Starting phenix.real_space_refine on Sat Dec 28 13:31:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whc_21671/12_2024/6whc_21671.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whc_21671/12_2024/6whc_21671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6whc_21671/12_2024/6whc_21671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whc_21671/12_2024/6whc_21671.map" model { file = "/net/cci-nas-00/data/ceres_data/6whc_21671/12_2024/6whc_21671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whc_21671/12_2024/6whc_21671.cif" } resolution = 3.4 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= 0.002 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 55 5.16 5 C 5528 2.51 5 N 1528 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8709 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1823 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2547 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 363 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2765 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 186 Time building chain proxies: 5.23, per 1000 atoms: 0.60 Number of scatterers: 8709 At special positions: 0 Unit cell: (92.13, 101.26, 161.85, 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 55 16.00 O 1598 8.00 N 1528 7.00 C 5528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.02 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 37.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.596A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.812A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.913A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.654A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.591A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.536A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.703A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.792A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.551A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.551A pdb=" N GLU E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 19 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS E 20 " --> pdb=" O GLU E 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 26 " --> pdb=" O PHE E 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.928A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 28 through 39 removed outlier: 3.985A pdb=" N GLU R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS R 37 " --> pdb=" O PHE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 50 removed outlier: 3.560A pdb=" N HIS R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU R 47 " --> pdb=" O CYS R 43 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER R 48 " --> pdb=" O HIS R 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 163 removed outlier: 3.781A pdb=" N MET R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR R 146 " --> pdb=" O GLN R 142 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU R 158 " --> pdb=" O GLY R 154 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA R 161 " --> pdb=" O LEU R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 202 removed outlier: 3.822A pdb=" N LYS R 187 " --> pdb=" O SER R 183 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 255 removed outlier: 3.632A pdb=" N VAL R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA R 222 " --> pdb=" O ASP R 218 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY R 223 " --> pdb=" O GLY R 219 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE R 230 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL R 236 " --> pdb=" O GLN R 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 277 removed outlier: 4.020A pdb=" N ALA R 274 " --> pdb=" O ILE R 270 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 278 through 289 removed outlier: 3.563A pdb=" N VAL R 285 " --> pdb=" O PRO R 281 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU R 288 " --> pdb=" O VAL R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 330 Proline residue: R 310 - end of helix removed outlier: 3.515A pdb=" N ILE R 315 " --> pdb=" O VAL R 311 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 348 Processing helix chain 'R' and resid 361 through 365 removed outlier: 3.632A pdb=" N VAL R 364 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 400 removed outlier: 3.977A pdb=" N LEU R 388 " --> pdb=" O PHE R 384 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL R 396 " --> pdb=" O GLN R 392 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA R 397 " --> pdb=" O GLY R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 418 removed outlier: 3.880A pdb=" N GLU R 410 " --> pdb=" O GLU R 406 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG R 417 " --> pdb=" O ARG R 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.627A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.551A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.565A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.308A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.081A 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: 6.673A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.277A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.525A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.539A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.602A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.709A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 77 through 80 removed outlier: 4.194A pdb=" N VAL R 96 " --> pdb=" O ILE R 79 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 984 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: 2.39 Time building geometry restraints manager: 2.61 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: 1779 1.33 - 1.45: 2177 1.45 - 1.57: 4865 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8897 Sorted by residual: bond pdb=" N ALA N 101 " pdb=" CA ALA N 101 " ideal model delta sigma weight residual 1.453 1.483 -0.029 8.30e-03 1.45e+04 1.26e+01 bond pdb=" CA ALA N 101 " pdb=" CB ALA N 101 " ideal model delta sigma weight residual 1.536 1.501 0.035 1.23e-02 6.61e+03 8.30e+00 bond pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.22e-02 6.72e+03 7.78e+00 bond pdb=" N CYS N 107 " pdb=" CA CYS N 107 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.50e+00 bond pdb=" N ARG R 378 " pdb=" CA ARG R 378 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.31e+00 ... (remaining 8892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 11546 1.73 - 3.45: 446 3.45 - 5.18: 46 5.18 - 6.90: 16 6.90 - 8.63: 8 Bond angle restraints: 12062 Sorted by residual: angle pdb=" C ASP N 109 " pdb=" CA ASP N 109 " pdb=" CB ASP N 109 " ideal model delta sigma weight residual 111.18 104.50 6.68 1.56e+00 4.11e-01 1.83e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.05 128.74 -5.69 1.57e+00 4.06e-01 1.31e+01 angle pdb=" N LYS R 349 " pdb=" CA LYS R 349 " pdb=" C LYS R 349 " ideal model delta sigma weight residual 114.56 110.01 4.55 1.27e+00 6.20e-01 1.28e+01 angle pdb=" C THR A 369 " pdb=" N GLU A 370 " pdb=" CA GLU A 370 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" N GLU E 21 " pdb=" CA GLU E 21 " pdb=" C GLU E 21 " ideal model delta sigma weight residual 111.07 107.53 3.54 1.07e+00 8.73e-01 1.09e+01 ... (remaining 12057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4698 17.79 - 35.58: 480 35.58 - 53.38: 66 53.38 - 71.17: 15 71.17 - 88.96: 11 Dihedral angle restraints: 5270 sinusoidal: 2007 harmonic: 3263 Sorted by residual: dihedral pdb=" CB CYS R 58 " pdb=" SG CYS R 58 " pdb=" SG CYS R 100 " pdb=" CB CYS R 100 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CA ILE R 355 " pdb=" C ILE R 355 " pdb=" N PRO R 356 " pdb=" CA PRO R 356 " ideal model delta harmonic sigma weight residual -180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " pdb=" SG CYS R 294 " pdb=" CB CYS R 294 " ideal model delta sinusoidal sigma weight residual 93.00 133.20 -40.20 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1074 0.058 - 0.116: 218 0.116 - 0.174: 42 0.174 - 0.232: 9 0.232 - 0.290: 2 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA GLU B 130 " pdb=" N GLU B 130 " pdb=" C GLU B 130 " pdb=" CB GLU B 130 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1342 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.24e+00 pdb=" N PRO B 236 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 274 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO R 275 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO C 55 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.033 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1679 2.77 - 3.30: 7669 3.30 - 3.84: 14504 3.84 - 4.37: 16487 4.37 - 4.90: 28357 Nonbonded interactions: 68696 Sorted by model distance: nonbonded pdb=" N GLU B 130 " pdb=" OE1 GLU B 130 " model vdw 2.238 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.246 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.302 3.040 ... (remaining 68691 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=0.00 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: 0.960 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.004 0.045 8897 Z= 0.255 Angle : 0.788 8.629 12062 Z= 0.471 Chirality : 0.051 0.290 1345 Planarity : 0.006 0.067 1548 Dihedral : 14.512 88.960 3143 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % 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: -4.67 (0.20), residues: 1104 helix: -4.41 (0.10), residues: 392 sheet: -2.10 (0.35), residues: 197 loop : -2.25 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.010 0.001 TYR N 32 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8439 (pt0) cc_final: 0.8002 (mt0) REVERT: C 29 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8501 (mtpp) REVERT: E 9 ASP cc_start: 0.9154 (t0) cc_final: 0.8911 (t70) REVERT: E 10 TYR cc_start: 0.8823 (t80) cc_final: 0.8564 (t80) REVERT: E 14 LEU cc_start: 0.9072 (mt) cc_final: 0.8866 (mt) REVERT: N 43 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7761 (mtpp) REVERT: N 86 LEU cc_start: 0.9079 (mm) cc_final: 0.8492 (tt) REVERT: R 231 MET cc_start: 0.8932 (tmm) cc_final: 0.8181 (tmm) REVERT: R 238 ASN cc_start: 0.8061 (t0) cc_final: 0.7799 (t0) REVERT: R 290 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7711 (mm-30) REVERT: R 298 ASN cc_start: 0.7889 (t0) cc_final: 0.6980 (t0) REVERT: R 301 MET cc_start: 0.7712 (mmm) cc_final: 0.6959 (mmp) REVERT: R 362 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7067 (tm-30) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2281 time to fit residues: 60.8397 Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.2980 chunk 82 optimal weight: 0.0000 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.0670 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 267 GLN A 278 ASN B 62 HIS B 119 ASN B 293 ASN B 295 ASN C 18 GLN E 28 ASN N 31 ASN R 339 HIS R 392 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8897 Z= 0.159 Angle : 0.587 7.063 12062 Z= 0.306 Chirality : 0.042 0.205 1345 Planarity : 0.005 0.051 1548 Dihedral : 4.597 26.119 1216 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.11 % Allowed : 15.89 % Favored : 83.00 % 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: -2.85 (0.22), residues: 1104 helix: -2.15 (0.20), residues: 389 sheet: -1.65 (0.35), residues: 205 loop : -1.63 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 339 PHE 0.020 0.001 PHE E 22 TYR 0.032 0.001 TYR R 145 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8512 (pt0) cc_final: 0.8077 (mt0) REVERT: B 119 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7605 (m-40) REVERT: C 21 MET cc_start: 0.5005 (ptt) cc_final: 0.4490 (ppp) REVERT: C 29 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8680 (mtpp) REVERT: N 43 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7765 (mtpp) REVERT: N 86 LEU cc_start: 0.9068 (mm) cc_final: 0.8564 (tt) REVERT: R 290 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7851 (mm-30) REVERT: R 295 TRP cc_start: 0.8150 (m-10) cc_final: 0.7741 (m-10) REVERT: R 298 ASN cc_start: 0.7849 (t0) cc_final: 0.6958 (t0) REVERT: R 301 MET cc_start: 0.7372 (mmm) cc_final: 0.6977 (mmp) REVERT: R 362 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6915 (tm-30) outliers start: 10 outliers final: 5 residues processed: 172 average time/residue: 0.2162 time to fit residues: 51.1909 Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 23 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 0.0070 chunk 79 optimal weight: 30.0000 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 295 ASN B 340 ASN C 59 ASN E 3 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8897 Z= 0.164 Angle : 0.540 7.389 12062 Z= 0.282 Chirality : 0.041 0.187 1345 Planarity : 0.004 0.047 1548 Dihedral : 4.363 26.917 1216 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.22 % Allowed : 17.33 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.91 (0.24), residues: 1104 helix: -0.90 (0.25), residues: 395 sheet: -1.52 (0.35), residues: 203 loop : -1.31 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS A 220 PHE 0.015 0.001 PHE N 103 TYR 0.022 0.001 TYR R 145 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8507 (pt0) cc_final: 0.8089 (mt0) REVERT: N 43 LYS cc_start: 0.8186 (mmmm) cc_final: 0.7692 (mtpp) REVERT: N 86 LEU cc_start: 0.9090 (mm) cc_final: 0.8587 (tt) REVERT: N 89 GLU cc_start: 0.8532 (pm20) cc_final: 0.8309 (pm20) REVERT: R 231 MET cc_start: 0.8754 (tmm) cc_final: 0.8466 (tmm) REVERT: R 241 TRP cc_start: 0.8038 (t-100) cc_final: 0.7572 (m-90) REVERT: R 290 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7868 (mm-30) REVERT: R 295 TRP cc_start: 0.8158 (m-10) cc_final: 0.7751 (m-10) REVERT: R 298 ASN cc_start: 0.7852 (t0) cc_final: 0.7319 (t0) REVERT: R 301 MET cc_start: 0.7420 (mmm) cc_final: 0.7061 (mmp) REVERT: R 362 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6997 (tm-30) outliers start: 20 outliers final: 8 residues processed: 161 average time/residue: 0.1959 time to fit residues: 44.9729 Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8897 Z= 0.224 Angle : 0.549 8.030 12062 Z= 0.286 Chirality : 0.042 0.171 1345 Planarity : 0.003 0.046 1548 Dihedral : 4.338 28.782 1216 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.78 % Allowed : 19.56 % Favored : 78.67 % 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: -1.43 (0.25), residues: 1104 helix: -0.22 (0.26), residues: 396 sheet: -1.62 (0.33), residues: 222 loop : -1.09 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.016 0.001 PHE N 108 TYR 0.009 0.001 TYR R 400 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8485 (pt0) cc_final: 0.8082 (mt0) REVERT: R 241 TRP cc_start: 0.8185 (t-100) cc_final: 0.7625 (m-90) REVERT: R 290 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7942 (mm-30) REVERT: R 295 TRP cc_start: 0.8272 (m-10) cc_final: 0.7846 (m-10) REVERT: R 298 ASN cc_start: 0.7840 (t0) cc_final: 0.7309 (t0) REVERT: R 301 MET cc_start: 0.7445 (mmm) cc_final: 0.7117 (mmp) outliers start: 16 outliers final: 11 residues processed: 155 average time/residue: 0.2123 time to fit residues: 45.4989 Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 119 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8897 Z= 0.154 Angle : 0.538 9.091 12062 Z= 0.277 Chirality : 0.041 0.162 1345 Planarity : 0.003 0.046 1548 Dihedral : 4.198 28.746 1216 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.33 % Allowed : 20.67 % Favored : 77.00 % 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: -1.10 (0.25), residues: 1104 helix: 0.15 (0.27), residues: 394 sheet: -1.45 (0.33), residues: 219 loop : -0.99 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS E 1 PHE 0.012 0.001 PHE A 212 TYR 0.016 0.001 TYR B 111 ARG 0.003 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8478 (pt0) cc_final: 0.8104 (mt0) REVERT: N 86 LEU cc_start: 0.9114 (mm) cc_final: 0.8403 (tt) REVERT: R 29 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7134 (mmt) REVERT: R 231 MET cc_start: 0.8877 (tmm) cc_final: 0.8500 (tmm) REVERT: R 241 TRP cc_start: 0.8074 (t-100) cc_final: 0.7670 (m-90) REVERT: R 290 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7945 (mm-30) REVERT: R 295 TRP cc_start: 0.8279 (m-10) cc_final: 0.7854 (m-10) REVERT: R 298 ASN cc_start: 0.7824 (t0) cc_final: 0.7292 (t0) REVERT: R 301 MET cc_start: 0.7440 (mmm) cc_final: 0.7116 (mmp) outliers start: 21 outliers final: 16 residues processed: 158 average time/residue: 0.2088 time to fit residues: 45.7088 Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8897 Z= 0.264 Angle : 0.586 9.785 12062 Z= 0.301 Chirality : 0.043 0.184 1345 Planarity : 0.004 0.051 1548 Dihedral : 4.439 40.176 1216 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.44 % Allowed : 21.22 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.99 (0.26), residues: 1104 helix: 0.35 (0.27), residues: 397 sheet: -1.57 (0.32), residues: 227 loop : -0.92 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 220 PHE 0.019 0.001 PHE N 108 TYR 0.019 0.001 TYR B 111 ARG 0.010 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.060 Fit side-chains REVERT: A 28 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8532 (ttpt) REVERT: A 35 GLN cc_start: 0.8458 (pt0) cc_final: 0.8110 (mt0) REVERT: R 29 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7172 (mmt) REVERT: R 231 MET cc_start: 0.8906 (tmm) cc_final: 0.8575 (tmm) REVERT: R 241 TRP cc_start: 0.8289 (t-100) cc_final: 0.7706 (m-90) REVERT: R 290 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7948 (mm-30) REVERT: R 298 ASN cc_start: 0.7869 (t0) cc_final: 0.7388 (t0) REVERT: R 301 MET cc_start: 0.7510 (mmm) cc_final: 0.7179 (mmp) outliers start: 22 outliers final: 15 residues processed: 148 average time/residue: 0.2120 time to fit residues: 43.8913 Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8897 Z= 0.195 Angle : 0.568 10.570 12062 Z= 0.290 Chirality : 0.042 0.168 1345 Planarity : 0.003 0.044 1548 Dihedral : 4.323 37.060 1216 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.00 % Allowed : 21.33 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.81 (0.26), residues: 1104 helix: 0.52 (0.27), residues: 394 sheet: -1.40 (0.33), residues: 221 loop : -0.88 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS E 1 PHE 0.016 0.001 PHE N 108 TYR 0.016 0.001 TYR B 111 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.108 Fit side-chains REVERT: A 28 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8523 (ttpt) REVERT: A 35 GLN cc_start: 0.8442 (pt0) cc_final: 0.8108 (mt0) REVERT: B 155 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7634 (t0) REVERT: B 172 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: B 220 GLN cc_start: 0.7777 (mt0) cc_final: 0.7562 (mt0) REVERT: N 83 MET cc_start: 0.7810 (mtt) cc_final: 0.7588 (mtt) REVERT: R 231 MET cc_start: 0.8881 (tmm) cc_final: 0.8585 (tmm) REVERT: R 241 TRP cc_start: 0.8166 (t-100) cc_final: 0.7670 (m-90) REVERT: R 290 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7905 (mm-30) REVERT: R 298 ASN cc_start: 0.7862 (t0) cc_final: 0.7386 (t0) REVERT: R 301 MET cc_start: 0.7496 (mmm) cc_final: 0.7170 (mmp) outliers start: 27 outliers final: 15 residues processed: 160 average time/residue: 0.2049 time to fit residues: 45.8047 Evaluate side-chains 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8897 Z= 0.160 Angle : 0.572 9.882 12062 Z= 0.289 Chirality : 0.042 0.167 1345 Planarity : 0.003 0.045 1548 Dihedral : 4.189 34.658 1216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.44 % Allowed : 22.56 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.73 (0.26), residues: 1104 helix: 0.63 (0.27), residues: 392 sheet: -1.36 (0.34), residues: 218 loop : -0.88 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 1 PHE 0.011 0.001 PHE N 108 TYR 0.027 0.001 TYR E 10 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.165 Fit side-chains REVERT: A 28 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8501 (ttpt) REVERT: A 35 GLN cc_start: 0.8435 (pt0) cc_final: 0.8108 (mt0) REVERT: B 155 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7673 (t0) REVERT: B 172 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: R 241 TRP cc_start: 0.8166 (t-100) cc_final: 0.7645 (m-90) REVERT: R 290 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7895 (mm-30) REVERT: R 298 ASN cc_start: 0.7850 (t0) cc_final: 0.7377 (t0) REVERT: R 301 MET cc_start: 0.7495 (mmm) cc_final: 0.7186 (mmp) outliers start: 13 outliers final: 9 residues processed: 151 average time/residue: 0.2235 time to fit residues: 46.7170 Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 0.0030 chunk 63 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8897 Z= 0.160 Angle : 0.579 10.400 12062 Z= 0.292 Chirality : 0.042 0.216 1345 Planarity : 0.003 0.045 1548 Dihedral : 4.159 34.609 1216 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.56 % Allowed : 22.56 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.65 (0.26), residues: 1104 helix: 0.72 (0.27), residues: 392 sheet: -1.27 (0.34), residues: 218 loop : -0.88 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.000 HIS E 1 PHE 0.011 0.001 PHE N 108 TYR 0.029 0.001 TYR E 10 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.907 Fit side-chains REVERT: A 28 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8499 (ttpt) REVERT: A 35 GLN cc_start: 0.8432 (pt0) cc_final: 0.8110 (mt0) REVERT: B 155 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7650 (t0) REVERT: B 172 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: B 217 MET cc_start: 0.7696 (pmm) cc_final: 0.7450 (pmm) REVERT: R 145 TYR cc_start: 0.7594 (p90) cc_final: 0.7355 (p90) REVERT: R 195 ASP cc_start: 0.7752 (m-30) cc_final: 0.7511 (m-30) REVERT: R 241 TRP cc_start: 0.8161 (t-100) cc_final: 0.7691 (m-90) REVERT: R 290 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7892 (mm-30) REVERT: R 298 ASN cc_start: 0.7884 (t0) cc_final: 0.7415 (t0) REVERT: R 301 MET cc_start: 0.7500 (mmm) cc_final: 0.7172 (mmp) outliers start: 14 outliers final: 9 residues processed: 154 average time/residue: 0.2125 time to fit residues: 45.4314 Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8897 Z= 0.198 Angle : 0.592 9.551 12062 Z= 0.299 Chirality : 0.043 0.260 1345 Planarity : 0.004 0.055 1548 Dihedral : 4.219 34.782 1216 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.33 % Allowed : 22.67 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.56 (0.26), residues: 1104 helix: 0.78 (0.27), residues: 394 sheet: -1.29 (0.33), residues: 221 loop : -0.78 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS E 1 PHE 0.016 0.001 PHE N 108 TYR 0.020 0.001 TYR E 10 ARG 0.014 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.973 Fit side-chains REVERT: A 35 GLN cc_start: 0.8437 (pt0) cc_final: 0.8125 (mt0) REVERT: B 155 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7698 (t0) REVERT: B 172 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: B 234 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8977 (m-80) REVERT: R 145 TYR cc_start: 0.7612 (p90) cc_final: 0.7326 (p90) REVERT: R 195 ASP cc_start: 0.7731 (m-30) cc_final: 0.7499 (m-30) REVERT: R 241 TRP cc_start: 0.8240 (t-100) cc_final: 0.7744 (m-90) REVERT: R 290 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7895 (mm-30) REVERT: R 298 ASN cc_start: 0.7862 (t0) cc_final: 0.7375 (t0) REVERT: R 301 MET cc_start: 0.7528 (mmm) cc_final: 0.7206 (mmp) outliers start: 12 outliers final: 9 residues processed: 148 average time/residue: 0.2215 time to fit residues: 45.5329 Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 40.0000 chunk 4 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.124956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087801 restraints weight = 17060.423| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.38 r_work: 0.3258 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8897 Z= 0.172 Angle : 0.583 8.992 12062 Z= 0.293 Chirality : 0.042 0.259 1345 Planarity : 0.003 0.045 1548 Dihedral : 4.158 34.437 1216 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.44 % Allowed : 22.78 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.50 (0.26), residues: 1104 helix: 0.86 (0.27), residues: 393 sheet: -1.29 (0.33), residues: 223 loop : -0.74 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS E 1 PHE 0.014 0.001 PHE N 108 TYR 0.020 0.001 TYR E 10 ARG 0.003 0.000 ARG N 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.71 seconds wall clock time: 38 minutes 58.05 seconds (2338.05 seconds total)