Starting phenix.real_space_refine on Fri Oct 23 06:28:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nt8_49755/10_2026/9nt8_49755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nt8_49755/10_2026/9nt8_49755.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/9nt8_49755/10_2026/9nt8_49755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nt8_49755/10_2026/9nt8_49755.map" model { file = "/net/cci-nas-00/data/ceres_data/9nt8_49755/10_2026/9nt8_49755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nt8_49755/10_2026/9nt8_49755.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5515 2.51 5 N 1531 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8694 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2647 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 584 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TRP:plan': 8, 'GLU:plan': 10, 'GLN:plan1': 7, 'ARG:plan': 8, 'TYR:plan': 7, 'ASP:plan': 9, 'PHE:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 294 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1934 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 123 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8694 At special positions: 0 Unit cell: (89.0517, 101.395, 169.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1601 8.00 N 1531 7.00 C 5515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.61 Conformation dependent library (CDL) restraints added in 525.6 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 43.3% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'R' and resid 33 through 53 removed outlier: 4.632A pdb=" N TRP R 39 " --> pdb=" O THR R 35 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU R 52 " --> pdb=" O ARG R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 95 removed outlier: 3.983A pdb=" N SER R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL R 95 " --> pdb=" O TRP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 169 removed outlier: 3.589A pdb=" N TYR R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE R 156 " --> pdb=" O TYR R 152 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 207 removed outlier: 3.508A pdb=" N VAL R 194 " --> pdb=" O ARG R 190 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR R 207 " --> pdb=" O TRP R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 223 removed outlier: 3.781A pdb=" N LEU R 218 " --> pdb=" O TRP R 214 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.613A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP R 243 " --> pdb=" O ALA R 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 245 " --> pdb=" O TYR R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 removed outlier: 3.716A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 290 removed outlier: 3.765A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.565A pdb=" N ILE R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.507A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.550A pdb=" N PHE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 361 removed outlier: 3.665A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE R 357 " --> pdb=" O THR R 353 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 Processing helix chain 'R' and resid 380 through 393 removed outlier: 3.932A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 403 Processing helix chain 'R' and resid 406 through 420 removed outlier: 3.792A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.536A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.566A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.787A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.007A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.527A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.349A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.560A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.543A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.803A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 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 8 through 24 removed outlier: 3.571A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.671A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.579A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.625A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 28 removed outlier: 3.945A pdb=" N VAL P 16 " --> pdb=" O PHE P 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER P 17 " --> pdb=" O THR P 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 101 through 102 removed outlier: 4.426A pdb=" N TYR R 101 " --> pdb=" O ASP R 122 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP R 122 " --> pdb=" O TYR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.590A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.661A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.948A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.802A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.824A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.983A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.756A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.995A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.526A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1125 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: 1.36 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1540 1.32 - 1.45: 2338 1.45 - 1.57: 4917 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 8860 Sorted by residual: bond pdb=" C GLN R 45 " pdb=" N CYS R 46 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" C ARG R 40 " pdb=" O ARG R 40 " ideal model delta sigma weight residual 1.237 1.278 -0.042 1.17e-02 7.31e+03 1.26e+01 bond pdb=" N ILE R 308 " pdb=" CA ILE R 308 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" N VAL R 83 " pdb=" CA VAL R 83 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 8855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 11520 2.22 - 4.44: 446 4.44 - 6.66: 42 6.66 - 8.89: 2 8.89 - 11.11: 1 Bond angle restraints: 12011 Sorted by residual: angle pdb=" C THR R 35 " pdb=" N VAL R 36 " pdb=" CA VAL R 36 " ideal model delta sigma weight residual 121.97 110.86 11.11 1.80e+00 3.09e-01 3.81e+01 angle pdb=" O GLN R 45 " pdb=" C GLN R 45 " pdb=" N CYS R 46 " ideal model delta sigma weight residual 122.15 128.57 -6.42 1.14e+00 7.69e-01 3.18e+01 angle pdb=" N PRO R 77 " pdb=" CA PRO R 77 " pdb=" C PRO R 77 " ideal model delta sigma weight residual 111.22 118.52 -7.30 1.40e+00 5.10e-01 2.72e+01 angle pdb=" N ILE R 345 " pdb=" CA ILE R 345 " pdb=" C ILE R 345 " ideal model delta sigma weight residual 110.62 105.57 5.05 1.02e+00 9.61e-01 2.45e+01 angle pdb=" N TYR R 291 " pdb=" CA TYR R 291 " pdb=" C TYR R 291 " ideal model delta sigma weight residual 111.36 116.74 -5.38 1.09e+00 8.42e-01 2.43e+01 ... (remaining 12006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4780 17.95 - 35.90: 387 35.90 - 53.86: 63 53.86 - 71.81: 7 71.81 - 89.76: 9 Dihedral angle restraints: 5246 sinusoidal: 1929 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -124.33 38.33 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C ARG R 43 " pdb=" N ARG R 43 " pdb=" CA ARG R 43 " pdb=" CB ARG R 43 " ideal model delta harmonic sigma weight residual -122.60 -112.80 -9.80 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 5243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1164 0.073 - 0.147: 144 0.147 - 0.220: 45 0.220 - 0.293: 11 0.293 - 0.366: 2 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA ARG R 43 " pdb=" N ARG R 43 " pdb=" C ARG R 43 " pdb=" CB ARG R 43 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ILE R 345 " pdb=" N ILE R 345 " pdb=" C ILE R 345 " pdb=" CB ILE R 345 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA VAL R 83 " pdb=" N VAL R 83 " pdb=" C VAL R 83 " pdb=" CB VAL R 83 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1363 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU R 364 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLU R 364 " 0.077 2.00e-02 2.50e+03 pdb=" O GLU R 364 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL R 365 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 289 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C TYR R 289 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR R 289 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU R 290 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 43 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG R 43 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG R 43 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG R 44 " -0.019 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 416 2.73 - 3.27: 8309 3.27 - 3.82: 12898 3.82 - 4.36: 16137 4.36 - 4.90: 28153 Nonbonded interactions: 65913 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.188 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" OG SER G 31 " model vdw 2.280 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.309 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.314 3.040 ... (remaining 65908 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: 3.070 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 0.048 8862 Z= 0.406 Angle : 0.829 11.108 12015 Z= 0.608 Chirality : 0.060 0.366 1366 Planarity : 0.004 0.047 1538 Dihedral : 13.526 89.759 3090 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1118 helix: 0.04 (0.23), residues: 419 sheet: 1.14 (0.34), residues: 216 loop : -0.54 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.025 0.001 TYR R 148 PHE 0.015 0.001 PHE R 381 TRP 0.012 0.001 TRP R 284 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.41 ( 8860) covalent geometry : angle 0.82941 / 0.61 (12011) SS BOND : bond 0.00173 / 0.09 ( 2) SS BOND : angle 0.65012 / 0.35 ( 4) hydrogen bonds : bond 0.30191 / 22.95 ( 391) hydrogen bonds : angle 7.62776 / 5.58 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: R 303 MET cc_start: 0.4222 (mmt) cc_final: 0.3702 (mtt) REVERT: R 414 ARG cc_start: 0.5771 (mmt90) cc_final: 0.4669 (mmp-170) REVERT: R 421 ARG cc_start: 0.4327 (ptt180) cc_final: 0.3890 (pmt170) REVERT: A 60 MET cc_start: 0.6168 (mtt) cc_final: 0.5922 (mtt) REVERT: B 212 ASP cc_start: 0.7742 (t0) cc_final: 0.7534 (t0) REVERT: N 34 MET cc_start: 0.8781 (mmm) cc_final: 0.8526 (mmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.6180 time to fit residues: 87.6065 Evaluate side-chains 93 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 88 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.196138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148781 restraints weight = 8897.608| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.94 r_work: 0.3337 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8862 Z= 0.141 Angle : 0.524 7.964 12015 Z= 0.292 Chirality : 0.042 0.148 1366 Planarity : 0.004 0.047 1538 Dihedral : 4.022 25.334 1232 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.61 % Allowed : 9.34 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1118 helix: 1.06 (0.24), residues: 433 sheet: 1.49 (0.35), residues: 208 loop : -0.72 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.011 0.001 TYR B 105 PHE 0.015 0.001 PHE B 199 TRP 0.009 0.001 TRP R 306 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 8860) covalent geometry : angle 0.52395 / 0.29 (12011) SS BOND : bond 0.00059 / 0.03 ( 2) SS BOND : angle 0.71849 / 0.41 ( 4) hydrogen bonds : bond 0.06743 / 5.19 ( 391) hydrogen bonds : angle 4.67777 / 3.41 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.335 Fit side-chains REVERT: R 157 SER cc_start: 0.8199 (m) cc_final: 0.7936 (t) REVERT: R 414 ARG cc_start: 0.5341 (mmt90) cc_final: 0.4348 (mmp-170) REVERT: R 421 ARG cc_start: 0.4442 (ptt180) cc_final: 0.3950 (pmt170) REVERT: A 20 ARG cc_start: 0.7331 (ptp-170) cc_final: 0.6640 (tpt170) REVERT: A 314 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: B 23 LYS cc_start: 0.8191 (tttt) cc_final: 0.7513 (tppt) REVERT: B 197 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8093 (ttm-80) REVERT: B 219 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7743 (mtm180) REVERT: G 32 LYS cc_start: 0.8658 (tptt) cc_final: 0.7818 (ttpt) REVERT: N 34 MET cc_start: 0.8788 (mmm) cc_final: 0.8471 (mmm) outliers start: 14 outliers final: 5 residues processed: 106 average time/residue: 0.6834 time to fit residues: 76.2494 Evaluate side-chains 96 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [77, 65, 71, 1, 103, 29, 21, 73, 56, 33, 37] chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.198930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149358 restraints weight = 8688.828| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.69 r_work: 0.3401 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8862 Z= 0.128 Angle : 0.496 7.399 12015 Z= 0.272 Chirality : 0.041 0.142 1366 Planarity : 0.003 0.048 1538 Dihedral : 4.007 26.492 1232 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.31 % Allowed : 10.84 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1118 helix: 1.48 (0.25), residues: 435 sheet: 1.55 (0.35), residues: 208 loop : -0.72 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 267 TYR 0.017 0.001 TYR N 80 PHE 0.014 0.001 PHE B 199 TRP 0.011 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8860) covalent geometry : angle 0.49585 / 0.27 (12011) SS BOND : bond 0.00087 / 0.05 ( 2) SS BOND : angle 1.03436 / 0.58 ( 4) hydrogen bonds : bond 0.05818 / 4.49 ( 391) hydrogen bonds : angle 4.26338 / 3.10 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.302 Fit side-chains REVERT: R 157 SER cc_start: 0.8241 (m) cc_final: 0.7970 (t) REVERT: R 271 SER cc_start: 0.7571 (p) cc_final: 0.7256 (m) REVERT: R 414 ARG cc_start: 0.5444 (mmt90) cc_final: 0.4395 (mmp-170) REVERT: R 421 ARG cc_start: 0.4478 (ptt180) cc_final: 0.3990 (pmt170) REVERT: A 20 ARG cc_start: 0.7231 (ptp-170) cc_final: 0.6521 (tpt170) REVERT: A 59 GLN cc_start: 0.6747 (tm-30) cc_final: 0.6526 (tm130) REVERT: A 314 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: B 16 ASN cc_start: 0.7653 (m-40) cc_final: 0.7279 (m-40) REVERT: B 23 LYS cc_start: 0.8196 (tttt) cc_final: 0.6854 (mptt) REVERT: B 188 MET cc_start: 0.8393 (mmm) cc_final: 0.8136 (mmp) REVERT: B 214 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7527 (mmm160) REVERT: B 219 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7525 (mtm180) REVERT: B 325 MET cc_start: 0.8520 (tpp) cc_final: 0.8252 (tpp) REVERT: G 32 LYS cc_start: 0.8695 (tptt) cc_final: 0.7785 (ttpt) REVERT: N 34 MET cc_start: 0.8730 (mmm) cc_final: 0.8374 (mmm) REVERT: N 77 ASN cc_start: 0.8051 (m-40) cc_final: 0.7850 (m110) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 0.6267 time to fit residues: 72.2004 Evaluate side-chains 102 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [8, 71, 60, 74, 86, 90, 51, 58, 103, 23, 41] chunk 8 optimal weight: 50.0000 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.199783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150418 restraints weight = 8831.150| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.68 r_work: 0.3404 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8862 Z= 0.110 Angle : 0.458 5.824 12015 Z= 0.252 Chirality : 0.040 0.136 1366 Planarity : 0.003 0.048 1538 Dihedral : 3.873 25.100 1232 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.65 % Allowed : 11.53 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1118 helix: 1.77 (0.25), residues: 435 sheet: 1.43 (0.35), residues: 214 loop : -0.72 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 267 TYR 0.024 0.001 TYR N 80 PHE 0.014 0.001 PHE R 280 TRP 0.010 0.001 TRP R 243 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8860) covalent geometry : angle 0.45797 / 0.25 (12011) SS BOND : bond 0.00087 / 0.05 ( 2) SS BOND : angle 0.82212 / 0.46 ( 4) hydrogen bonds : bond 0.04765 / 3.68 ( 391) hydrogen bonds : angle 4.01179 / 2.91 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.328 Fit side-chains REVERT: R 157 SER cc_start: 0.8158 (m) cc_final: 0.7936 (t) REVERT: R 233 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.5315 (mmm) REVERT: R 385 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4760 (t80) REVERT: A 20 ARG cc_start: 0.7202 (ptp-170) cc_final: 0.6528 (tpt170) REVERT: A 31 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: A 343 ASP cc_start: 0.7624 (m-30) cc_final: 0.7289 (m-30) REVERT: B 23 LYS cc_start: 0.8200 (tttt) cc_final: 0.6830 (mptt) REVERT: B 188 MET cc_start: 0.8357 (mmm) cc_final: 0.8118 (mmp) REVERT: B 197 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.7616 (mpt90) REVERT: B 214 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7491 (mmm160) REVERT: G 32 LYS cc_start: 0.8674 (tptt) cc_final: 0.7852 (ttpt) REVERT: N 34 MET cc_start: 0.8684 (mmm) cc_final: 0.8335 (mmm) REVERT: N 83 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8738 (mtp) outliers start: 23 outliers final: 9 residues processed: 100 average time/residue: 0.5533 time to fit residues: 59.0968 Evaluate side-chains 92 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 385 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [52, 95, 56, 47, 96, 84, 50, 100, 79, 88, 5] chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.195148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144941 restraints weight = 8744.532| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.73 r_work: 0.3379 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8862 Z= 0.182 Angle : 0.567 9.308 12015 Z= 0.304 Chirality : 0.043 0.154 1366 Planarity : 0.004 0.050 1538 Dihedral : 4.247 29.039 1232 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.88 % Allowed : 11.88 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1118 helix: 1.51 (0.25), residues: 441 sheet: 1.51 (0.35), residues: 204 loop : -0.91 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 267 TYR 0.023 0.002 TYR N 80 PHE 0.018 0.002 PHE N 108 TRP 0.014 0.002 TRP B 82 HIS 0.012 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 8860) covalent geometry : angle 0.56624 / 0.30 (12011) SS BOND : bond 0.00150 / 0.08 ( 2) SS BOND : angle 1.38487 / 0.70 ( 4) hydrogen bonds : bond 0.05906 / 4.59 ( 391) hydrogen bonds : angle 4.21215 / 3.06 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.314 Fit side-chains REVERT: R 157 SER cc_start: 0.8213 (m) cc_final: 0.7964 (t) REVERT: R 233 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.5490 (mmm) REVERT: R 385 PHE cc_start: 0.5139 (OUTLIER) cc_final: 0.4776 (t80) REVERT: R 414 ARG cc_start: 0.5499 (mmt90) cc_final: 0.4478 (mmp-170) REVERT: R 421 ARG cc_start: 0.4603 (ptt180) cc_final: 0.4098 (pmt170) REVERT: A 20 ARG cc_start: 0.7312 (ptp-170) cc_final: 0.6596 (tpt170) REVERT: A 38 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7604 (mmt90) REVERT: A 314 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: B 23 LYS cc_start: 0.8418 (tttt) cc_final: 0.7936 (tttm) REVERT: B 188 MET cc_start: 0.8473 (mmm) cc_final: 0.8259 (mmp) REVERT: B 197 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.7690 (mpt90) REVERT: B 214 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7545 (mmm160) REVERT: B 219 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7627 (mtm180) REVERT: B 325 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8162 (mmt) REVERT: G 32 LYS cc_start: 0.8707 (tptt) cc_final: 0.7890 (ttpt) REVERT: N 34 MET cc_start: 0.8701 (mmm) cc_final: 0.8408 (mmm) outliers start: 25 outliers final: 10 residues processed: 106 average time/residue: 0.6479 time to fit residues: 72.4823 Evaluate side-chains 107 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 385 PHE Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [94, 63, 90, 72, 78, 11, 75, 44, 77, 109, 30] chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148604 restraints weight = 8769.755| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.60 r_work: 0.3325 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8862 Z= 0.169 Angle : 0.548 8.279 12015 Z= 0.295 Chirality : 0.043 0.151 1366 Planarity : 0.004 0.052 1538 Dihedral : 4.251 28.895 1232 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.88 % Allowed : 12.80 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1118 helix: 1.52 (0.25), residues: 441 sheet: 1.35 (0.35), residues: 205 loop : -0.98 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 267 TYR 0.013 0.002 TYR R 402 PHE 0.018 0.002 PHE A 212 TRP 0.014 0.002 TRP B 82 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8860) covalent geometry : angle 0.54740 / 0.30 (12011) SS BOND : bond 0.00163 / 0.09 ( 2) SS BOND : angle 1.34438 / 0.68 ( 4) hydrogen bonds : bond 0.05661 / 4.40 ( 391) hydrogen bonds : angle 4.13923 / 3.01 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.314 Fit side-chains REVERT: R 157 SER cc_start: 0.8159 (m) cc_final: 0.7891 (t) REVERT: R 233 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5471 (mmm) REVERT: R 385 PHE cc_start: 0.5291 (OUTLIER) cc_final: 0.4895 (t80) REVERT: R 414 ARG cc_start: 0.5476 (mmt90) cc_final: 0.4412 (mmp-170) REVERT: R 418 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5780 (mt-10) REVERT: R 421 ARG cc_start: 0.4619 (ptt180) cc_final: 0.4126 (pmt170) REVERT: A 20 ARG cc_start: 0.7248 (ptp-170) cc_final: 0.6456 (tpt170) REVERT: A 38 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7523 (mmt90) REVERT: A 314 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: B 23 LYS cc_start: 0.8353 (tttt) cc_final: 0.7840 (tttm) REVERT: B 59 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: B 123 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 188 MET cc_start: 0.8478 (mmm) cc_final: 0.8269 (mmp) REVERT: B 197 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.7625 (mpt90) REVERT: B 214 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7611 (mmm-85) REVERT: B 219 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7581 (mtm180) REVERT: G 32 LYS cc_start: 0.8661 (tptt) cc_final: 0.7935 (ttmt) REVERT: N 17 SER cc_start: 0.8742 (m) cc_final: 0.8487 (m) outliers start: 25 outliers final: 10 residues processed: 102 average time/residue: 0.6844 time to fit residues: 73.5758 Evaluate side-chains 103 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 385 PHE Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [1, 18, 23, 54, 78, 19, 72, 59, 11, 84, 20] chunk 1 optimal weight: 120.0000 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.0270 chunk 54 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.196941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150286 restraints weight = 8773.652| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.64 r_work: 0.3346 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8862 Z= 0.123 Angle : 0.483 6.516 12015 Z= 0.264 Chirality : 0.041 0.144 1366 Planarity : 0.003 0.051 1538 Dihedral : 4.038 27.311 1232 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.31 % Allowed : 13.73 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1118 helix: 1.77 (0.25), residues: 440 sheet: 1.25 (0.35), residues: 210 loop : -0.95 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 267 TYR 0.023 0.001 TYR N 80 PHE 0.014 0.001 PHE R 280 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8860) covalent geometry : angle 0.48241 / 0.26 (12011) SS BOND : bond 0.00092 / 0.05 ( 2) SS BOND : angle 1.03910 / 0.55 ( 4) hydrogen bonds : bond 0.04869 / 3.78 ( 391) hydrogen bonds : angle 3.96326 / 2.89 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.332 Fit side-chains REVERT: R 157 SER cc_start: 0.8136 (m) cc_final: 0.7871 (t) REVERT: R 414 ARG cc_start: 0.5561 (mmt90) cc_final: 0.4495 (mmp-170) REVERT: R 418 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5753 (mt-10) REVERT: R 421 ARG cc_start: 0.4622 (ptt180) cc_final: 0.4141 (pmt170) REVERT: A 20 ARG cc_start: 0.7246 (ptp-170) cc_final: 0.6437 (tpt170) REVERT: A 31 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: A 38 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7467 (mmt90) REVERT: A 314 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: B 23 LYS cc_start: 0.8299 (tttt) cc_final: 0.7588 (tppt) REVERT: B 197 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.7655 (mpt90) REVERT: B 214 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7607 (mmm-85) REVERT: B 219 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7516 (mtm180) REVERT: G 32 LYS cc_start: 0.8666 (tptt) cc_final: 0.7954 (ttmt) REVERT: N 17 SER cc_start: 0.8718 (m) cc_final: 0.8459 (m) outliers start: 20 outliers final: 8 residues processed: 102 average time/residue: 0.6716 time to fit residues: 72.1743 Evaluate side-chains 101 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [21, 52, 49, 103, 100, 62, 85, 94, 110, 93, 102] chunk 21 optimal weight: 7.9990 chunk 52 optimal weight: 0.0000 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 110 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 36 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.198717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151072 restraints weight = 8709.330| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.65 r_work: 0.3361 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8862 Z= 0.103 Angle : 0.450 6.136 12015 Z= 0.248 Chirality : 0.040 0.141 1366 Planarity : 0.003 0.051 1538 Dihedral : 3.842 25.894 1232 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.31 % Allowed : 14.07 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1118 helix: 2.00 (0.25), residues: 440 sheet: 1.32 (0.36), residues: 201 loop : -0.93 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 267 TYR 0.019 0.001 TYR N 80 PHE 0.013 0.001 PHE R 280 TRP 0.011 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 8860) covalent geometry : angle 0.45026 / 0.25 (12011) SS BOND : bond 0.00063 / 0.03 ( 2) SS BOND : angle 0.86794 / 0.47 ( 4) hydrogen bonds : bond 0.04295 / 3.33 ( 391) hydrogen bonds : angle 3.82658 / 2.78 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.309 Fit side-chains REVERT: R 157 SER cc_start: 0.8108 (m) cc_final: 0.7814 (t) REVERT: R 418 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5687 (mt-10) REVERT: R 421 ARG cc_start: 0.4550 (ptt180) cc_final: 0.4097 (pmt170) REVERT: A 20 ARG cc_start: 0.7187 (ptp-170) cc_final: 0.6398 (tpt170) REVERT: A 38 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7449 (mmt90) REVERT: A 314 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: A 343 ASP cc_start: 0.7667 (m-30) cc_final: 0.7349 (m-30) REVERT: B 23 LYS cc_start: 0.8244 (tttt) cc_final: 0.6816 (mptt) REVERT: B 197 ARG cc_start: 0.8449 (ttp-110) cc_final: 0.7694 (mpt90) REVERT: B 214 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: B 219 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7494 (mtm180) REVERT: G 32 LYS cc_start: 0.8650 (tptt) cc_final: 0.7953 (ttmt) REVERT: N 17 SER cc_start: 0.8586 (m) cc_final: 0.8332 (m) REVERT: N 34 MET cc_start: 0.8638 (mmm) cc_final: 0.8335 (mmm) outliers start: 20 outliers final: 7 residues processed: 101 average time/residue: 0.5912 time to fit residues: 63.4909 Evaluate side-chains 96 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [11, 54, 26, 66, 92, 41, 90, 30, 16, 33, 107] chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 36 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.197687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151265 restraints weight = 8687.594| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.63 r_work: 0.3350 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8862 Z= 0.115 Angle : 0.471 6.241 12015 Z= 0.258 Chirality : 0.040 0.144 1366 Planarity : 0.003 0.050 1538 Dihedral : 3.885 26.621 1232 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.19 % Allowed : 14.53 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1118 helix: 2.00 (0.25), residues: 440 sheet: 1.33 (0.35), residues: 208 loop : -0.88 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 267 TYR 0.020 0.001 TYR N 80 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8860) covalent geometry : angle 0.47093 / 0.26 (12011) SS BOND : bond 0.00059 / 0.03 ( 2) SS BOND : angle 0.97861 / 0.52 ( 4) hydrogen bonds : bond 0.04502 / 3.50 ( 391) hydrogen bonds : angle 3.87520 / 2.81 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.312 Fit side-chains REVERT: R 157 SER cc_start: 0.8118 (m) cc_final: 0.7828 (t) REVERT: R 418 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5599 (mt-10) REVERT: A 20 ARG cc_start: 0.7201 (ptp-170) cc_final: 0.6377 (tpt170) REVERT: A 31 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: A 38 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7489 (mmt90) REVERT: A 240 ASP cc_start: 0.7334 (m-30) cc_final: 0.7124 (p0) REVERT: A 314 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: A 343 ASP cc_start: 0.7676 (m-30) cc_final: 0.7370 (m-30) REVERT: B 16 ASN cc_start: 0.7677 (m-40) cc_final: 0.7429 (m-40) REVERT: B 23 LYS cc_start: 0.8284 (tttt) cc_final: 0.6855 (mptt) REVERT: B 197 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.7662 (mpt90) REVERT: B 214 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7633 (mmm-85) REVERT: B 219 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7557 (mtm180) REVERT: G 32 LYS cc_start: 0.8662 (tptt) cc_final: 0.7963 (ttmt) REVERT: N 17 SER cc_start: 0.8589 (m) cc_final: 0.8336 (m) outliers start: 19 outliers final: 8 residues processed: 97 average time/residue: 0.5962 time to fit residues: 61.3756 Evaluate side-chains 97 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [70, 18, 50, 15, 76, 58, 60, 42, 52, 5, 49] chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 5 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151153 restraints weight = 8752.078| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.66 r_work: 0.3339 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8862 Z= 0.112 Angle : 0.461 5.746 12015 Z= 0.253 Chirality : 0.040 0.142 1366 Planarity : 0.003 0.050 1538 Dihedral : 3.857 26.439 1232 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.61 % Allowed : 15.11 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1118 helix: 2.07 (0.25), residues: 440 sheet: 1.30 (0.34), residues: 213 loop : -0.81 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 267 TYR 0.021 0.001 TYR N 80 PHE 0.013 0.001 PHE R 280 TRP 0.011 0.001 TRP R 243 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8860) covalent geometry : angle 0.46076 / 0.25 (12011) SS BOND : bond 0.00080 / 0.04 ( 2) SS BOND : angle 0.92392 / 0.49 ( 4) hydrogen bonds : bond 0.04362 / 3.39 ( 391) hydrogen bonds : angle 3.84542 / 2.79 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.318 Fit side-chains REVERT: R 157 SER cc_start: 0.8140 (m) cc_final: 0.7852 (t) REVERT: R 418 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5697 (mt-10) REVERT: R 421 ARG cc_start: 0.4569 (ptt180) cc_final: 0.4116 (pmt170) REVERT: A 20 ARG cc_start: 0.7226 (ptp-170) cc_final: 0.6408 (tpt170) REVERT: A 31 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: A 38 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7501 (mmt90) REVERT: A 240 ASP cc_start: 0.7435 (m-30) cc_final: 0.7174 (p0) REVERT: A 314 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: A 343 ASP cc_start: 0.7708 (m-30) cc_final: 0.7402 (m-30) REVERT: B 16 ASN cc_start: 0.7710 (m-40) cc_final: 0.7418 (m-40) REVERT: B 23 LYS cc_start: 0.8303 (tttt) cc_final: 0.6876 (mptt) REVERT: B 197 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7648 (mpt90) REVERT: B 214 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7618 (mmm-85) REVERT: B 219 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7592 (mtm180) REVERT: G 32 LYS cc_start: 0.8682 (tptt) cc_final: 0.7984 (ttmt) REVERT: N 17 SER cc_start: 0.8580 (m) cc_final: 0.8349 (m) outliers start: 14 outliers final: 7 residues processed: 95 average time/residue: 0.6302 time to fit residues: 63.2619 Evaluate side-chains 98 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: [97, 95, 77, 22, 12, 40, 86, 102, 89, 10, 96] chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.0170 chunk 86 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.198324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151214 restraints weight = 8649.100| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.62 r_work: 0.3461 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8862 Z= 0.107 Angle : 0.456 5.687 12015 Z= 0.250 Chirality : 0.040 0.142 1366 Planarity : 0.003 0.051 1538 Dihedral : 3.816 26.167 1232 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.85 % Allowed : 14.99 % Favored : 83.16 % 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 are not related in a simple way. whole: 1.19 (0.25), residues: 1118 helix: 2.09 (0.25), residues: 441 sheet: 1.32 (0.34), residues: 213 loop : -0.78 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 267 TYR 0.020 0.001 TYR N 80 PHE 0.013 0.001 PHE R 280 TRP 0.011 0.001 TRP R 243 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8860) covalent geometry : angle 0.45563 / 0.25 (12011) SS BOND : bond 0.00067 / 0.04 ( 2) SS BOND : angle 0.92289 / 0.50 ( 4) hydrogen bonds : bond 0.04280 / 3.32 ( 391) hydrogen bonds : angle 3.82089 / 2.77 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.01 seconds wall clock time: 49 minutes 10.21 seconds (2950.21 seconds total)