Starting phenix.real_space_refine on Mon Apr 28 01:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg1_29991/04_2025/8gg1_29991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg1_29991/04_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_29991/04_2025/8gg1_29991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg1_29991/04_2025/8gg1_29991.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg1_29991/04_2025/8gg1_29991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg1_29991/04_2025/8gg1_29991.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} 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, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 3} 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, 'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} 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: 5.37, per 1000 atoms: 0.79 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: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.92 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: 1.85 Time building geometry restraints manager: 2.28 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.740 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS R 296 PHE 0.011 0.001 PHE R 208 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.20950 ( 348) hydrogen bonds : angle 6.33847 ( 1017) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.99221 ( 2) covalent geometry : bond 0.00317 ( 6894) covalent geometry : angle 0.54412 ( 9406) *********************** 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 : 0.692 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: 1.1779 time to fit residues: 126.5631 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 : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 B 340 ASN R 51 ASN R 312 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106827 restraints weight = 8584.195| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.04 r_work: 0.3086 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6895 Z= 0.107 Angle : 0.477 6.527 9408 Z= 0.257 Chirality : 0.041 0.133 1109 Planarity : 0.003 0.031 1179 Dihedral : 6.682 106.831 985 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.36 % Allowed : 6.49 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.29), residues: 878 helix: 2.00 (0.26), residues: 399 sheet: 0.53 (0.41), residues: 164 loop : -0.68 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.005 0.001 HIS R 296 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 348) hydrogen bonds : angle 4.24504 ( 1017) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.78827 ( 2) covalent geometry : bond 0.00216 ( 6894) covalent geometry : angle 0.47728 ( 9406) *********************** 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 94 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.877 Fit side-chains REVERT: B 36 ASN cc_start: 0.8251 (m-40) cc_final: 0.7282 (p0) REVERT: B 314 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6242 (ttm170) outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 1.1276 time to fit residues: 107.6293 Evaluate side-chains 83 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 320 THR Chi-restraints excluded: chain B residue 314 ARG 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 31 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 0.0010 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 9 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 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 = 0.3566 r_free = 0.3566 target = 0.135348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107609 restraints weight = 8522.887| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.03 r_work: 0.3103 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1435 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= 0.086 Angle : 0.436 6.504 9408 Z= 0.234 Chirality : 0.040 0.140 1109 Planarity : 0.003 0.028 1179 Dihedral : 6.418 107.245 985 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.66 % Allowed : 9.50 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 878 helix: 2.37 (0.27), residues: 395 sheet: 0.78 (0.41), residues: 164 loop : -0.64 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 348) hydrogen bonds : angle 3.91442 ( 1017) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.63965 ( 2) covalent geometry : bond 0.00168 ( 6894) covalent geometry : angle 0.43634 ( 9406) *********************** 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 103 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.704 Fit side-chains REVERT: B 36 ASN cc_start: 0.8263 (m-40) cc_final: 0.7300 (p0) REVERT: B 219 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.6925 (mtt90) REVERT: B 314 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6352 (ttm170) outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 1.1384 time to fit residues: 116.8992 Evaluate side-chains 88 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.0010 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN B 237 ASN B 340 ASN R 51 ASN R 296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107325 restraints weight = 8662.192| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.03 r_work: 0.3092 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6895 Z= 0.099 Angle : 0.452 6.588 9408 Z= 0.243 Chirality : 0.040 0.149 1109 Planarity : 0.003 0.028 1179 Dihedral : 6.326 107.759 985 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.81 % Allowed : 12.22 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 878 helix: 2.55 (0.27), residues: 392 sheet: 0.83 (0.41), residues: 164 loop : -0.75 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 348) hydrogen bonds : angle 3.83851 ( 1017) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.69006 ( 2) covalent geometry : bond 0.00213 ( 6894) covalent geometry : angle 0.45169 ( 9406) *********************** 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 99 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.877 Fit side-chains REVERT: B 36 ASN cc_start: 0.8299 (m-40) cc_final: 0.7314 (p0) REVERT: B 219 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6908 (mtt90) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 1.1950 time to fit residues: 114.8016 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 : 0.699 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 219 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 29 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 183 HIS B 340 ASN R 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103942 restraints weight = 8493.599| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.02 r_work: 0.3063 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6895 Z= 0.121 Angle : 0.478 6.596 9408 Z= 0.256 Chirality : 0.041 0.150 1109 Planarity : 0.003 0.030 1179 Dihedral : 6.381 107.567 985 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.26 % Allowed : 13.27 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 878 helix: 2.53 (0.27), residues: 392 sheet: 0.83 (0.41), residues: 164 loop : -0.78 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR A 339 ARG 0.003 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 348) hydrogen bonds : angle 3.88698 ( 1017) SS BOND : bond 0.00323 ( 1) SS BOND : angle 0.76926 ( 2) covalent geometry : bond 0.00281 ( 6894) covalent geometry : angle 0.47805 ( 9406) *********************** 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 100 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.782 Fit side-chains REVERT: B 32 GLN cc_start: 0.7751 (mt0) cc_final: 0.7531 (mt0) REVERT: B 36 ASN cc_start: 0.8295 (m-40) cc_final: 0.7274 (p0) REVERT: B 219 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.6914 (mtt90) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 1.1141 time to fit residues: 107.3995 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 : 0.738 ------------------------------------------------------------------------------- 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 G residue 19 LEU 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 78 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS 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 = 0.3514 r_free = 0.3514 target = 0.131145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103254 restraints weight = 8467.004| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.01 r_work: 0.3045 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6895 Z= 0.119 Angle : 0.476 6.575 9408 Z= 0.257 Chirality : 0.041 0.162 1109 Planarity : 0.003 0.029 1179 Dihedral : 6.369 108.161 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.26 % Allowed : 14.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 878 helix: 2.54 (0.27), residues: 392 sheet: 0.76 (0.41), residues: 166 loop : -0.78 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.003 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 348) hydrogen bonds : angle 3.87540 ( 1017) SS BOND : bond 0.00314 ( 1) SS BOND : angle 0.75815 ( 2) covalent geometry : bond 0.00274 ( 6894) covalent geometry : angle 0.47619 ( 9406) *********************** 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 100 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.797 Fit side-chains REVERT: B 36 ASN cc_start: 0.8348 (m-40) cc_final: 0.7293 (p0) REVERT: B 59 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 156 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: B 219 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6895 (mtt90) REVERT: B 314 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7010 (ptp-170) outliers start: 15 outliers final: 9 residues processed: 94 average time/residue: 1.1073 time to fit residues: 110.0641 Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106197 restraints weight = 8568.245| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.99 r_work: 0.3071 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6895 Z= 0.103 Angle : 0.459 6.548 9408 Z= 0.247 Chirality : 0.040 0.168 1109 Planarity : 0.003 0.027 1179 Dihedral : 6.290 108.091 985 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 : 2.11 % Allowed : 15.54 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 878 helix: 2.63 (0.27), residues: 391 sheet: 0.82 (0.41), residues: 164 loop : -0.76 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 348) hydrogen bonds : angle 3.81898 ( 1017) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.67398 ( 2) covalent geometry : bond 0.00228 ( 6894) covalent geometry : angle 0.45913 ( 9406) *********************** 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 102 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.791 Fit side-chains REVERT: B 36 ASN cc_start: 0.8358 (m-40) cc_final: 0.7282 (p0) REVERT: B 217 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8101 (pmm) REVERT: B 219 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.6825 (mtt90) REVERT: B 314 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7023 (ptp-170) REVERT: R 297 VAL cc_start: 0.7837 (OUTLIER) cc_final: 0.7599 (p) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 1.1286 time to fit residues: 112.3653 Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103215 restraints weight = 8501.551| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.02 r_work: 0.3058 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6895 Z= 0.118 Angle : 0.478 6.532 9408 Z= 0.257 Chirality : 0.041 0.155 1109 Planarity : 0.003 0.029 1179 Dihedral : 6.322 108.108 985 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.41 % Allowed : 15.69 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 878 helix: 2.57 (0.27), residues: 392 sheet: 0.76 (0.41), residues: 166 loop : -0.74 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 348) hydrogen bonds : angle 3.85906 ( 1017) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.84057 ( 2) covalent geometry : bond 0.00273 ( 6894) covalent geometry : angle 0.47763 ( 9406) *********************** 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 94 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.751 Fit side-chains REVERT: B 59 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: B 156 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: B 217 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7923 (pmm) REVERT: B 219 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6867 (mtt90) REVERT: B 314 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.6936 (ptp-170) REVERT: R 231 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7210 (tt0) REVERT: R 297 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7602 (p) outliers start: 16 outliers final: 8 residues processed: 87 average time/residue: 1.2006 time to fit residues: 110.2111 Evaluate side-chains 92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.0030 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 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 = 0.3507 r_free = 0.3507 target = 0.131755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104974 restraints weight = 8533.931| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.85 r_work: 0.3053 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6895 Z= 0.102 Angle : 0.458 6.507 9408 Z= 0.247 Chirality : 0.040 0.169 1109 Planarity : 0.003 0.027 1179 Dihedral : 6.233 107.337 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.41 % Allowed : 15.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.29), residues: 878 helix: 2.65 (0.27), residues: 392 sheet: 0.82 (0.41), residues: 164 loop : -0.75 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 348) hydrogen bonds : angle 3.79842 ( 1017) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.81208 ( 2) covalent geometry : bond 0.00225 ( 6894) covalent geometry : angle 0.45758 ( 9406) *********************** 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 101 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.703 Fit side-chains REVERT: A 211 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7901 (mmtt) REVERT: B 156 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: B 217 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8163 (pmm) REVERT: B 219 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.6923 (mtt90) REVERT: B 314 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7137 (ptp-170) REVERT: R 297 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7763 (p) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 1.1621 time to fit residues: 116.5871 Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 6 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 = 0.3504 r_free = 0.3504 target = 0.131555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104703 restraints weight = 8647.244| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.86 r_work: 0.3046 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6895 Z= 0.105 Angle : 0.471 7.501 9408 Z= 0.254 Chirality : 0.041 0.175 1109 Planarity : 0.003 0.027 1179 Dihedral : 6.251 107.307 985 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.26 % Allowed : 16.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.29), residues: 878 helix: 2.65 (0.27), residues: 392 sheet: 0.80 (0.41), residues: 166 loop : -0.71 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.009 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.003 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 348) hydrogen bonds : angle 3.80452 ( 1017) SS BOND : bond 0.00215 ( 1) SS BOND : angle 0.79502 ( 2) covalent geometry : bond 0.00234 ( 6894) covalent geometry : angle 0.47073 ( 9406) ********************** 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 98 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.792 Fit side-chains REVERT: B 217 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8159 (pmm) REVERT: B 219 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.6922 (mtt90) REVERT: B 314 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7080 (ptp-170) REVERT: R 231 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7262 (tt0) REVERT: R 297 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7762 (p) outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 1.1683 time to fit residues: 114.7550 Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG 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 11 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103222 restraints weight = 8557.665| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.85 r_work: 0.3039 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1760 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= 0.122 Angle : 0.490 6.907 9408 Z= 0.264 Chirality : 0.041 0.162 1109 Planarity : 0.003 0.029 1179 Dihedral : 6.273 107.113 985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.11 % Allowed : 16.59 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.29), residues: 878 helix: 2.57 (0.27), residues: 392 sheet: 0.71 (0.40), residues: 172 loop : -0.69 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 348) hydrogen bonds : angle 3.86987 ( 1017) SS BOND : bond 0.00263 ( 1) SS BOND : angle 0.82042 ( 2) covalent geometry : bond 0.00282 ( 6894) covalent geometry : angle 0.48988 ( 9406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4748.27 seconds wall clock time: 81 minutes 43.64 seconds (4903.64 seconds total)