Starting phenix.real_space_refine on Mon Jul 28 05:59:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nts_0510/07_2025/6nts_0510.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nts_0510/07_2025/6nts_0510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nts_0510/07_2025/6nts_0510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nts_0510/07_2025/6nts_0510.map" model { file = "/net/cci-nas-00/data/ceres_data/6nts_0510/07_2025/6nts_0510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nts_0510/07_2025/6nts_0510.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 S 57 5.16 5 C 6378 2.51 5 N 1654 2.21 5 O 1862 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9956 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2976 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain: "C" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2399 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'L2J': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.57, per 1000 atoms: 0.66 Number of scatterers: 9956 At special positions: 0 Unit cell: (96.824, 110.656, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 57 16.00 F 3 9.00 O 1862 8.00 N 1654 7.00 C 6378 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: 2.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 3 sheets defined 74.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 Processing helix chain 'A' and resid 24 through 43 removed outlier: 3.506A pdb=" N ARG A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 59 removed outlier: 5.099A pdb=" N LEU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.149A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.867A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.736A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.837A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.804A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.692A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.529A pdb=" N ARG A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 5.081A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.698A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.398A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.666A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.907A pdb=" N ALA A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.743A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.567A pdb=" N LYS A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.821A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.565A pdb=" N VAL A 321 " --> pdb=" O CYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.767A pdb=" N LYS A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.935A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.806A pdb=" N ILE A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.680A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 removed outlier: 3.816A pdb=" N VAL A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.760A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.626A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.956A pdb=" N PHE A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.599A pdb=" N CYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.556A pdb=" N ARG A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.957A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 removed outlier: 3.799A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.734A pdb=" N THR A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 529 removed outlier: 3.611A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix removed outlier: 3.575A pdb=" N ALA A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 removed outlier: 4.549A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.538A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix removed outlier: 3.814A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.037A pdb=" N GLN B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 91 through 111 removed outlier: 3.930A pdb=" N GLU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.668A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 4.230A pdb=" N LEU B 161 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 200 through 218 removed outlier: 3.565A pdb=" N ARG B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.552A pdb=" N LEU B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.713A pdb=" N LEU B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.698A pdb=" N THR B 281 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.856A pdb=" N PHE B 299 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.698A pdb=" N VAL B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.600A pdb=" N MET B 328 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 362 removed outlier: 4.465A pdb=" N LYS B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.623A pdb=" N LYS B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 391 through 402 removed outlier: 4.139A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.540A pdb=" N VAL B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.548A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.601A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.154A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.108A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.503A pdb=" N PHE C 220 " --> pdb=" O ASP C 202 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.57: 10076 1.57 - 1.92: 84 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.97: 1 Bond restraints: 10161 Sorted by residual: bond pdb=" C10 MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.427 2.965 -1.538 2.00e-02 2.50e+03 5.92e+03 bond pdb=" C02 L2J A 601 " pdb=" C03 L2J A 601 " ideal model delta sigma weight residual 1.396 1.293 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " ideal model delta sigma weight residual 1.388 1.488 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.327 1.231 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C07 L2J A 601 " pdb=" C08 L2J A 601 " ideal model delta sigma weight residual 1.402 1.320 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 10156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 13721 3.18 - 6.35: 53 6.35 - 9.53: 1 9.53 - 12.70: 3 12.70 - 15.88: 2 Bond angle restraints: 13780 Sorted by residual: angle pdb=" O03 L2J A 601 " pdb=" S01 L2J A 601 " pdb=" O04 L2J A 601 " ideal model delta sigma weight residual 116.82 100.94 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " pdb=" C10 MLL C 309 " ideal model delta sigma weight residual 117.67 133.31 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C19 L2J A 601 " pdb=" S01 L2J A 601 " pdb=" N02 L2J A 601 " ideal model delta sigma weight residual 100.55 111.98 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " pdb=" C05 L2J A 601 " ideal model delta sigma weight residual 119.28 108.25 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 110.79 121.00 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 13775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5703 17.83 - 35.65: 387 35.65 - 53.48: 69 53.48 - 71.31: 16 71.31 - 89.14: 12 Dihedral angle restraints: 6187 sinusoidal: 2536 harmonic: 3651 Sorted by residual: dihedral pdb=" CA ARG A 537 " pdb=" C ARG A 537 " pdb=" N PHE A 538 " pdb=" CA PHE A 538 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA HIS B 364 " pdb=" C HIS B 364 " pdb=" N PHE B 365 " pdb=" CA PHE B 365 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB GLU C 188 " pdb=" CG GLU C 188 " pdb=" CD GLU C 188 " pdb=" OE1 GLU C 188 " ideal model delta sinusoidal sigma weight residual 0.00 -89.14 89.14 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 6184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1080 0.027 - 0.055: 309 0.055 - 0.082: 116 0.082 - 0.110: 54 0.110 - 0.137: 13 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C18 L2J A 601 " pdb=" C13 L2J A 601 " pdb=" C17 L2J A 601 " pdb=" N01 L2J A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.45 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL C 52 " pdb=" N VAL C 52 " pdb=" C VAL C 52 " pdb=" CB VAL C 52 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PHE A 538 " pdb=" N PHE A 538 " pdb=" C PHE A 538 " pdb=" CB PHE A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1569 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 90 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO A 91 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 86 " 0.010 2.00e-02 2.50e+03 6.28e-03 7.89e-01 pdb=" CG TYR C 86 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 86 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 86 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 86 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 50 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.53e-01 pdb=" N PRO C 51 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.011 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 39 2.51 - 3.11: 7867 3.11 - 3.71: 15828 3.71 - 4.30: 21974 4.30 - 4.90: 35746 Nonbonded interactions: 81454 Sorted by model distance: nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 1.917 2.400 nonbonded pdb=" O GLY A 275 " pdb=" OG1 THR A 279 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.222 2.320 nonbonded pdb=" NE2 HIS C 59 " pdb="MN MN C 402 " model vdw 2.235 2.400 nonbonded pdb=" O GLY A 513 " pdb=" OG1 THR A 517 " model vdw 2.264 3.040 ... (remaining 81449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.64 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: 3.110 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.780 Find NCS groups from input model: 0.240 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.016 1.538 10161 Z= 0.780 Angle : 0.516 15.879 13780 Z= 0.247 Chirality : 0.034 0.137 1572 Planarity : 0.002 0.023 1764 Dihedral : 13.181 89.136 3809 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.22), residues: 1231 helix: -1.17 (0.17), residues: 793 sheet: -1.94 (0.87), residues: 35 loop : -1.41 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP A 257 HIS 0.003 0.000 HIS B 364 PHE 0.008 0.001 PHE A 538 TYR 0.013 0.001 TYR C 86 ARG 0.002 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.12700 ( 528) hydrogen bonds : angle 5.16110 ( 1536) covalent geometry : bond 0.01559 (10161) covalent geometry : angle 0.51645 (13780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.8284 (pp20) cc_final: 0.8055 (pp20) REVERT: B 78 CYS cc_start: 0.8890 (m) cc_final: 0.8648 (m) REVERT: B 110 THR cc_start: 0.8511 (p) cc_final: 0.8237 (p) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2652 time to fit residues: 44.1695 Evaluate side-chains 50 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** B 268 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 = 0.3562 r_free = 0.3562 target = 0.055615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047886 restraints weight = 63905.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.049124 restraints weight = 35528.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.049994 restraints weight = 23324.278| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10161 Z= 0.156 Angle : 0.641 10.993 13780 Z= 0.314 Chirality : 0.041 0.183 1572 Planarity : 0.004 0.061 1764 Dihedral : 4.398 26.065 1366 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.18 % Allowed : 5.88 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.24), residues: 1231 helix: -0.16 (0.19), residues: 813 sheet: -0.96 (0.97), residues: 31 loop : -0.89 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 477 HIS 0.010 0.001 HIS C 241 PHE 0.035 0.001 PHE A 538 TYR 0.015 0.001 TYR A 155 ARG 0.004 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 528) hydrogen bonds : angle 4.20869 ( 1536) covalent geometry : bond 0.00352 (10161) covalent geometry : angle 0.64089 (13780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 CYS cc_start: 0.8939 (m) cc_final: 0.8715 (m) REVERT: B 112 ARG cc_start: 0.6682 (tpt170) cc_final: 0.5942 (tpt-90) REVERT: B 326 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8532 (mm-30) REVERT: B 425 MET cc_start: 0.7086 (ptp) cc_final: 0.6796 (ptp) outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 0.2458 time to fit residues: 23.8748 Evaluate side-chains 50 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 90 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 444 ASN B 111 ASN C 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.051799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.044316 restraints weight = 65297.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.045480 restraints weight = 36219.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046321 restraints weight = 23719.999| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10161 Z= 0.140 Angle : 0.584 6.091 13780 Z= 0.291 Chirality : 0.041 0.139 1572 Planarity : 0.004 0.060 1764 Dihedral : 4.325 21.747 1366 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.09 % Allowed : 8.24 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1231 helix: 0.35 (0.19), residues: 809 sheet: -0.40 (1.07), residues: 31 loop : -0.51 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 156 HIS 0.005 0.001 HIS B 280 PHE 0.028 0.001 PHE A 538 TYR 0.011 0.001 TYR B 107 ARG 0.004 0.001 ARG C 239 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 528) hydrogen bonds : angle 4.04171 ( 1536) covalent geometry : bond 0.00316 (10161) covalent geometry : angle 0.58433 (13780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: B 112 ARG cc_start: 0.6819 (tpt170) cc_final: 0.6142 (tpt-90) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 0.1982 time to fit residues: 17.3728 Evaluate side-chains 45 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 165 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.051523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043960 restraints weight = 65021.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.045161 restraints weight = 36308.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.046008 restraints weight = 23951.117| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10161 Z= 0.106 Angle : 0.549 8.707 13780 Z= 0.270 Chirality : 0.039 0.135 1572 Planarity : 0.003 0.036 1764 Dihedral : 4.098 17.629 1366 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 9.14 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1231 helix: 0.57 (0.19), residues: 824 sheet: -0.10 (1.10), residues: 31 loop : -0.42 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 156 HIS 0.002 0.000 HIS C 59 PHE 0.023 0.001 PHE A 538 TYR 0.015 0.001 TYR B 400 ARG 0.002 0.000 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 528) hydrogen bonds : angle 3.94811 ( 1536) covalent geometry : bond 0.00241 (10161) covalent geometry : angle 0.54861 (13780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: B 112 ARG cc_start: 0.6839 (tpt170) cc_final: 0.6590 (tpt170) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.2134 time to fit residues: 17.2469 Evaluate side-chains 47 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 387 ASN A 444 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.049822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.042322 restraints weight = 64978.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.043501 restraints weight = 36546.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.044326 restraints weight = 24287.052| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10161 Z= 0.118 Angle : 0.568 7.270 13780 Z= 0.278 Chirality : 0.039 0.129 1572 Planarity : 0.003 0.037 1764 Dihedral : 4.061 19.468 1366 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.54 % Allowed : 10.14 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1231 helix: 0.76 (0.19), residues: 821 sheet: 0.14 (1.11), residues: 31 loop : -0.29 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 156 HIS 0.002 0.001 HIS B 280 PHE 0.018 0.001 PHE A 538 TYR 0.010 0.001 TYR B 107 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 528) hydrogen bonds : angle 3.96915 ( 1536) covalent geometry : bond 0.00272 (10161) covalent geometry : angle 0.56779 (13780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.8397 (ttp) cc_final: 0.7778 (ttp) outliers start: 17 outliers final: 9 residues processed: 50 average time/residue: 0.1901 time to fit residues: 15.1810 Evaluate side-chains 46 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.049040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.041606 restraints weight = 65182.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042773 restraints weight = 36562.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043591 restraints weight = 24136.778| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10161 Z= 0.118 Angle : 0.558 6.838 13780 Z= 0.274 Chirality : 0.039 0.133 1572 Planarity : 0.003 0.037 1764 Dihedral : 4.036 19.759 1366 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.09 % Allowed : 11.13 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1231 helix: 0.87 (0.19), residues: 823 sheet: 0.27 (1.07), residues: 31 loop : -0.23 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 156 HIS 0.003 0.000 HIS C 63 PHE 0.016 0.001 PHE A 538 TYR 0.022 0.001 TYR A 60 ARG 0.002 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 528) hydrogen bonds : angle 3.95304 ( 1536) covalent geometry : bond 0.00275 (10161) covalent geometry : angle 0.55849 (13780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 350 MET cc_start: 0.8604 (ttp) cc_final: 0.8120 (ttp) REVERT: A 521 MET cc_start: 0.8032 (mpp) cc_final: 0.7128 (mtm) outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 0.1926 time to fit residues: 14.6631 Evaluate side-chains 45 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.041567 restraints weight = 65855.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.042757 restraints weight = 36436.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043593 restraints weight = 23862.611| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10161 Z= 0.101 Angle : 0.550 8.008 13780 Z= 0.267 Chirality : 0.039 0.132 1572 Planarity : 0.003 0.038 1764 Dihedral : 3.961 19.621 1366 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 11.58 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1231 helix: 0.94 (0.19), residues: 824 sheet: 0.32 (1.09), residues: 31 loop : -0.18 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 PHE 0.016 0.001 PHE A 538 TYR 0.010 0.001 TYR B 107 ARG 0.004 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.02722 ( 528) hydrogen bonds : angle 3.89315 ( 1536) covalent geometry : bond 0.00232 (10161) covalent geometry : angle 0.55001 (13780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.7973 (mpp) cc_final: 0.7151 (mtm) outliers start: 14 outliers final: 10 residues processed: 44 average time/residue: 0.1673 time to fit residues: 12.6469 Evaluate side-chains 45 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 64 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 119 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.049636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042161 restraints weight = 64529.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.043373 restraints weight = 35814.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.044199 restraints weight = 23473.751| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10161 Z= 0.096 Angle : 0.544 7.847 13780 Z= 0.263 Chirality : 0.038 0.131 1572 Planarity : 0.003 0.039 1764 Dihedral : 3.848 19.831 1366 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.09 % Allowed : 11.58 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1231 helix: 1.07 (0.19), residues: 811 sheet: 0.39 (1.08), residues: 31 loop : -0.10 (0.35), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.002 0.000 HIS A 119 PHE 0.014 0.001 PHE A 538 TYR 0.011 0.001 TYR B 400 ARG 0.003 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 528) hydrogen bonds : angle 3.84791 ( 1536) covalent geometry : bond 0.00214 (10161) covalent geometry : angle 0.54351 (13780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 521 MET cc_start: 0.7971 (mpp) cc_final: 0.7170 (mtm) outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 0.1970 time to fit residues: 14.6590 Evaluate side-chains 43 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** B 268 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 = 0.3367 r_free = 0.3367 target = 0.048936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.041649 restraints weight = 64861.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.042825 restraints weight = 36506.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.043624 restraints weight = 24049.005| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10161 Z= 0.105 Angle : 0.562 8.748 13780 Z= 0.272 Chirality : 0.039 0.132 1572 Planarity : 0.003 0.041 1764 Dihedral : 3.884 20.494 1366 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 11.95 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1231 helix: 1.10 (0.19), residues: 812 sheet: 0.23 (1.01), residues: 31 loop : -0.09 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 PHE 0.015 0.001 PHE A 538 TYR 0.010 0.001 TYR B 107 ARG 0.004 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 528) hydrogen bonds : angle 3.84808 ( 1536) covalent geometry : bond 0.00244 (10161) covalent geometry : angle 0.56198 (13780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 350 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7753 (ttp) REVERT: A 521 MET cc_start: 0.8005 (mpp) cc_final: 0.7220 (mtm) outliers start: 10 outliers final: 9 residues processed: 42 average time/residue: 0.1732 time to fit residues: 12.5127 Evaluate side-chains 43 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 0.0070 chunk 0 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.049316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041884 restraints weight = 65091.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.043097 restraints weight = 35911.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.043928 restraints weight = 23395.172| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10161 Z= 0.095 Angle : 0.557 8.702 13780 Z= 0.268 Chirality : 0.038 0.133 1572 Planarity : 0.003 0.041 1764 Dihedral : 3.825 20.159 1366 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.90 % Allowed : 12.13 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1231 helix: 1.13 (0.19), residues: 808 sheet: 0.10 (0.98), residues: 31 loop : -0.05 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 PHE 0.014 0.001 PHE A 538 TYR 0.010 0.001 TYR B 107 ARG 0.003 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.02481 ( 528) hydrogen bonds : angle 3.80320 ( 1536) covalent geometry : bond 0.00212 (10161) covalent geometry : angle 0.55666 (13780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.1796 time to fit residues: 13.4289 Evaluate side-chains 42 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.0040 chunk 15 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.040632 restraints weight = 64855.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041776 restraints weight = 36352.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042568 restraints weight = 24005.626| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10161 Z= 0.130 Angle : 0.593 9.005 13780 Z= 0.289 Chirality : 0.040 0.155 1572 Planarity : 0.003 0.041 1764 Dihedral : 3.964 21.522 1366 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.81 % Allowed : 12.49 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1231 helix: 1.09 (0.19), residues: 814 sheet: -0.31 (0.82), residues: 42 loop : -0.04 (0.35), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 477 HIS 0.007 0.001 HIS B 289 PHE 0.016 0.001 PHE A 538 TYR 0.010 0.001 TYR B 107 ARG 0.003 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 528) hydrogen bonds : angle 3.91977 ( 1536) covalent geometry : bond 0.00305 (10161) covalent geometry : angle 0.59317 (13780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.30 seconds wall clock time: 54 minutes 30.23 seconds (3270.23 seconds total)