Starting phenix.real_space_refine on Tue Mar 3 18:59:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpc_32682/03_2026/7wpc_32682_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpc_32682/03_2026/7wpc_32682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2026/7wpc_32682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2026/7wpc_32682.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2026/7wpc_32682_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2026/7wpc_32682_neut.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Zn 1 6.06 5 S 44 5.16 5 Cl 1 4.86 5 C 5162 2.51 5 N 1335 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8057 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1582 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 183} Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1518 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 3 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.84, per 1000 atoms: 0.23 Number of scatterers: 8057 At special positions: 0 Unit cell: (99.704, 98.056, 127.72, 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) Zn 1 29.99 Cl 1 17.00 S 44 16.00 O 1514 8.00 N 1335 7.00 C 5162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN A 340 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 546 " " NAG E 1 " - " ASN B 340 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 190.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 44.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.958A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.992A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.972A pdb=" N TYR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 368 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.557A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.509A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.809A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.047A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.590A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.611A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.718A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.558A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.503A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.646A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.929A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 303 through 316 Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.640A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.604A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.795A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.728A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.536A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.501A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.648A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.594A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.809A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.884A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.506A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.693A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.579A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 353 through 355 removed outlier: 4.169A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.772A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.661A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2559 1.35 - 1.47: 2162 1.47 - 1.59: 3493 1.59 - 1.71: 0 1.71 - 1.83: 65 Bond restraints: 8279 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N VAL B 480 " pdb=" CA VAL B 480 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N TYR B 486 " pdb=" CA TYR B 486 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.59e+00 bond pdb=" N LEU B 514 " pdb=" CA LEU B 514 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.54e+00 bond pdb=" N CYS B 485 " pdb=" CA CYS B 485 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.38e+00 ... (remaining 8274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10925 1.89 - 3.78: 267 3.78 - 5.68: 39 5.68 - 7.57: 12 7.57 - 9.46: 4 Bond angle restraints: 11247 Sorted by residual: angle pdb=" N VAL D 339 " pdb=" CA VAL D 339 " pdb=" C VAL D 339 " ideal model delta sigma weight residual 113.71 108.44 5.27 9.50e-01 1.11e+00 3.07e+01 angle pdb=" CA GLY B 482 " pdb=" C GLY B 482 " pdb=" O GLY B 482 " ideal model delta sigma weight residual 122.01 118.07 3.94 9.70e-01 1.06e+00 1.65e+01 angle pdb=" N GLY A 499 " pdb=" CA GLY A 499 " pdb=" C GLY A 499 " ideal model delta sigma weight residual 111.34 118.64 -7.30 1.82e+00 3.02e-01 1.61e+01 angle pdb=" N GLU D 145 " pdb=" CA GLU D 145 " pdb=" C GLU D 145 " ideal model delta sigma weight residual 109.81 118.47 -8.66 2.21e+00 2.05e-01 1.54e+01 angle pdb=" CA PHE B 512 " pdb=" CB PHE B 512 " pdb=" CG PHE B 512 " ideal model delta sigma weight residual 113.80 117.43 -3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 11242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 4594 22.38 - 44.76: 320 44.76 - 67.15: 35 67.15 - 89.53: 7 89.53 - 111.91: 25 Dihedral angle restraints: 4981 sinusoidal: 2101 harmonic: 2880 Sorted by residual: dihedral pdb=" CA PHE A 372 " pdb=" C PHE A 372 " pdb=" N THR A 373 " pdb=" CA THR A 373 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C3 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sinusoidal sigma weight residual -55.55 56.36 -111.91 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" N2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sinusoidal sigma weight residual -178.19 -66.52 -111.67 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 4978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1033 0.064 - 0.129: 152 0.129 - 0.193: 6 0.193 - 0.258: 4 0.258 - 0.322: 2 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CA LEU B 515 " pdb=" N LEU B 515 " pdb=" C LEU B 515 " pdb=" CB LEU B 515 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.35e+00 chirality pdb=" CA ASN B 484 " pdb=" N ASN B 484 " pdb=" C ASN B 484 " pdb=" CB ASN B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1194 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 564 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 565 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 565 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 565 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO D 500 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 582 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D 583 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.031 5.00e-02 4.00e+02 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1689 2.78 - 3.31: 6569 3.31 - 3.84: 13351 3.84 - 4.37: 15369 4.37 - 4.90: 26616 Nonbonded interactions: 63594 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 902 " model vdw 2.253 2.230 nonbonded pdb=" O THR D 118 " pdb=" OG1 THR D 122 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 412 " pdb=" OD2 ASP B 417 " model vdw 2.337 3.040 nonbonded pdb=" OG SER D 109 " pdb=" OD1 ASP D 111 " model vdw 2.349 3.040 nonbonded pdb=" OG SER B 466 " pdb=" OE1 GLU B 468 " model vdw 2.354 3.040 ... (remaining 63589 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 329 through 369 or resid 372 through 499 or resid 501 thro \ ugh 515 or resid 523 through 525)) selection = (chain 'B' and resid 329 through 525) } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.520 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8297 Z= 0.202 Angle : 0.723 9.460 11288 Z= 0.420 Chirality : 0.048 0.322 1197 Planarity : 0.006 0.063 1448 Dihedral : 17.016 111.911 3103 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.20), residues: 968 helix: -2.98 (0.17), residues: 385 sheet: -0.65 (0.53), residues: 69 loop : -2.98 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 514 TYR 0.013 0.001 TYR D 183 PHE 0.018 0.001 PHE B 512 TRP 0.011 0.001 TRP D 477 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8279) covalent geometry : angle 0.72033 (11247) SS BOND : bond 0.00220 ( 10) SS BOND : angle 0.83161 ( 20) hydrogen bonds : bond 0.21225 ( 280) hydrogen bonds : angle 7.90010 ( 795) metal coordination : bond 0.05708 ( 1) link_BETA1-4 : bond 0.00728 ( 2) link_BETA1-4 : angle 0.80704 ( 6) link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 1.88729 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.278 Fit side-chains REVERT: A 362 TYR cc_start: 0.8789 (m-80) cc_final: 0.8561 (m-80) REVERT: A 436 ASN cc_start: 0.8211 (t0) cc_final: 0.8009 (t0) REVERT: B 383 LYS cc_start: 0.1328 (pttp) cc_final: 0.0891 (mtmt) REVERT: B 415 ILE cc_start: 0.7493 (mm) cc_final: 0.7243 (pp) REVERT: D 126 ILE cc_start: 0.7831 (mt) cc_final: 0.7627 (mt) REVERT: D 271 TRP cc_start: 0.8191 (m-90) cc_final: 0.7451 (m-90) REVERT: D 362 THR cc_start: 0.7658 (m) cc_final: 0.7366 (m) REVERT: D 527 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6923 (tm-30) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.4822 time to fit residues: 105.1684 Evaluate side-chains 169 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0060 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 overall best weight: 0.2050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 445 ASN A 471 GLN A 478 ASN B 357 ASN B 457 ASN B 484 ASN D 33 ASN D 51 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 61 ASN D 154 ASN D 194 ASN D 221 GLN D 277 ASN D 300 GLN D 505 HIS D 522 GLN D 531 GLN D 599 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.180225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150643 restraints weight = 11636.959| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.12 r_work: 0.3796 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8297 Z= 0.126 Angle : 0.553 10.279 11288 Z= 0.273 Chirality : 0.045 0.269 1197 Planarity : 0.005 0.050 1448 Dihedral : 13.559 100.205 1221 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.62 % Allowed : 14.37 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.24), residues: 968 helix: -1.46 (0.23), residues: 402 sheet: -0.30 (0.58), residues: 72 loop : -2.31 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 192 TYR 0.015 0.001 TYR D 202 PHE 0.018 0.001 PHE D 314 TRP 0.011 0.001 TRP D 477 HIS 0.008 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8279) covalent geometry : angle 0.54496 (11247) SS BOND : bond 0.00165 ( 10) SS BOND : angle 0.65558 ( 20) hydrogen bonds : bond 0.03855 ( 280) hydrogen bonds : angle 5.05129 ( 795) metal coordination : bond 0.01028 ( 1) link_BETA1-4 : bond 0.00463 ( 2) link_BETA1-4 : angle 2.16919 ( 6) link_NAG-ASN : bond 0.00468 ( 5) link_NAG-ASN : angle 2.21971 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8054 (ttp80) REVERT: A 436 ASN cc_start: 0.8494 (t0) cc_final: 0.8286 (t160) REVERT: B 383 LYS cc_start: 0.1842 (pttp) cc_final: 0.0859 (mtmt) REVERT: B 515 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5635 (mm) REVERT: D 82 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6735 (mtp) REVERT: D 117 ASN cc_start: 0.8267 (m-40) cc_final: 0.7986 (m-40) REVERT: D 145 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6088 (pm20) REVERT: D 271 TRP cc_start: 0.8554 (m-90) cc_final: 0.7900 (m-90) outliers start: 14 outliers final: 4 residues processed: 191 average time/residue: 0.4963 time to fit residues: 100.9292 Evaluate side-chains 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.3980 chunk 56 optimal weight: 0.0000 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 overall best weight: 0.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 445 ASN B 391 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 505 HIS D 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144804 restraints weight = 11281.322| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.09 r_work: 0.3710 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8297 Z= 0.144 Angle : 0.566 11.351 11288 Z= 0.277 Chirality : 0.044 0.247 1197 Planarity : 0.004 0.041 1448 Dihedral : 11.820 96.822 1221 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.78 % Allowed : 14.95 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.25), residues: 968 helix: -0.73 (0.25), residues: 404 sheet: 0.04 (0.61), residues: 72 loop : -2.08 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 192 TYR 0.024 0.001 TYR D 50 PHE 0.013 0.001 PHE D 523 TRP 0.008 0.001 TRP D 478 HIS 0.007 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8279) covalent geometry : angle 0.55312 (11247) SS BOND : bond 0.00134 ( 10) SS BOND : angle 0.50983 ( 20) hydrogen bonds : bond 0.03815 ( 280) hydrogen bonds : angle 4.60457 ( 795) metal coordination : bond 0.00199 ( 1) link_BETA1-4 : bond 0.00443 ( 2) link_BETA1-4 : angle 2.49795 ( 6) link_NAG-ASN : bond 0.00286 ( 5) link_NAG-ASN : angle 2.92607 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8043 (ttp80) REVERT: A 362 TYR cc_start: 0.8815 (m-80) cc_final: 0.8577 (m-80) REVERT: B 383 LYS cc_start: 0.2218 (pttp) cc_final: 0.0829 (mtmt) REVERT: D 52 THR cc_start: 0.8142 (m) cc_final: 0.7933 (m) REVERT: D 82 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7072 (mtp) REVERT: D 117 ASN cc_start: 0.8272 (m-40) cc_final: 0.8006 (m-40) REVERT: D 271 TRP cc_start: 0.8635 (m-90) cc_final: 0.8162 (m-90) REVERT: D 476 LYS cc_start: 0.8224 (tppp) cc_final: 0.7800 (tppp) outliers start: 24 outliers final: 8 residues processed: 189 average time/residue: 0.5324 time to fit residues: 106.5710 Evaluate side-chains 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 81 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 37 optimal weight: 0.3980 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 378 HIS D 505 HIS D 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.173782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142819 restraints weight = 11485.854| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.13 r_work: 0.3669 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8297 Z= 0.136 Angle : 0.526 7.725 11288 Z= 0.261 Chirality : 0.044 0.251 1197 Planarity : 0.004 0.038 1448 Dihedral : 10.772 96.808 1219 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.01 % Allowed : 17.50 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.26), residues: 968 helix: -0.21 (0.26), residues: 400 sheet: 0.01 (0.60), residues: 70 loop : -1.97 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 192 TYR 0.019 0.001 TYR D 202 PHE 0.016 0.001 PHE A 389 TRP 0.010 0.001 TRP A 433 HIS 0.007 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8279) covalent geometry : angle 0.51864 (11247) SS BOND : bond 0.00123 ( 10) SS BOND : angle 0.52863 ( 20) hydrogen bonds : bond 0.03561 ( 280) hydrogen bonds : angle 4.47757 ( 795) metal coordination : bond 0.00322 ( 1) link_BETA1-4 : bond 0.00388 ( 2) link_BETA1-4 : angle 2.21265 ( 6) link_NAG-ASN : bond 0.00229 ( 5) link_NAG-ASN : angle 2.05751 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.2565 (pttp) cc_final: 0.0796 (mtmt) REVERT: D 117 ASN cc_start: 0.8237 (m-40) cc_final: 0.7992 (m-40) REVERT: D 155 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7063 (m) REVERT: D 225 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 271 TRP cc_start: 0.8662 (m-90) cc_final: 0.8293 (m-90) REVERT: D 363 LYS cc_start: 0.8150 (mmpt) cc_final: 0.7899 (mmpt) REVERT: D 476 LYS cc_start: 0.8354 (tppp) cc_final: 0.7938 (tppp) REVERT: D 557 MET cc_start: 0.8757 (tmm) cc_final: 0.8455 (tmm) outliers start: 26 outliers final: 9 residues processed: 191 average time/residue: 0.5264 time to fit residues: 106.3677 Evaluate side-chains 178 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN D 58 ASN D 239 HIS D 388 GLN D 505 HIS D 599 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.166556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134061 restraints weight = 11217.724| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.18 r_work: 0.3611 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 8297 Z= 0.229 Angle : 0.611 8.992 11288 Z= 0.303 Chirality : 0.048 0.246 1197 Planarity : 0.004 0.037 1448 Dihedral : 10.462 91.489 1219 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.71 % Allowed : 17.15 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.26), residues: 968 helix: -0.16 (0.26), residues: 402 sheet: 0.14 (0.61), residues: 70 loop : -1.92 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 192 TYR 0.029 0.002 TYR D 50 PHE 0.017 0.002 PHE D 523 TRP 0.012 0.002 TRP D 477 HIS 0.007 0.002 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8279) covalent geometry : angle 0.60006 (11247) SS BOND : bond 0.00199 ( 10) SS BOND : angle 0.83318 ( 20) hydrogen bonds : bond 0.04282 ( 280) hydrogen bonds : angle 4.58631 ( 795) metal coordination : bond 0.00551 ( 1) link_BETA1-4 : bond 0.00299 ( 2) link_BETA1-4 : angle 1.93952 ( 6) link_NAG-ASN : bond 0.00872 ( 5) link_NAG-ASN : angle 2.98950 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7252 (pt) REVERT: B 383 LYS cc_start: 0.3248 (pttp) cc_final: 0.0819 (mtmt) REVERT: D 102 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.5740 (pp30) REVERT: D 117 ASN cc_start: 0.8298 (m-40) cc_final: 0.8038 (m-40) REVERT: D 155 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7801 (m) REVERT: D 215 TYR cc_start: 0.8208 (m-80) cc_final: 0.7899 (m-80) REVERT: D 225 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: D 363 LYS cc_start: 0.8204 (mmpt) cc_final: 0.7921 (mmpt) REVERT: D 557 MET cc_start: 0.8800 (tmm) cc_final: 0.8523 (tmm) outliers start: 32 outliers final: 13 residues processed: 184 average time/residue: 0.5091 time to fit residues: 99.2913 Evaluate side-chains 184 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 0.0970 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 74 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 175 GLN D 194 ASN D 552 GLN D 599 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.167389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135050 restraints weight = 11184.220| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.15 r_work: 0.3623 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8297 Z= 0.160 Angle : 0.563 8.212 11288 Z= 0.279 Chirality : 0.045 0.260 1197 Planarity : 0.004 0.049 1448 Dihedral : 10.019 88.065 1219 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.90 % Allowed : 18.19 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.26), residues: 968 helix: -0.02 (0.27), residues: 401 sheet: 0.33 (0.61), residues: 70 loop : -1.81 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 192 TYR 0.030 0.001 TYR D 50 PHE 0.019 0.001 PHE A 389 TRP 0.013 0.001 TRP D 477 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8279) covalent geometry : angle 0.55440 (11247) SS BOND : bond 0.00154 ( 10) SS BOND : angle 0.61232 ( 20) hydrogen bonds : bond 0.03795 ( 280) hydrogen bonds : angle 4.55986 ( 795) metal coordination : bond 0.00294 ( 1) link_BETA1-4 : bond 0.00408 ( 2) link_BETA1-4 : angle 1.93324 ( 6) link_NAG-ASN : bond 0.00506 ( 5) link_NAG-ASN : angle 2.47343 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.3217 (pttp) cc_final: 0.0921 (mttp) REVERT: D 52 THR cc_start: 0.8455 (m) cc_final: 0.8219 (m) REVERT: D 102 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.5667 (pp30) REVERT: D 117 ASN cc_start: 0.8265 (m-40) cc_final: 0.8002 (m-40) REVERT: D 155 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7713 (m) REVERT: D 215 TYR cc_start: 0.8192 (m-80) cc_final: 0.7873 (m-80) REVERT: D 225 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: D 347 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8127 (p) REVERT: D 363 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7944 (mmpt) REVERT: D 557 MET cc_start: 0.8774 (tmm) cc_final: 0.8458 (tmm) outliers start: 25 outliers final: 8 residues processed: 182 average time/residue: 0.5589 time to fit residues: 107.5403 Evaluate side-chains 176 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.4980 chunk 82 optimal weight: 0.2980 chunk 81 optimal weight: 0.2980 chunk 55 optimal weight: 0.0870 chunk 92 optimal weight: 0.4980 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 175 GLN D 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.170647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139028 restraints weight = 11335.125| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.15 r_work: 0.3622 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8297 Z= 0.152 Angle : 0.560 9.286 11288 Z= 0.278 Chirality : 0.045 0.267 1197 Planarity : 0.004 0.055 1448 Dihedral : 9.566 83.840 1219 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.78 % Allowed : 18.42 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 968 helix: 0.10 (0.27), residues: 402 sheet: 0.42 (0.61), residues: 70 loop : -1.76 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 192 TYR 0.031 0.001 TYR D 50 PHE 0.021 0.001 PHE A 389 TRP 0.013 0.001 TRP D 477 HIS 0.006 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8279) covalent geometry : angle 0.55150 (11247) SS BOND : bond 0.00151 ( 10) SS BOND : angle 0.60152 ( 20) hydrogen bonds : bond 0.03750 ( 280) hydrogen bonds : angle 4.53342 ( 795) metal coordination : bond 0.00272 ( 1) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 1.91716 ( 6) link_NAG-ASN : bond 0.00484 ( 5) link_NAG-ASN : angle 2.52271 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.2952 (pttp) cc_final: 0.0747 (mttp) REVERT: D 87 GLU cc_start: 0.7339 (mp0) cc_final: 0.7130 (mm-30) REVERT: D 102 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.5680 (pp30) REVERT: D 117 ASN cc_start: 0.8261 (m-40) cc_final: 0.8008 (m-40) REVERT: D 215 TYR cc_start: 0.8185 (m-80) cc_final: 0.7861 (m-80) REVERT: D 225 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: D 347 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8169 (p) REVERT: D 363 LYS cc_start: 0.8202 (mmpt) cc_final: 0.7912 (mmpt) REVERT: D 557 MET cc_start: 0.8778 (tmm) cc_final: 0.8463 (tmm) outliers start: 24 outliers final: 11 residues processed: 185 average time/residue: 0.5561 time to fit residues: 108.6295 Evaluate side-chains 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 84 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 GLN D 175 GLN D 388 GLN D 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.166623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134136 restraints weight = 11157.596| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.18 r_work: 0.3616 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8297 Z= 0.176 Angle : 0.585 9.506 11288 Z= 0.290 Chirality : 0.046 0.272 1197 Planarity : 0.004 0.055 1448 Dihedral : 9.102 78.042 1219 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.32 % Allowed : 19.00 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.26), residues: 968 helix: 0.09 (0.27), residues: 402 sheet: 0.52 (0.61), residues: 70 loop : -1.70 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 192 TYR 0.027 0.001 TYR D 50 PHE 0.020 0.001 PHE A 389 TRP 0.013 0.001 TRP D 477 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8279) covalent geometry : angle 0.57648 (11247) SS BOND : bond 0.00163 ( 10) SS BOND : angle 0.68068 ( 20) hydrogen bonds : bond 0.03898 ( 280) hydrogen bonds : angle 4.60661 ( 795) metal coordination : bond 0.00385 ( 1) link_BETA1-4 : bond 0.00562 ( 2) link_BETA1-4 : angle 1.96680 ( 6) link_NAG-ASN : bond 0.00474 ( 5) link_NAG-ASN : angle 2.56058 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.3075 (pttp) cc_final: 0.0557 (mttp) REVERT: D 102 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.5759 (pp30) REVERT: D 117 ASN cc_start: 0.8251 (m-40) cc_final: 0.7998 (m-40) REVERT: D 215 TYR cc_start: 0.8229 (m-80) cc_final: 0.7899 (m-80) REVERT: D 225 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: D 227 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: D 347 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8205 (p) REVERT: D 363 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7904 (mmpt) REVERT: D 557 MET cc_start: 0.8771 (tmm) cc_final: 0.8472 (tmm) outliers start: 20 outliers final: 12 residues processed: 184 average time/residue: 0.5722 time to fit residues: 111.0648 Evaluate side-chains 188 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 65 optimal weight: 0.0270 chunk 57 optimal weight: 0.5980 chunk 84 optimal weight: 0.0370 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN D 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139584 restraints weight = 11253.594| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.10 r_work: 0.3635 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8297 Z= 0.135 Angle : 0.577 10.747 11288 Z= 0.283 Chirality : 0.044 0.266 1197 Planarity : 0.004 0.062 1448 Dihedral : 8.642 71.810 1219 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.09 % Allowed : 20.05 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.27), residues: 968 helix: 0.16 (0.27), residues: 403 sheet: 0.59 (0.61), residues: 70 loop : -1.63 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 192 TYR 0.025 0.001 TYR D 50 PHE 0.022 0.001 PHE A 389 TRP 0.010 0.001 TRP D 477 HIS 0.006 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8279) covalent geometry : angle 0.56844 (11247) SS BOND : bond 0.00154 ( 10) SS BOND : angle 0.57553 ( 20) hydrogen bonds : bond 0.03672 ( 280) hydrogen bonds : angle 4.55940 ( 795) metal coordination : bond 0.00198 ( 1) link_BETA1-4 : bond 0.00624 ( 2) link_BETA1-4 : angle 2.01894 ( 6) link_NAG-ASN : bond 0.00462 ( 5) link_NAG-ASN : angle 2.56264 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.2948 (pttp) cc_final: 0.0594 (mttp) REVERT: D 117 ASN cc_start: 0.8249 (m-40) cc_final: 0.7994 (m-40) REVERT: D 215 TYR cc_start: 0.8179 (m-80) cc_final: 0.7862 (m-80) REVERT: D 225 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: D 227 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: D 266 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 347 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8234 (p) REVERT: D 363 LYS cc_start: 0.8173 (mmpt) cc_final: 0.7882 (mmpt) REVERT: D 557 MET cc_start: 0.8758 (tmm) cc_final: 0.8468 (tmm) outliers start: 18 outliers final: 10 residues processed: 183 average time/residue: 0.5640 time to fit residues: 108.9821 Evaluate side-chains 186 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 3 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 72 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 61 optimal weight: 0.0980 chunk 56 optimal weight: 0.0870 chunk 92 optimal weight: 0.9990 overall best weight: 0.0952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141899 restraints weight = 11362.429| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.10 r_work: 0.3665 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8297 Z= 0.100 Angle : 0.561 9.709 11288 Z= 0.274 Chirality : 0.043 0.236 1197 Planarity : 0.004 0.054 1448 Dihedral : 7.973 62.455 1219 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.85 % Allowed : 20.51 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.27), residues: 968 helix: 0.30 (0.27), residues: 402 sheet: 0.71 (0.61), residues: 70 loop : -1.55 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 192 TYR 0.023 0.001 TYR D 202 PHE 0.022 0.001 PHE A 389 TRP 0.009 0.001 TRP A 433 HIS 0.006 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8279) covalent geometry : angle 0.55138 (11247) SS BOND : bond 0.00138 ( 10) SS BOND : angle 0.45738 ( 20) hydrogen bonds : bond 0.03309 ( 280) hydrogen bonds : angle 4.43186 ( 795) metal coordination : bond 0.00092 ( 1) link_BETA1-4 : bond 0.00740 ( 2) link_BETA1-4 : angle 2.07216 ( 6) link_NAG-ASN : bond 0.00486 ( 5) link_NAG-ASN : angle 2.55544 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.2754 (pttp) cc_final: 0.0526 (mtmt) REVERT: D 49 ASN cc_start: 0.7720 (m-40) cc_final: 0.7350 (m110) REVERT: D 117 ASN cc_start: 0.8213 (m-40) cc_final: 0.7959 (m-40) REVERT: D 215 TYR cc_start: 0.8085 (m-80) cc_final: 0.7758 (m-80) REVERT: D 225 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: D 227 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: D 363 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7876 (mmpt) REVERT: D 557 MET cc_start: 0.8715 (tmm) cc_final: 0.8453 (tmm) outliers start: 16 outliers final: 9 residues processed: 188 average time/residue: 0.5580 time to fit residues: 110.7519 Evaluate side-chains 182 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 505 HIS D 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134871 restraints weight = 11255.118| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.17 r_work: 0.3604 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8297 Z= 0.221 Angle : 0.621 8.606 11288 Z= 0.306 Chirality : 0.048 0.204 1197 Planarity : 0.004 0.063 1448 Dihedral : 7.748 57.135 1219 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.62 % Allowed : 21.78 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.27), residues: 968 helix: 0.19 (0.27), residues: 402 sheet: 0.42 (0.60), residues: 70 loop : -1.56 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 192 TYR 0.023 0.002 TYR D 202 PHE 0.018 0.001 PHE A 389 TRP 0.011 0.001 TRP D 477 HIS 0.009 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 8279) covalent geometry : angle 0.61128 (11247) SS BOND : bond 0.00193 ( 10) SS BOND : angle 0.77582 ( 20) hydrogen bonds : bond 0.04137 ( 280) hydrogen bonds : angle 4.57789 ( 795) metal coordination : bond 0.00489 ( 1) link_BETA1-4 : bond 0.00664 ( 2) link_BETA1-4 : angle 2.17675 ( 6) link_NAG-ASN : bond 0.00538 ( 5) link_NAG-ASN : angle 2.73680 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4301.17 seconds wall clock time: 73 minutes 38.06 seconds (4418.06 seconds total)