 time to fit residues: 6.9820 Evaluate side-chains 79 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 8 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3526 r_free = 0.3526 target = 0.112457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.088350 restraints weight = 14213.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090967 restraints weight = 7813.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092746 restraints weight = 5343.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094080 restraints weight = 4170.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094973 restraints weight = 3499.721| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6630 Z= 0.190 Angle : 0.496 5.998 9105 Z= 0.276 Chirality : 0.042 0.139 1108 Planarity : 0.003 0.046 1167 Dihedral : 8.045 154.473 1031 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.01 % Allowed : 17.23 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.28), residues: 936 helix: 2.96 (0.26), residues: 423 sheet: -0.40 (0.41), residues: 164 loop : -1.06 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 131 TYR 0.020 0.001 TYR R 308 PHE 0.018 0.002 PHE B 235 TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 6629) covalent geometry : angle 0.49648 ( 9103) SS BOND : bond 0.00372 ( 1) SS BOND : angle 0.44133 ( 2) hydrogen bonds : bond 0.04723 ( 349) hydrogen bonds : angle 3.74283 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.295 Fit side-chains REVERT: A 344 GLU cc_start: 0.8248 (tp30) cc_final: 0.8001 (tp30) REVERT: B 262 MET cc_start: 0.8237 (tpp) cc_final: 0.7931 (tpp) REVERT: G 48 ASP cc_start: 0.8893 (t70) cc_final: 0.8132 (t0) REVERT: R 312 ASN cc_start: 0.8501 (t0) cc_final: 0.8111 (t0) outliers start: 15 outliers final: 14 residues processed: 81 average time/residue: 0.0616 time to fit residues: 7.5045 Evaluate side-chains 83 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 4 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088715 restraints weight = 14283.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091365 restraints weight = 7807.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093199 restraints weight = 5339.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094522 restraints weight = 4144.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095346 restraints weight = 3469.300| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6630 Z= 0.160 Angle : 0.468 5.928 9105 Z= 0.260 Chirality : 0.041 0.137 1108 Planarity : 0.003 0.048 1167 Dihedral : 7.978 154.411 1031 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.41 % Allowed : 17.64 % Favored : 78.96 % 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: 1.29 (0.28), residues: 936 helix: 2.89 (0.26), residues: 424 sheet: -0.49 (0.40), residues: 167 loop : -1.09 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 131 TYR 0.022 0.001 TYR R 308 PHE 0.016 0.001 PHE R 217 TRP 0.011 0.001 TRP R 313 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6629) covalent geometry : angle 0.46754 ( 9103) SS BOND : bond 0.00349 ( 1) SS BOND : angle 0.31651 ( 2) hydrogen bonds : bond 0.04425 ( 349) hydrogen bonds : angle 3.68457 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.282 Fit side-chains REVERT: A 344 GLU cc_start: 0.8283 (tp30) cc_final: 0.8035 (tp30) REVERT: B 262 MET cc_start: 0.8195 (tpp) cc_final: 0.7875 (tpp) REVERT: G 48 ASP cc_start: 0.8905 (t70) cc_final: 0.8479 (t0) REVERT: R 312 ASN cc_start: 0.8466 (t0) cc_final: 0.7559 (t0) REVERT: R 316 TYR cc_start: 0.8518 (m-10) cc_final: 0.8055 (m-10) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.0639 time to fit residues: 7.9174 Evaluate side-chains 83 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3524 r_free = 0.3524 target = 0.112322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088265 restraints weight = 14436.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090918 restraints weight = 7890.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092748 restraints weight = 5376.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094063 restraints weight = 4163.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.094943 restraints weight = 3500.590| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6630 Z= 0.168 Angle : 0.484 5.948 9105 Z= 0.268 Chirality : 0.042 0.138 1108 Planarity : 0.003 0.048 1167 Dihedral : 7.935 154.814 1031 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.41 % Allowed : 17.43 % Favored : 79.16 % 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: 1.24 (0.28), residues: 936 helix: 2.82 (0.26), residues: 423 sheet: -0.46 (0.40), residues: 178 loop : -1.12 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 131 TYR 0.021 0.001 TYR R 308 PHE 0.014 0.001 PHE B 235 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6629) covalent geometry : angle 0.48354 ( 9103) SS BOND : bond 0.00361 ( 1) SS BOND : angle 0.34693 ( 2) hydrogen bonds : bond 0.04543 ( 349) hydrogen bonds : angle 3.73307 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.255 Fit side-chains REVERT: A 344 GLU cc_start: 0.8246 (tp30) cc_final: 0.7984 (tp30) REVERT: B 262 MET cc_start: 0.8234 (tpp) cc_final: 0.7896 (tpp) REVERT: G 48 ASP cc_start: 0.8881 (t70) cc_final: 0.8453 (t0) REVERT: R 312 ASN cc_start: 0.8463 (t0) cc_final: 0.8074 (t0) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.0658 time to fit residues: 8.1304 Evaluate side-chains 86 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.0270 chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091292 restraints weight = 14060.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094016 restraints weight = 7660.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.095945 restraints weight = 5192.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097221 restraints weight = 4005.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098100 restraints weight = 3361.335| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 6630 Z= 0.093 Angle : 0.422 5.894 9105 Z= 0.231 Chirality : 0.040 0.132 1108 Planarity : 0.003 0.044 1167 Dihedral : 7.651 151.473 1031 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.20 % Allowed : 18.64 % Favored : 79.16 % 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 (0.28), residues: 936 helix: 3.02 (0.25), residues: 424 sheet: -0.19 (0.41), residues: 170 loop : -1.13 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 342 TYR 0.022 0.001 TYR R 308 PHE 0.009 0.001 PHE B 199 TRP 0.008 0.001 TRP R 109 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 6629) covalent geometry : angle 0.42201 ( 9103) SS BOND : bond 0.00368 ( 1) SS BOND : angle 0.27567 ( 2) hydrogen bonds : bond 0.03485 ( 349) hydrogen bonds : angle 3.44543 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.253 Fit side-chains REVERT: A 344 GLU cc_start: 0.8212 (tp30) cc_final: 0.7960 (tp30) REVERT: B 262 MET cc_start: 0.8165 (tpp) cc_final: 0.7836 (tpp) outliers start: 11 outliers final: 11 residues processed: 80 average time/residue: 0.0644 time to fit residues: 7.4958 Evaluate side-chains 79 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 0.0980 chunk 38 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.117687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093546 restraints weight = 14098.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096350 restraints weight = 7625.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098305 restraints weight = 5133.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099696 restraints weight = 3939.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100616 restraints weight = 3275.029| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 6630 Z= 0.079 Angle : 0.410 6.450 9105 Z= 0.219 Chirality : 0.040 0.130 1108 Planarity : 0.003 0.040 1167 Dihedral : 7.339 147.874 1031 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.60 % Allowed : 19.84 % Favored : 78.56 % 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: 1.68 (0.28), residues: 936 helix: 3.18 (0.25), residues: 424 sheet: -0.06 (0.41), residues: 174 loop : -1.02 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 342 TYR 0.024 0.001 TYR R 308 PHE 0.022 0.001 PHE R 217 TRP 0.008 0.001 TRP R 109 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00154 ( 6629) covalent geometry : angle 0.41026 ( 9103) SS BOND : bond 0.00348 ( 1) SS BOND : angle 0.26167 ( 2) hydrogen bonds : bond 0.02936 ( 349) hydrogen bonds : angle 3.30376 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1324.97 seconds wall clock time: 23 minutes 27.17 seconds (1407.17 seconds total)