Starting phenix.real_space_refine on Wed Nov 19 00:49:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ces_7464/11_2025/6ces_7464_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ces_7464/11_2025/6ces_7464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ces_7464/11_2025/6ces_7464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ces_7464/11_2025/6ces_7464.map" model { file = "/net/cci-nas-00/data/ceres_data/6ces_7464/11_2025/6ces_7464_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ces_7464/11_2025/6ces_7464_neut.cif" } resolution = 4.0 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 111 5.16 5 C 12147 2.51 5 N 3205 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2579 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 3 Chain: "M" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4084 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 34, 'TRANS': 484} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 7349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7349 Classifications: {'peptide': 901} Link IDs: {'PTRANS': 44, 'TRANS': 856} Chain breaks: 10 Chain: "A" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2459 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain: "C" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2485 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.22 Number of scatterers: 18988 At special positions: 0 Unit cell: (132.3, 130.95, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 3 15.00 O 3522 8.00 N 3205 7.00 C 12147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 959.9 milliseconds 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4514 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 18 sheets defined 36.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'N' and resid 39 through 46 Processing helix chain 'N' and resid 98 through 116 removed outlier: 3.979A pdb=" N VAL N 102 " --> pdb=" O LEU N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 120 removed outlier: 3.828A pdb=" N SER N 120 " --> pdb=" O SER N 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 117 through 120' Processing helix chain 'N' and resid 121 through 142 removed outlier: 4.058A pdb=" N VAL N 129 " --> pdb=" O LYS N 125 " (cutoff:3.500A) Proline residue: N 130 - end of helix removed outlier: 4.119A pdb=" N ASN N 140 " --> pdb=" O LEU N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 184 removed outlier: 3.563A pdb=" N ASP N 183 " --> pdb=" O ASP N 180 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE N 184 " --> pdb=" O LYS N 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 180 through 184' Processing helix chain 'N' and resid 190 through 197 Processing helix chain 'N' and resid 198 through 201 removed outlier: 4.602A pdb=" N ASP N 201 " --> pdb=" O PRO N 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 198 through 201' Processing helix chain 'N' and resid 204 through 212 removed outlier: 4.004A pdb=" N SER N 210 " --> pdb=" O ILE N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 216 through 231 Processing helix chain 'N' and resid 254 through 264 removed outlier: 4.651A pdb=" N LYS N 258 " --> pdb=" O LEU N 254 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER N 259 " --> pdb=" O VAL N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 286 removed outlier: 5.111A pdb=" N PHE N 282 " --> pdb=" O LEU N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 327 removed outlier: 3.533A pdb=" N LEU N 326 " --> pdb=" O ILE N 323 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN N 327 " --> pdb=" O ARG N 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 323 through 327' Processing helix chain 'N' and resid 351 through 359 Processing helix chain 'N' and resid 361 through 369 Processing helix chain 'M' and resid 63 through 74 removed outlier: 3.964A pdb=" N LEU M 73 " --> pdb=" O LEU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 150 Processing helix chain 'M' and resid 160 through 173 removed outlier: 3.805A pdb=" N LEU M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 173 " --> pdb=" O LEU M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 195 Processing helix chain 'M' and resid 203 through 213 Processing helix chain 'M' and resid 245 through 252 removed outlier: 4.408A pdb=" N GLU M 249 " --> pdb=" O PRO M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 270 Processing helix chain 'M' and resid 293 through 305 Processing helix chain 'M' and resid 336 through 346 removed outlier: 3.657A pdb=" N SER M 346 " --> pdb=" O VAL M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 359 removed outlier: 3.653A pdb=" N SER M 358 " --> pdb=" O HIS M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 379 Proline residue: M 371 - end of helix Processing helix chain 'M' and resid 381 through 387 Processing helix chain 'M' and resid 390 through 393 removed outlier: 3.653A pdb=" N MET M 393 " --> pdb=" O LEU M 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 393' Processing helix chain 'M' and resid 394 through 402 Processing helix chain 'M' and resid 476 through 486 Processing helix chain 'M' and resid 492 through 501 Processing helix chain 'M' and resid 514 through 520 Processing helix chain 'M' and resid 523 through 532 Processing helix chain 'M' and resid 538 through 546 removed outlier: 4.137A pdb=" N PHE M 544 " --> pdb=" O LEU M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 558 through 567 removed outlier: 4.100A pdb=" N ALA M 562 " --> pdb=" O ASP M 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 4.405A pdb=" N THR D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.544A pdb=" N MET D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 210 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.888A pdb=" N GLU D 236 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 237 " --> pdb=" O PHE D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 237' Processing helix chain 'D' and resid 268 through 287 removed outlier: 3.669A pdb=" N VAL D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 305 through 318 Processing helix chain 'D' and resid 346 through 358 removed outlier: 3.510A pdb=" N MET D 350 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 749 removed outlier: 3.555A pdb=" N THR D 749 " --> pdb=" O LYS D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.955A pdb=" N GLU D 801 " --> pdb=" O GLN D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 991 removed outlier: 3.648A pdb=" N GLU D 979 " --> pdb=" O ALA D 975 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 991 " --> pdb=" O VAL D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1102 Proline residue: D1100 - end of helix Processing helix chain 'D' and resid 1179 through 1185 Processing helix chain 'D' and resid 1206 through 1218 Processing helix chain 'D' and resid 1222 through 1232 removed outlier: 3.925A pdb=" N MET D1226 " --> pdb=" O GLN D1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1312 removed outlier: 4.034A pdb=" N GLU D1307 " --> pdb=" O LEU D1303 " (cutoff:3.500A) Proline residue: D1309 - end of helix Processing helix chain 'D' and resid 1394 through 1411 removed outlier: 3.857A pdb=" N LEU D1398 " --> pdb=" O THR D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1464 through 1484 removed outlier: 3.706A pdb=" N ARG D1468 " --> pdb=" O THR D1464 " (cutoff:3.500A) Processing helix chain 'D' and resid 1566 through 1581 Processing helix chain 'D' and resid 1585 through 1596 Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.602A pdb=" N ARG A 37 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 39 " --> pdb=" O THR A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 39' Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.649A pdb=" N ILE A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 Processing helix chain 'A' and resid 133 through 152 Processing helix chain 'A' and resid 167 through 181 Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 225 through 244 removed outlier: 4.682A pdb=" N GLU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 298 removed outlier: 4.144A pdb=" N HIS A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.505A pdb=" N PHE C 92 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU C 94 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 94' Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 126 through 134 removed outlier: 3.975A pdb=" N TYR C 130 " --> pdb=" O PRO C 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 156 through 168 removed outlier: 4.605A pdb=" N LYS C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 removed outlier: 3.715A pdb=" N ILE C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 280 through 298 removed outlier: 3.758A pdb=" N LEU C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 367 removed outlier: 4.663A pdb=" N PHE C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 22 through 27 removed outlier: 8.450A pdb=" N ILE N 7 " --> pdb=" O ASP N 90 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP N 90 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU N 82 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU M 130 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL M 94 " --> pdb=" O PHE M 128 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE M 128 " --> pdb=" O VAL M 94 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS M 96 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL M 126 " --> pdb=" O HIS M 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 144 through 148 Processing sheet with id=AA3, first strand: chain 'N' and resid 174 through 177 Processing sheet with id=AA4, first strand: chain 'M' and resid 47 through 49 Processing sheet with id=AA5, first strand: chain 'M' and resid 405 through 410 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 134 Processing sheet with id=AA8, first strand: chain 'D' and resid 131 through 134 removed outlier: 5.581A pdb=" N ALA D 141 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR D 103 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU D 143 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU D 101 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 100 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ARG D 165 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU D 102 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 123 through 127 Processing sheet with id=AB1, first strand: chain 'D' and resid 238 through 242 removed outlier: 3.762A pdb=" N LYS D 247 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN D 260 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL D 216 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET D 170 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL D 334 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR D 172 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE D 336 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE D 174 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL D 364 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER D 333 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU D 366 " --> pdb=" O SER D 333 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL D 335 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 295 through 296 removed outlier: 5.193A pdb=" N VAL D 216 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN D 260 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP D 253 " --> pdb=" O TYR D 836 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 342 through 345 removed outlier: 6.291A pdb=" N PHE D 343 " --> pdb=" O LYS D 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 770 through 774 removed outlier: 6.671A pdb=" N THR D 771 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLY D 857 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY D 773 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR D 852 " --> pdb=" O LYS D 868 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL D 872 " --> pdb=" O ASP D 867 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1352 through 1357 removed outlier: 3.720A pdb=" N LEU D1415 " --> pdb=" O ALA D1300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1439 through 1441 removed outlier: 3.607A pdb=" N ILE D1441 " --> pdb=" O TYR D1546 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL D1509 " --> pdb=" O HIS D1504 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 45 through 52 removed outlier: 3.876A pdb=" N LEU A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 8 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TRP A 61 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 10 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 63 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 12 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A 88 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU A 125 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR A 90 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 213 through 218 removed outlier: 7.110A pdb=" N VAL A 213 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU A 207 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER A 251 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR C 327 " --> pdb=" O CYS C 339 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 144 removed outlier: 5.974A pdb=" N TYR C 142 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET C 171 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N HIS C 212 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE C 173 " --> pdb=" O HIS C 212 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 214 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 175 " --> pdb=" O SER C 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 707 hydrogen bonds defined for protein. 2046 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: 3.37 Time building geometry restraints manager: 2.40 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: 4649 1.33 - 1.45: 4089 1.45 - 1.58: 10497 1.58 - 1.70: 6 1.70 - 1.82: 172 Bond restraints: 19413 Sorted by residual: bond pdb=" O2B GNP A 500 " pdb=" PB GNP A 500 " ideal model delta sigma weight residual 1.505 1.604 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C4 GNP A 500 " pdb=" C5 GNP A 500 " ideal model delta sigma weight residual 1.382 1.464 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O1G GNP A 500 " pdb=" PG GNP A 500 " ideal model delta sigma weight residual 1.531 1.608 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O3G GNP A 500 " pdb=" PG GNP A 500 " ideal model delta sigma weight residual 1.532 1.609 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C ASP C 125 " pdb=" N PRO C 126 " ideal model delta sigma weight residual 1.336 1.381 -0.046 1.23e-02 6.61e+03 1.39e+01 ... (remaining 19408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 25311 3.01 - 6.03: 781 6.03 - 9.04: 161 9.04 - 12.05: 31 12.05 - 15.07: 9 Bond angle restraints: 26293 Sorted by residual: angle pdb=" C VAL C 277 " pdb=" N ASP C 278 " pdb=" CA ASP C 278 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.07e+01 angle pdb=" C PRO M 502 " pdb=" N ALA M 503 " pdb=" CA ALA M 503 " ideal model delta sigma weight residual 121.54 131.72 -10.18 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C LYS M 87 " pdb=" N ILE M 88 " pdb=" CA ILE M 88 " ideal model delta sigma weight residual 122.27 127.87 -5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" C PRO D1495 " pdb=" N ALA D1496 " pdb=" CA ALA D1496 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" C TYR N 245 " pdb=" N CYS N 246 " pdb=" CA CYS N 246 " ideal model delta sigma weight residual 120.06 126.14 -6.08 1.19e+00 7.06e-01 2.61e+01 ... (remaining 26288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 10811 17.39 - 34.78: 765 34.78 - 52.16: 140 52.16 - 69.55: 5 69.55 - 86.94: 7 Dihedral angle restraints: 11728 sinusoidal: 4803 harmonic: 6925 Sorted by residual: dihedral pdb=" CA ARG D1583 " pdb=" C ARG D1583 " pdb=" N ASP D1584 " pdb=" CA ASP D1584 " ideal model delta harmonic sigma weight residual -180.00 -126.01 -53.99 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA ASN M 379 " pdb=" C ASN M 379 " pdb=" N PRO M 380 " pdb=" CA PRO M 380 " ideal model delta harmonic sigma weight residual 180.00 133.77 46.23 0 5.00e+00 4.00e-02 8.55e+01 dihedral pdb=" CA GLU D 288 " pdb=" C GLU D 288 " pdb=" N GLN D 289 " pdb=" CA GLN D 289 " ideal model delta harmonic sigma weight residual -180.00 -136.20 -43.80 0 5.00e+00 4.00e-02 7.68e+01 ... (remaining 11725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2451 0.086 - 0.171: 418 0.171 - 0.257: 59 0.257 - 0.342: 5 0.342 - 0.428: 4 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CB ILE C 237 " pdb=" CA ILE C 237 " pdb=" CG1 ILE C 237 " pdb=" CG2 ILE C 237 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CB ILE M 11 " pdb=" CA ILE M 11 " pdb=" CG1 ILE M 11 " pdb=" CG2 ILE M 11 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA THR M 441 " pdb=" N THR M 441 " pdb=" C THR M 441 " pdb=" CB THR M 441 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 2934 not shown) Planarity restraints: 3363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 298 " -0.031 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C GLU A 298 " 0.105 2.00e-02 2.50e+03 pdb=" O GLU A 298 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 299 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 173 " 0.038 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP A 173 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 173 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 173 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 173 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 173 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 173 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 173 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 173 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN M 379 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO M 380 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO M 380 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO M 380 " 0.055 5.00e-02 4.00e+02 ... (remaining 3360 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3107 2.77 - 3.30: 17747 3.30 - 3.83: 29799 3.83 - 4.37: 32999 4.37 - 4.90: 55519 Nonbonded interactions: 139171 Sorted by model distance: nonbonded pdb=" O THR N 58 " pdb=" O LYS M 87 " model vdw 2.231 3.040 nonbonded pdb=" O VAL M 67 " pdb=" OG1 THR M 71 " model vdw 2.267 3.040 nonbonded pdb=" O ALA A 172 " pdb=" OG SER A 175 " model vdw 2.268 3.040 nonbonded pdb=" O ILE N 354 " pdb=" OG1 THR N 358 " model vdw 2.277 3.040 nonbonded pdb=" O ASP A 44 " pdb=" OH TYR A 73 " model vdw 2.279 3.040 ... (remaining 139166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.980 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.007 0.099 19413 Z= 0.329 Angle : 1.322 15.065 26293 Z= 0.694 Chirality : 0.067 0.428 2937 Planarity : 0.010 0.100 3363 Dihedral : 12.250 86.941 7214 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.43 % Allowed : 16.77 % Favored : 82.80 % Rotamer: Outliers : 0.99 % Allowed : 6.24 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.67 % Twisted General : 0.72 % 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: -5.29 (0.13), residues: 2302 helix: -2.85 (0.13), residues: 750 sheet: -2.32 (0.23), residues: 404 loop : -4.57 (0.13), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 111 TYR 0.031 0.004 TYR D 226 PHE 0.036 0.004 PHE C 226 TRP 0.069 0.004 TRP A 173 HIS 0.015 0.003 HIS D1186 Details of bonding type rmsd covalent geometry : bond 0.00713 (19413) covalent geometry : angle 1.32248 (26293) hydrogen bonds : bond 0.10020 ( 695) hydrogen bonds : angle 7.40989 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 306 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 269 THR cc_start: 0.6837 (m) cc_final: 0.6543 (p) REVERT: M 250 ARG cc_start: 0.5318 (tmt90) cc_final: 0.5036 (ttp80) REVERT: M 262 LEU cc_start: 0.8210 (mt) cc_final: 0.7534 (mm) REVERT: M 404 ILE cc_start: 0.7430 (mm) cc_final: 0.6864 (mm) REVERT: M 530 MET cc_start: 0.7151 (mmm) cc_final: 0.6948 (mmt) REVERT: D 59 LYS cc_start: 0.6301 (mtpp) cc_final: 0.5880 (mmpt) REVERT: D 853 TRP cc_start: 0.8470 (p-90) cc_final: 0.8240 (p-90) REVERT: D 868 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8022 (mmtm) REVERT: D 1253 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: A 3 ASN cc_start: 0.7359 (t0) cc_final: 0.6811 (m-40) REVERT: A 90 TYR cc_start: 0.8382 (t80) cc_final: 0.8179 (t80) REVERT: A 252 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6275 (ppp) REVERT: A 266 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7014 (m-10) REVERT: C 67 MET cc_start: 0.3730 (mtt) cc_final: 0.3417 (ppp) outliers start: 21 outliers final: 4 residues processed: 324 average time/residue: 0.1673 time to fit residues: 79.0436 Evaluate side-chains 174 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 205 HIS N 321 ASN M 50 ASN M 144 ASN M 192 HIS ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 485 ASN M 493 HIS D 45 ASN D 176 GLN D 197 ASN D 261 ASN D 303 GLN D 311 ASN D 315 ASN D 383 HIS D 384 ASN D 797 GLN D 809 GLN D 981 GLN D 994 ASN ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 HIS D1406 HIS D1478 HIS D1551 ASN A 49 HIS A 59 ASN A 179 GLN A 186 GLN A 258 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 111 ASN C 196 HIS C 200 ASN C 364 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.123090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106453 restraints weight = 64445.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106202 restraints weight = 52057.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.106925 restraints weight = 38991.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107257 restraints weight = 31092.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107313 restraints weight = 28433.562| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19413 Z= 0.139 Angle : 0.794 10.230 26293 Z= 0.410 Chirality : 0.046 0.247 2937 Planarity : 0.007 0.085 3363 Dihedral : 8.397 84.178 2579 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.86 % Favored : 86.10 % Rotamer: Outliers : 2.84 % Allowed : 9.83 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.32 % 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: -4.21 (0.15), residues: 2302 helix: -1.31 (0.17), residues: 760 sheet: -1.99 (0.24), residues: 396 loop : -4.31 (0.14), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 204 TYR 0.024 0.002 TYR C 165 PHE 0.028 0.002 PHE D1289 TRP 0.038 0.002 TRP D1405 HIS 0.005 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00296 (19413) covalent geometry : angle 0.79363 (26293) hydrogen bonds : bond 0.04569 ( 695) hydrogen bonds : angle 6.03732 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 112 LEU cc_start: 0.8795 (mt) cc_final: 0.8520 (mt) REVERT: M 250 ARG cc_start: 0.5541 (tmt90) cc_final: 0.5190 (ttp80) REVERT: M 393 MET cc_start: 0.8053 (ppp) cc_final: 0.7804 (ppp) REVERT: M 439 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7479 (tt) REVERT: M 531 TYR cc_start: 0.4884 (m-80) cc_final: 0.4413 (m-80) REVERT: D 868 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7471 (tppt) REVERT: D 1095 GLU cc_start: 0.7982 (pp20) cc_final: 0.7633 (tm-30) REVERT: D 1405 TRP cc_start: 0.8578 (p90) cc_final: 0.8055 (p90) REVERT: D 1465 TYR cc_start: 0.5068 (OUTLIER) cc_final: 0.3829 (t80) REVERT: A 3 ASN cc_start: 0.7009 (t0) cc_final: 0.6651 (m-40) REVERT: A 6 MET cc_start: 0.6731 (mmp) cc_final: 0.5964 (mmm) REVERT: C 85 MET cc_start: 0.6015 (mpp) cc_final: 0.5748 (mpp) REVERT: C 209 GLU cc_start: 0.3431 (OUTLIER) cc_final: 0.3174 (pp20) REVERT: C 269 TYR cc_start: 0.2041 (m-80) cc_final: 0.1837 (m-80) outliers start: 60 outliers final: 25 residues processed: 269 average time/residue: 0.1440 time to fit residues: 59.4600 Evaluate side-chains 200 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 79 MET Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 979 GLU Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 107 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 227 optimal weight: 30.0000 chunk 155 optimal weight: 0.0470 chunk 83 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 323 ASN D 809 GLN ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.117796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.100879 restraints weight = 64796.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.099852 restraints weight = 54177.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.100518 restraints weight = 44859.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.100806 restraints weight = 36908.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100997 restraints weight = 32819.755| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19413 Z= 0.221 Angle : 0.866 11.090 26293 Z= 0.449 Chirality : 0.049 0.234 2937 Planarity : 0.007 0.113 3363 Dihedral : 8.353 89.438 2576 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.20 % Favored : 83.71 % Rotamer: Outliers : 3.78 % Allowed : 13.23 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.32 % 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: -3.81 (0.16), residues: 2302 helix: -0.78 (0.18), residues: 777 sheet: -1.98 (0.24), residues: 407 loop : -4.20 (0.15), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.023 0.002 TYR D 775 PHE 0.027 0.002 PHE D 760 TRP 0.037 0.002 TRP D1405 HIS 0.008 0.001 HIS N 363 Details of bonding type rmsd covalent geometry : bond 0.00501 (19413) covalent geometry : angle 0.86613 (26293) hydrogen bonds : bond 0.05260 ( 695) hydrogen bonds : angle 6.11292 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 175 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 112 LEU cc_start: 0.8676 (mt) cc_final: 0.8431 (mt) REVERT: N 282 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7052 (t80) REVERT: M 73 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7629 (pp) REVERT: M 250 ARG cc_start: 0.5537 (tmt90) cc_final: 0.5082 (ttp80) REVERT: M 480 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: D 303 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: D 853 TRP cc_start: 0.8561 (p-90) cc_final: 0.8177 (p-90) REVERT: D 868 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7682 (tppt) REVERT: D 995 ARG cc_start: 0.6088 (ttt180) cc_final: 0.5506 (mtp180) REVERT: D 1095 GLU cc_start: 0.7744 (pp20) cc_final: 0.7466 (tm-30) REVERT: D 1184 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6891 (ptt) REVERT: D 1253 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7564 (m-10) REVERT: D 1465 TYR cc_start: 0.4974 (OUTLIER) cc_final: 0.3941 (t80) REVERT: D 1548 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.7327 (t-100) REVERT: A 189 MET cc_start: 0.7083 (tmm) cc_final: 0.6550 (tmm) REVERT: A 271 TYR cc_start: 0.7029 (m-80) cc_final: 0.6503 (m-80) REVERT: A 276 MET cc_start: 0.8280 (tpp) cc_final: 0.7842 (tpp) REVERT: C 85 MET cc_start: 0.5591 (mpp) cc_final: 0.5363 (mpp) outliers start: 80 outliers final: 39 residues processed: 243 average time/residue: 0.1299 time to fit residues: 50.7644 Evaluate side-chains 199 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 217 LEU Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 375 SER Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 1184 MET Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1375 HIS Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 95 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.120395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.103558 restraints weight = 64540.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103465 restraints weight = 52682.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.103795 restraints weight = 41293.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104194 restraints weight = 36900.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104336 restraints weight = 30894.688| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19413 Z= 0.148 Angle : 0.782 11.953 26293 Z= 0.399 Chirality : 0.046 0.216 2937 Planarity : 0.006 0.110 3363 Dihedral : 7.838 87.140 2576 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.07 % Favored : 85.84 % Rotamer: Outliers : 3.21 % Allowed : 15.83 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.32 % 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: -3.47 (0.16), residues: 2302 helix: -0.43 (0.19), residues: 781 sheet: -1.86 (0.24), residues: 389 loop : -4.01 (0.15), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 204 TYR 0.021 0.002 TYR M 208 PHE 0.025 0.002 PHE N 87 TRP 0.026 0.002 TRP D1405 HIS 0.003 0.001 HIS D1478 Details of bonding type rmsd covalent geometry : bond 0.00327 (19413) covalent geometry : angle 0.78151 (26293) hydrogen bonds : bond 0.04407 ( 695) hydrogen bonds : angle 5.72461 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 180 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 112 LEU cc_start: 0.8859 (mt) cc_final: 0.8624 (mt) REVERT: M 73 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7725 (pp) REVERT: M 250 ARG cc_start: 0.5449 (tmt90) cc_final: 0.5058 (ttp80) REVERT: M 395 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8221 (m) REVERT: M 527 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7979 (tp30) REVERT: D 853 TRP cc_start: 0.8509 (p-90) cc_final: 0.8189 (p-90) REVERT: D 868 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7558 (tppt) REVERT: D 995 ARG cc_start: 0.6135 (ttt180) cc_final: 0.5517 (mtp180) REVERT: D 1095 GLU cc_start: 0.7688 (pp20) cc_final: 0.7386 (tm-30) REVERT: D 1184 MET cc_start: 0.7094 (ptt) cc_final: 0.6813 (ptt) REVERT: D 1253 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: D 1405 TRP cc_start: 0.8609 (p90) cc_final: 0.8142 (p90) REVERT: D 1465 TYR cc_start: 0.4796 (OUTLIER) cc_final: 0.4023 (t80) REVERT: D 1573 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8822 (tt) REVERT: A 189 MET cc_start: 0.7094 (tmm) cc_final: 0.6514 (tmm) REVERT: A 223 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6801 (mpt-90) REVERT: A 276 MET cc_start: 0.8138 (tpp) cc_final: 0.7647 (tpp) REVERT: C 151 MET cc_start: 0.1611 (ptm) cc_final: 0.1352 (mtm) REVERT: C 269 TYR cc_start: 0.1851 (m-80) cc_final: 0.1382 (m-80) REVERT: C 288 MET cc_start: 0.7670 (tpp) cc_final: 0.7319 (tpp) outliers start: 68 outliers final: 44 residues processed: 234 average time/residue: 0.1334 time to fit residues: 49.5794 Evaluate side-chains 211 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain N residue 217 LEU Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 45 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.117266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100163 restraints weight = 64541.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099966 restraints weight = 52622.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.100351 restraints weight = 48737.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100689 restraints weight = 37750.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.100790 restraints weight = 33432.446| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19413 Z= 0.210 Angle : 0.829 11.049 26293 Z= 0.426 Chirality : 0.048 0.240 2937 Planarity : 0.007 0.117 3363 Dihedral : 7.993 88.003 2575 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.42 % Favored : 83.49 % Rotamer: Outliers : 4.54 % Allowed : 15.69 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.23 % 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: -3.41 (0.17), residues: 2302 helix: -0.33 (0.19), residues: 780 sheet: -1.93 (0.24), residues: 406 loop : -3.99 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 291 TYR 0.022 0.002 TYR M 208 PHE 0.023 0.002 PHE D 760 TRP 0.028 0.002 TRP D1405 HIS 0.007 0.001 HIS N 363 Details of bonding type rmsd covalent geometry : bond 0.00473 (19413) covalent geometry : angle 0.82898 (26293) hydrogen bonds : bond 0.04856 ( 695) hydrogen bonds : angle 5.88973 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 161 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 112 LEU cc_start: 0.8661 (mt) cc_final: 0.8402 (mt) REVERT: N 216 GLU cc_start: 0.6782 (tp30) cc_final: 0.6473 (tp30) REVERT: M 73 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7591 (pp) REVERT: D 303 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: D 369 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6665 (ptt) REVERT: D 828 PRO cc_start: 0.4341 (OUTLIER) cc_final: 0.4120 (Cg_exo) REVERT: D 1095 GLU cc_start: 0.7713 (pp20) cc_final: 0.7435 (tm-30) REVERT: D 1184 MET cc_start: 0.7148 (ptt) cc_final: 0.6755 (ptt) REVERT: D 1253 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: D 1405 TRP cc_start: 0.8642 (p90) cc_final: 0.8201 (p90) REVERT: D 1465 TYR cc_start: 0.5354 (OUTLIER) cc_final: 0.4602 (t80) REVERT: D 1548 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.7392 (t-100) REVERT: D 1573 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8628 (tt) REVERT: A 223 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.7026 (mpt-90) outliers start: 96 outliers final: 56 residues processed: 242 average time/residue: 0.1249 time to fit residues: 49.2195 Evaluate side-chains 219 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 154 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain N residue 217 LEU Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 363 HIS Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 828 PRO Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.118584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.101250 restraints weight = 64221.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101260 restraints weight = 52624.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101979 restraints weight = 39293.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.102352 restraints weight = 31919.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102436 restraints weight = 30263.898| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19413 Z= 0.163 Angle : 0.790 11.004 26293 Z= 0.403 Chirality : 0.047 0.229 2937 Planarity : 0.006 0.118 3363 Dihedral : 7.792 87.385 2575 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.73 % Favored : 85.19 % Rotamer: Outliers : 4.54 % Allowed : 16.26 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.27 % 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: -3.30 (0.17), residues: 2302 helix: -0.22 (0.19), residues: 780 sheet: -1.82 (0.25), residues: 388 loop : -3.94 (0.15), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.022 0.002 TYR M 208 PHE 0.022 0.002 PHE M 352 TRP 0.025 0.002 TRP D1548 HIS 0.010 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00363 (19413) covalent geometry : angle 0.78955 (26293) hydrogen bonds : bond 0.04481 ( 695) hydrogen bonds : angle 5.72046 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 167 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7320 (t-90) REVERT: N 112 LEU cc_start: 0.8629 (mt) cc_final: 0.8396 (mt) REVERT: N 282 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6514 (t80) REVERT: M 73 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7598 (pp) REVERT: M 439 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7693 (tt) REVERT: M 530 MET cc_start: 0.7331 (mmt) cc_final: 0.6971 (mtt) REVERT: D 303 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: D 369 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6441 (ptt) REVERT: D 868 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7454 (tppt) REVERT: D 982 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8123 (mt) REVERT: D 1095 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: D 1184 MET cc_start: 0.7195 (ptt) cc_final: 0.6715 (ptt) REVERT: D 1253 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7490 (m-10) REVERT: D 1405 TRP cc_start: 0.8585 (p90) cc_final: 0.8243 (p90) REVERT: D 1465 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.4568 (t80) REVERT: D 1480 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6629 (t80) REVERT: D 1548 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.7278 (t-100) REVERT: D 1573 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8553 (tt) REVERT: A 56 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 132 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7094 (m) REVERT: A 189 MET cc_start: 0.7232 (tmm) cc_final: 0.6658 (tmm) REVERT: A 223 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7081 (mtt-85) REVERT: A 271 TYR cc_start: 0.7031 (m-80) cc_final: 0.6666 (m-80) outliers start: 96 outliers final: 52 residues processed: 248 average time/residue: 0.1214 time to fit residues: 48.7053 Evaluate side-chains 225 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain N residue 217 LEU Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 363 HIS Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 375 SER Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1095 GLU Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1480 PHE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 217 optimal weight: 0.0020 chunk 203 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 405 GLN M 525 HIS ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.120701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.103907 restraints weight = 64631.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.103620 restraints weight = 56481.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.103962 restraints weight = 43406.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104252 restraints weight = 36591.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104390 restraints weight = 33582.820| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19413 Z= 0.136 Angle : 0.767 10.294 26293 Z= 0.387 Chirality : 0.046 0.221 2937 Planarity : 0.006 0.120 3363 Dihedral : 7.505 86.954 2575 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.51 % Favored : 85.45 % Rotamer: Outliers : 4.02 % Allowed : 17.67 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.27 % 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: -3.16 (0.17), residues: 2302 helix: -0.11 (0.19), residues: 785 sheet: -1.74 (0.25), residues: 388 loop : -3.87 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 204 TYR 0.025 0.001 TYR M 208 PHE 0.020 0.002 PHE N 87 TRP 0.024 0.002 TRP D1548 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00295 (19413) covalent geometry : angle 0.76702 (26293) hydrogen bonds : bond 0.04150 ( 695) hydrogen bonds : angle 5.56506 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 185 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: N 112 LEU cc_start: 0.8624 (mt) cc_final: 0.8415 (mt) REVERT: N 282 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6217 (t80) REVERT: M 73 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7593 (pp) REVERT: M 151 THR cc_start: 0.3198 (p) cc_final: 0.2979 (p) REVERT: M 397 MET cc_start: 0.7305 (ptt) cc_final: 0.7016 (ptp) REVERT: M 405 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6460 (tm-30) REVERT: M 439 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7472 (tt) REVERT: M 530 MET cc_start: 0.7212 (mmt) cc_final: 0.6890 (mtt) REVERT: D 369 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6003 (ptt) REVERT: D 853 TRP cc_start: 0.8526 (p-90) cc_final: 0.8220 (p-90) REVERT: D 995 ARG cc_start: 0.6571 (ttt180) cc_final: 0.5908 (mtp180) REVERT: D 1095 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: D 1184 MET cc_start: 0.7267 (ptt) cc_final: 0.6775 (ptt) REVERT: D 1253 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: D 1405 TRP cc_start: 0.8521 (p90) cc_final: 0.8254 (p90) REVERT: D 1465 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.4738 (t80) REVERT: D 1480 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6530 (t80) REVERT: D 1548 TRP cc_start: 0.9044 (OUTLIER) cc_final: 0.7116 (t-100) REVERT: D 1573 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 132 VAL cc_start: 0.7300 (OUTLIER) cc_final: 0.6927 (m) REVERT: A 189 MET cc_start: 0.7234 (tmm) cc_final: 0.6608 (tmm) REVERT: A 223 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6896 (mtt-85) REVERT: A 289 ASN cc_start: 0.7327 (m110) cc_final: 0.6348 (t0) REVERT: C 165 TYR cc_start: 0.5477 (OUTLIER) cc_final: 0.4948 (p90) REVERT: C 269 TYR cc_start: 0.1981 (m-80) cc_final: 0.1721 (m-80) REVERT: C 359 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7761 (p90) outliers start: 85 outliers final: 49 residues processed: 251 average time/residue: 0.1222 time to fit residues: 49.8688 Evaluate side-chains 232 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 363 HIS Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 375 SER Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 405 GLN Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1095 GLU Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1480 PHE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 201 optimal weight: 0.0570 chunk 232 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 153 optimal weight: 0.4980 chunk 181 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 525 HIS D 355 GLN ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.120225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103295 restraints weight = 64556.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103210 restraints weight = 52034.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103705 restraints weight = 39723.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104119 restraints weight = 33277.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104198 restraints weight = 30750.503| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19413 Z= 0.146 Angle : 0.778 10.877 26293 Z= 0.392 Chirality : 0.046 0.218 2937 Planarity : 0.006 0.126 3363 Dihedral : 7.444 87.593 2575 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.68 % Favored : 85.23 % Rotamer: Outliers : 3.97 % Allowed : 18.10 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.27 % 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: -3.10 (0.17), residues: 2302 helix: -0.08 (0.19), residues: 787 sheet: -1.64 (0.25), residues: 393 loop : -3.86 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 988 TYR 0.027 0.002 TYR M 208 PHE 0.021 0.002 PHE N 87 TRP 0.025 0.002 TRP D1548 HIS 0.007 0.001 HIS M 96 Details of bonding type rmsd covalent geometry : bond 0.00326 (19413) covalent geometry : angle 0.77787 (26293) hydrogen bonds : bond 0.04208 ( 695) hydrogen bonds : angle 5.53404 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 174 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7089 (t-90) REVERT: N 112 LEU cc_start: 0.8644 (mt) cc_final: 0.8430 (mt) REVERT: M 41 LYS cc_start: 0.5760 (mmpt) cc_final: 0.5301 (mmtm) REVERT: M 73 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7606 (pp) REVERT: M 397 MET cc_start: 0.7196 (ptt) cc_final: 0.6929 (ptp) REVERT: M 530 MET cc_start: 0.7203 (mmt) cc_final: 0.6997 (mtt) REVERT: D 303 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: D 369 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.5990 (ptt) REVERT: D 853 TRP cc_start: 0.8513 (p-90) cc_final: 0.8288 (p-90) REVERT: D 995 ARG cc_start: 0.6448 (ttt180) cc_final: 0.5808 (mtp180) REVERT: D 1095 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: D 1184 MET cc_start: 0.7117 (ptt) cc_final: 0.6623 (ptt) REVERT: D 1253 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: D 1405 TRP cc_start: 0.8509 (p90) cc_final: 0.8289 (p90) REVERT: D 1465 TYR cc_start: 0.5520 (OUTLIER) cc_final: 0.4741 (t80) REVERT: D 1480 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6644 (t80) REVERT: D 1548 TRP cc_start: 0.8999 (OUTLIER) cc_final: 0.7108 (t-100) REVERT: D 1573 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8832 (tt) REVERT: A 56 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 132 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.6944 (m) REVERT: A 189 MET cc_start: 0.7201 (tmm) cc_final: 0.6515 (tmm) REVERT: A 266 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6624 (m-10) REVERT: A 271 TYR cc_start: 0.6987 (m-80) cc_final: 0.6676 (m-80) REVERT: C 165 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.5011 (p90) REVERT: C 269 TYR cc_start: 0.2195 (m-80) cc_final: 0.1836 (m-80) REVERT: C 359 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7795 (p90) outliers start: 84 outliers final: 52 residues processed: 240 average time/residue: 0.1202 time to fit residues: 46.7465 Evaluate side-chains 234 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 363 HIS Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 375 SER Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1095 GLU Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1480 PHE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.120102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103211 restraints weight = 63887.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103274 restraints weight = 48863.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104053 restraints weight = 36551.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.104238 restraints weight = 30883.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.104270 restraints weight = 29527.368| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19413 Z= 0.148 Angle : 0.782 11.945 26293 Z= 0.393 Chirality : 0.046 0.217 2937 Planarity : 0.006 0.128 3363 Dihedral : 7.412 87.870 2575 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.90 % Favored : 85.01 % Rotamer: Outliers : 3.83 % Allowed : 18.43 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.23 % 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: -3.06 (0.17), residues: 2302 helix: -0.07 (0.19), residues: 787 sheet: -1.58 (0.25), residues: 391 loop : -3.83 (0.16), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 279 TYR 0.029 0.002 TYR M 208 PHE 0.020 0.002 PHE N 87 TRP 0.025 0.002 TRP D1548 HIS 0.006 0.001 HIS M 96 Details of bonding type rmsd covalent geometry : bond 0.00330 (19413) covalent geometry : angle 0.78217 (26293) hydrogen bonds : bond 0.04220 ( 695) hydrogen bonds : angle 5.55530 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 177 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7109 (t-90) REVERT: N 132 MET cc_start: 0.8717 (mtm) cc_final: 0.8482 (mtm) REVERT: M 41 LYS cc_start: 0.5446 (mmpt) cc_final: 0.4973 (mmtm) REVERT: M 73 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7639 (pp) REVERT: M 335 MET cc_start: 0.3004 (mtt) cc_final: 0.2638 (mtt) REVERT: M 397 MET cc_start: 0.7038 (ptt) cc_final: 0.6750 (ptp) REVERT: M 480 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: M 530 MET cc_start: 0.7173 (mmt) cc_final: 0.6968 (mtt) REVERT: D 303 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: D 369 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6037 (ptt) REVERT: D 995 ARG cc_start: 0.6431 (ttt180) cc_final: 0.5788 (mtp180) REVERT: D 1184 MET cc_start: 0.7114 (ptt) cc_final: 0.6624 (ptt) REVERT: D 1405 TRP cc_start: 0.8515 (p90) cc_final: 0.8315 (p90) REVERT: D 1465 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.4800 (t80) REVERT: D 1480 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6610 (t80) REVERT: D 1548 TRP cc_start: 0.9005 (OUTLIER) cc_final: 0.7113 (t-100) REVERT: D 1573 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 56 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 70 MET cc_start: 0.8460 (mmm) cc_final: 0.8111 (tpp) REVERT: A 132 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6931 (m) REVERT: A 189 MET cc_start: 0.7205 (tmm) cc_final: 0.6553 (tmm) REVERT: A 266 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: A 271 TYR cc_start: 0.7083 (m-80) cc_final: 0.6683 (m-80) REVERT: C 165 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.5215 (p90) REVERT: C 269 TYR cc_start: 0.2271 (m-80) cc_final: 0.1997 (m-80) REVERT: C 359 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7766 (p90) outliers start: 81 outliers final: 57 residues processed: 241 average time/residue: 0.1283 time to fit residues: 50.3991 Evaluate side-chains 238 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 167 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 363 HIS Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 375 SER Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1408 LYS Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1480 PHE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 94 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 155 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.120141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.103348 restraints weight = 64045.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.103223 restraints weight = 55902.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103453 restraints weight = 41487.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103728 restraints weight = 38115.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.103811 restraints weight = 35151.323| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19413 Z= 0.149 Angle : 0.797 15.438 26293 Z= 0.399 Chirality : 0.046 0.215 2937 Planarity : 0.006 0.132 3363 Dihedral : 7.384 87.814 2575 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.07 % Favored : 84.84 % Rotamer: Outliers : 3.64 % Allowed : 18.71 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.27 % 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: -3.06 (0.17), residues: 2302 helix: -0.11 (0.19), residues: 793 sheet: -1.53 (0.25), residues: 388 loop : -3.82 (0.16), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 988 TYR 0.032 0.002 TYR M 208 PHE 0.024 0.002 PHE D 986 TRP 0.025 0.002 TRP D1548 HIS 0.006 0.001 HIS M 96 Details of bonding type rmsd covalent geometry : bond 0.00334 (19413) covalent geometry : angle 0.79720 (26293) hydrogen bonds : bond 0.04243 ( 695) hydrogen bonds : angle 5.56509 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7125 (t-90) REVERT: N 132 MET cc_start: 0.8714 (mtm) cc_final: 0.8459 (mtm) REVERT: M 73 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7635 (pp) REVERT: M 318 TYR cc_start: 0.5610 (m-80) cc_final: 0.5404 (m-80) REVERT: M 335 MET cc_start: 0.2948 (mtt) cc_final: 0.2565 (mtt) REVERT: M 397 MET cc_start: 0.7129 (ptt) cc_final: 0.6818 (ptp) REVERT: M 480 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: M 530 MET cc_start: 0.7178 (mmt) cc_final: 0.6895 (mtt) REVERT: D 303 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: D 369 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6001 (ptt) REVERT: D 809 GLN cc_start: 0.6856 (tp40) cc_final: 0.6520 (tp40) REVERT: D 995 ARG cc_start: 0.6424 (ttt180) cc_final: 0.5799 (mtp180) REVERT: D 1184 MET cc_start: 0.7154 (ptt) cc_final: 0.6662 (ptt) REVERT: D 1405 TRP cc_start: 0.8509 (p90) cc_final: 0.8297 (p90) REVERT: D 1465 TYR cc_start: 0.5480 (OUTLIER) cc_final: 0.4799 (t80) REVERT: D 1480 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6681 (t80) REVERT: D 1548 TRP cc_start: 0.9071 (OUTLIER) cc_final: 0.7255 (t-100) REVERT: D 1573 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8779 (tt) REVERT: A 56 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8352 (tt) REVERT: A 132 VAL cc_start: 0.7191 (OUTLIER) cc_final: 0.6899 (m) REVERT: A 189 MET cc_start: 0.7197 (tmm) cc_final: 0.6546 (tmm) REVERT: A 266 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6500 (m-10) REVERT: A 271 TYR cc_start: 0.7075 (m-80) cc_final: 0.6711 (m-80) REVERT: C 165 TYR cc_start: 0.5707 (OUTLIER) cc_final: 0.5232 (p90) REVERT: C 269 TYR cc_start: 0.2222 (m-80) cc_final: 0.1868 (m-80) REVERT: C 359 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7791 (p90) outliers start: 77 outliers final: 54 residues processed: 231 average time/residue: 0.1188 time to fit residues: 44.9413 Evaluate side-chains 233 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 282 PHE Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 363 HIS Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 375 SER Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1408 LYS Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1480 PHE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 136 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 156 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 371 ASN M 339 ASN D 805 GLN ** D1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 178 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.113240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096707 restraints weight = 64416.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096143 restraints weight = 58245.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096664 restraints weight = 52758.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.096954 restraints weight = 42053.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097016 restraints weight = 37249.886| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 19413 Z= 0.335 Angle : 1.012 14.751 26293 Z= 0.520 Chirality : 0.054 0.230 2937 Planarity : 0.008 0.141 3363 Dihedral : 8.508 89.897 2575 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.25 % Favored : 81.67 % Rotamer: Outliers : 3.69 % Allowed : 18.95 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.74 % Twisted General : 0.36 % 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: -3.58 (0.16), residues: 2302 helix: -0.63 (0.18), residues: 784 sheet: -1.83 (0.25), residues: 394 loop : -4.04 (0.16), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 988 TYR 0.032 0.003 TYR M 208 PHE 0.046 0.003 PHE C 112 TRP 0.038 0.003 TRP D 402 HIS 0.011 0.002 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00771 (19413) covalent geometry : angle 1.01203 (26293) hydrogen bonds : bond 0.05969 ( 695) hydrogen bonds : angle 6.45278 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2693.77 seconds wall clock time: 47 minutes 44.34 seconds (2864.34 seconds total)