Starting phenix.real_space_refine on Thu Jul 2 21:40:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2026/7pmb_13527.cif" } resolution = 3.6 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= 0.001 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 P 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6441 2.51 5 N 1719 2.21 5 O 1884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10113 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6043 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 27, 'TRANS': 711} Chain breaks: 6 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.74, per 1000 atoms: 0.17 Number of scatterers: 10113 At special positions: 0 Unit cell: (107.06, 136.74, 150.52, 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) S 63 16.00 P 4 15.00 Mg 2 11.99 O 1884 8.00 N 1719 7.00 C 6441 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 268.1 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 14 sheets defined 56.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.175A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.769A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.543A pdb=" N ARG A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.184A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.720A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.954A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.148A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.191A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.535A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.886A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.590A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.700A pdb=" N PHE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.965A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.590A pdb=" N ILE A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.831A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.522A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.591A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.625A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.627A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.643A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.920A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.038A pdb=" N LYS A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 4.056A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.438A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 removed outlier: 4.145A pdb=" N ASN A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.580A pdb=" N TRP A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.675A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.925A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.860A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.885A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.846A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.783A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.880A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.118A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.496A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.989A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.522A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.611A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.974A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.722A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.561A pdb=" N LEU A 107 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.888A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.980A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.464A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 512 hydrogen bonds defined for protein. 1437 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: 1.11 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1687 1.32 - 1.44: 2731 1.44 - 1.57: 5801 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10327 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.60e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.33e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 10322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13543 2.38 - 4.76: 349 4.76 - 7.14: 45 7.14 - 9.51: 7 9.51 - 11.89: 4 Bond angle restraints: 13948 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.81 11.89 1.80e+00 3.09e-01 4.37e+01 angle pdb=" CA TRP C 356 " pdb=" CB TRP C 356 " pdb=" CG TRP C 356 " ideal model delta sigma weight residual 113.60 122.80 -9.20 1.90e+00 2.77e-01 2.34e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.81 -4.81 1.10e+00 8.26e-01 1.91e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.21 4.19 1.00e+00 1.00e+00 1.75e+01 ... (remaining 13943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.17: 5976 27.17 - 54.34: 190 54.34 - 81.51: 41 81.51 - 108.69: 9 108.69 - 135.86: 4 Dihedral angle restraints: 6220 sinusoidal: 2554 harmonic: 3666 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.86 -135.86 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 71.60 -131.60 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 67.63 -127.64 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 6217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.021: 1522 1.021 - 2.041: 0 2.041 - 3.062: 0 3.062 - 4.082: 0 4.082 - 5.103: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.39 4.92 2.00e-01 2.50e+01 6.05e+02 chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1521 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 28 " 0.133 9.50e-02 1.11e+02 7.79e-02 3.35e+01 pdb=" NE ARG C 28 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG C 28 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG C 28 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG C 28 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.140 9.50e-02 1.11e+02 7.83e-02 3.01e+01 pdb=" NE ARG A 677 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 477 " -0.001 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 477 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 477 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 477 " 0.050 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 18 2.37 - 3.00: 5558 3.00 - 3.63: 14983 3.63 - 4.27: 22360 4.27 - 4.90: 37639 Nonbonded interactions: 80558 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 1.947 2.170 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.021 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.136 2.170 nonbonded pdb=" OH TYR A 528 " pdb=" O ALA A 547 " model vdw 2.162 3.040 ... (remaining 80553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.006 0.122 10329 Z= 0.279 Angle : 0.936 11.894 13954 Z= 0.545 Chirality : 0.190 5.103 1524 Planarity : 0.009 0.117 1777 Dihedral : 15.726 135.857 3850 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1224 helix: -1.69 (0.17), residues: 566 sheet: 0.17 (0.36), residues: 155 loop : 0.23 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.013 ARG C 28 TYR 0.050 0.007 TYR A 477 PHE 0.031 0.003 PHE C 255 TRP 0.054 0.004 TRP C 356 HIS 0.008 0.002 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.28 (10327) covalent geometry : angle 0.93188 / 0.54 (13948) hydrogen bonds : bond 0.15763 / 10.15 ( 510) hydrogen bonds : angle 7.48772 / 5.24 ( 1437) link_TRANS : bond 0.00923 / 0.48 ( 2) link_TRANS : angle 4.22853 / 2.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8082 (p0) cc_final: 0.7874 (p0) REVERT: A 790 MET cc_start: -0.0217 (ppp) cc_final: -0.0449 (ptm) REVERT: C 313 MET cc_start: 0.8525 (mmm) cc_final: 0.8321 (tpt) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.0862 time to fit residues: 16.8170 Evaluate side-chains 80 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0270 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 147 HIS A 264 GLN A 290 GLN A 354 HIS A 373 HIS A 398 ASN A 463 GLN A 755 GLN C 121 GLN C 161 HIS C 162 ASN C 173 HIS C 371 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.072678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052445 restraints weight = 39562.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054347 restraints weight = 18883.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055568 restraints weight = 11644.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056388 restraints weight = 8394.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.056900 restraints weight = 6700.650| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10329 Z= 0.147 Angle : 0.694 10.731 13954 Z= 0.355 Chirality : 0.044 0.176 1524 Planarity : 0.005 0.045 1777 Dihedral : 9.846 133.725 1388 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.11 % Allowed : 5.57 % Favored : 93.31 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.23), residues: 1224 helix: 0.76 (0.21), residues: 587 sheet: 0.80 (0.38), residues: 150 loop : 0.54 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 152 TYR 0.015 0.001 TYR A 50 PHE 0.026 0.002 PHE C 375 TRP 0.022 0.002 TRP A 484 HIS 0.006 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (10327) covalent geometry : angle 0.69418 / 0.35 (13948) hydrogen bonds : bond 0.04166 / 2.65 ( 510) hydrogen bonds : angle 5.37392 / 3.66 ( 1437) link_TRANS : bond 0.00335 / 0.16 ( 2) link_TRANS : angle 1.06916 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.6947 (m-10) cc_final: 0.6541 (m-80) REVERT: B 120 MET cc_start: 0.7472 (mmp) cc_final: 0.6650 (mmm) REVERT: A 132 MET cc_start: 0.7465 (ppp) cc_final: 0.6249 (ppp) REVERT: A 715 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7695 (ptm) REVERT: A 788 MET cc_start: 0.4986 (ptp) cc_final: 0.4614 (mtt) REVERT: C 41 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8233 (tm-30) REVERT: C 107 GLU cc_start: 0.7161 (tt0) cc_final: 0.6652 (tt0) REVERT: C 217 CYS cc_start: 0.8717 (m) cc_final: 0.8317 (m) REVERT: C 227 MET cc_start: 0.8622 (tpp) cc_final: 0.8287 (tpp) REVERT: C 313 MET cc_start: 0.8970 (mmm) cc_final: 0.8685 (tpt) outliers start: 12 outliers final: 6 residues processed: 115 average time/residue: 0.0841 time to fit residues: 14.2702 Evaluate side-chains 81 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 715 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN ** C 111 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.071226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051066 restraints weight = 39290.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052948 restraints weight = 18910.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054186 restraints weight = 11702.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054968 restraints weight = 8412.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055494 restraints weight = 6738.331| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10329 Z= 0.181 Angle : 0.629 6.995 13954 Z= 0.320 Chirality : 0.043 0.198 1524 Planarity : 0.004 0.047 1777 Dihedral : 8.542 136.967 1387 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.21 % Allowed : 7.89 % Favored : 90.90 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1224 helix: 1.21 (0.22), residues: 601 sheet: 0.91 (0.40), residues: 144 loop : 0.54 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 343 TYR 0.015 0.001 TYR A 259 PHE 0.014 0.002 PHE C 255 TRP 0.015 0.002 TRP A 414 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (10327) covalent geometry : angle 0.62876 / 0.32 (13948) hydrogen bonds : bond 0.03912 / 2.50 ( 510) hydrogen bonds : angle 5.05580 / 3.43 ( 1437) link_TRANS : bond 0.00223 / 0.12 ( 2) link_TRANS : angle 0.58379 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 PHE cc_start: 0.3682 (t80) cc_final: 0.2661 (t80) REVERT: A 132 MET cc_start: 0.7583 (ppp) cc_final: 0.6043 (ppp) REVERT: A 788 MET cc_start: 0.5064 (ptp) cc_final: 0.4616 (mtt) REVERT: C 217 CYS cc_start: 0.8851 (m) cc_final: 0.8535 (m) REVERT: C 227 MET cc_start: 0.8600 (tpp) cc_final: 0.8173 (tpp) REVERT: C 241 GLU cc_start: 0.8102 (mp0) cc_final: 0.7872 (pm20) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 0.0698 time to fit residues: 9.5313 Evaluate side-chains 80 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain C residue 149 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049512 restraints weight = 39799.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051361 restraints weight = 19344.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052540 restraints weight = 12009.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053362 restraints weight = 8707.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053879 restraints weight = 6948.482| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10329 Z= 0.231 Angle : 0.649 8.229 13954 Z= 0.328 Chirality : 0.044 0.200 1524 Planarity : 0.004 0.038 1777 Dihedral : 8.205 140.062 1387 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.04 % Allowed : 9.38 % Favored : 88.58 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1224 helix: 1.23 (0.22), residues: 600 sheet: 0.93 (0.41), residues: 139 loop : 0.38 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.014 0.002 TYR A 259 PHE 0.023 0.002 PHE B 12 TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (10327) covalent geometry : angle 0.64895 / 0.33 (13948) hydrogen bonds : bond 0.03979 / 2.53 ( 510) hydrogen bonds : angle 5.06717 / 3.45 ( 1437) link_TRANS : bond 0.00235 / 0.12 ( 2) link_TRANS : angle 0.38523 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ASN cc_start: 0.9514 (m-40) cc_final: 0.8976 (p0) REVERT: A 132 MET cc_start: 0.7721 (ppp) cc_final: 0.7051 (ppp) REVERT: A 788 MET cc_start: 0.5176 (ptp) cc_final: 0.4740 (mtt) REVERT: C 217 CYS cc_start: 0.8965 (m) cc_final: 0.8646 (m) REVERT: C 227 MET cc_start: 0.8649 (tpp) cc_final: 0.8281 (tpp) outliers start: 22 outliers final: 12 residues processed: 88 average time/residue: 0.0715 time to fit residues: 9.4960 Evaluate side-chains 77 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 317 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 0.9990 chunk 96 optimal weight: 0.0010 chunk 10 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051175 restraints weight = 39119.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053061 restraints weight = 18704.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.054247 restraints weight = 11512.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055097 restraints weight = 8327.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055613 restraints weight = 6608.026| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10329 Z= 0.126 Angle : 0.588 8.648 13954 Z= 0.289 Chirality : 0.041 0.201 1524 Planarity : 0.004 0.039 1777 Dihedral : 7.781 138.283 1387 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.39 % Allowed : 10.58 % Favored : 88.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1224 helix: 1.50 (0.22), residues: 601 sheet: 1.03 (0.42), residues: 139 loop : 0.31 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.011 0.001 TYR A 259 PHE 0.019 0.001 PHE B 12 TRP 0.013 0.001 TRP A 484 HIS 0.013 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10327) covalent geometry : angle 0.58808 / 0.29 (13948) hydrogen bonds : bond 0.03453 / 2.19 ( 510) hydrogen bonds : angle 4.79942 / 3.25 ( 1437) link_TRANS : bond 0.00099 / 0.05 ( 2) link_TRANS : angle 0.39595 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 140 ASN cc_start: 0.9515 (m-40) cc_final: 0.8971 (p0) REVERT: A 132 MET cc_start: 0.7703 (ppp) cc_final: 0.7168 (ppp) REVERT: A 788 MET cc_start: 0.5183 (ptp) cc_final: 0.4727 (mtt) REVERT: C 54 VAL cc_start: 0.9272 (t) cc_final: 0.8513 (m) REVERT: C 217 CYS cc_start: 0.8971 (m) cc_final: 0.8622 (m) REVERT: C 227 MET cc_start: 0.8623 (tpp) cc_final: 0.8267 (tpp) REVERT: C 299 MET cc_start: 0.8836 (mmm) cc_final: 0.8628 (mmm) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.0880 time to fit residues: 11.8806 Evaluate side-chains 76 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051377 restraints weight = 39079.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053266 restraints weight = 18603.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054485 restraints weight = 11412.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055297 restraints weight = 8195.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055816 restraints weight = 6507.706| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10329 Z= 0.127 Angle : 0.585 9.272 13954 Z= 0.288 Chirality : 0.041 0.198 1524 Planarity : 0.003 0.039 1777 Dihedral : 7.507 132.019 1387 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.21 % Allowed : 12.16 % Favored : 86.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1224 helix: 1.49 (0.22), residues: 607 sheet: 1.14 (0.41), residues: 148 loop : 0.26 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.011 0.001 TYR A 259 PHE 0.029 0.001 PHE B 19 TRP 0.016 0.001 TRP A 484 HIS 0.007 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10327) covalent geometry : angle 0.58546 / 0.29 (13948) hydrogen bonds : bond 0.03360 / 2.14 ( 510) hydrogen bonds : angle 4.75731 / 3.21 ( 1437) link_TRANS : bond 0.00109 / 0.06 ( 2) link_TRANS : angle 0.24169 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7929 (ppp) cc_final: 0.7261 (ppp) REVERT: A 788 MET cc_start: 0.5065 (ptp) cc_final: 0.4525 (mtt) REVERT: C 217 CYS cc_start: 0.8965 (m) cc_final: 0.8615 (m) REVERT: C 227 MET cc_start: 0.8635 (tpp) cc_final: 0.8224 (tpp) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.0886 time to fit residues: 10.7651 Evaluate side-chains 73 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 0.0370 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS A 395 HIS A 657 HIS C 111 ASN C 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051420 restraints weight = 39102.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053340 restraints weight = 18819.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054574 restraints weight = 11650.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055391 restraints weight = 8418.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055909 restraints weight = 6712.781| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10329 Z= 0.116 Angle : 0.598 9.776 13954 Z= 0.290 Chirality : 0.041 0.194 1524 Planarity : 0.004 0.051 1777 Dihedral : 7.240 125.656 1387 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.30 % Allowed : 13.00 % Favored : 85.70 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1224 helix: 1.58 (0.22), residues: 604 sheet: 1.20 (0.40), residues: 154 loop : 0.22 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 343 TYR 0.011 0.001 TYR B 29 PHE 0.033 0.001 PHE B 12 TRP 0.017 0.001 TRP A 484 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10327) covalent geometry : angle 0.59796 / 0.29 (13948) hydrogen bonds : bond 0.03247 / 2.07 ( 510) hydrogen bonds : angle 4.64108 / 3.15 ( 1437) link_TRANS : bond 0.00087 / 0.04 ( 2) link_TRANS : angle 0.20425 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 788 MET cc_start: 0.4902 (ptp) cc_final: 0.4409 (mtt) REVERT: C 217 CYS cc_start: 0.8934 (m) cc_final: 0.8564 (m) REVERT: C 227 MET cc_start: 0.8544 (tpp) cc_final: 0.8262 (tpp) REVERT: C 299 MET cc_start: 0.8659 (mmm) cc_final: 0.8361 (mmm) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.0763 time to fit residues: 9.4444 Evaluate side-chains 74 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 0.0470 chunk 54 optimal weight: 0.0770 chunk 119 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051751 restraints weight = 38652.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053575 restraints weight = 18416.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.054751 restraints weight = 11418.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055567 restraints weight = 8278.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.056085 restraints weight = 6611.466| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10329 Z= 0.115 Angle : 0.602 10.663 13954 Z= 0.288 Chirality : 0.040 0.192 1524 Planarity : 0.003 0.043 1777 Dihedral : 7.108 121.939 1387 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.02 % Allowed : 13.46 % Favored : 85.52 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1224 helix: 1.66 (0.22), residues: 603 sheet: 1.23 (0.40), residues: 154 loop : 0.21 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.010 0.001 TYR A 259 PHE 0.013 0.001 PHE B 12 TRP 0.015 0.001 TRP A 484 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10327) covalent geometry : angle 0.60191 / 0.29 (13948) hydrogen bonds : bond 0.03212 / 2.04 ( 510) hydrogen bonds : angle 4.59655 / 3.11 ( 1437) link_TRANS : bond 0.00090 / 0.05 ( 2) link_TRANS : angle 0.18904 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7762 (ppp) cc_final: 0.6782 (ppp) REVERT: A 484 TRP cc_start: 0.7144 (t60) cc_final: 0.6821 (t60) REVERT: A 788 MET cc_start: 0.4805 (ptp) cc_final: 0.4264 (mtt) REVERT: C 217 CYS cc_start: 0.8912 (m) cc_final: 0.8547 (m) REVERT: C 227 MET cc_start: 0.8531 (tpp) cc_final: 0.8257 (tpp) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.0812 time to fit residues: 9.7464 Evaluate side-chains 73 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 97 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.071987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051817 restraints weight = 38877.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053708 restraints weight = 18708.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054933 restraints weight = 11550.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055766 restraints weight = 8296.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056273 restraints weight = 6606.975| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10329 Z= 0.109 Angle : 0.603 11.146 13954 Z= 0.286 Chirality : 0.040 0.188 1524 Planarity : 0.003 0.040 1777 Dihedral : 6.873 115.640 1387 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.93 % Allowed : 13.74 % Favored : 85.33 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1224 helix: 1.69 (0.22), residues: 604 sheet: 1.26 (0.40), residues: 154 loop : 0.18 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.009 0.001 TYR A 456 PHE 0.016 0.001 PHE B 12 TRP 0.016 0.001 TRP A 484 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10327) covalent geometry : angle 0.60273 / 0.29 (13948) hydrogen bonds : bond 0.03121 / 1.98 ( 510) hydrogen bonds : angle 4.53719 / 3.07 ( 1437) link_TRANS : bond 0.00074 / 0.04 ( 2) link_TRANS : angle 0.18277 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7813 (ppp) cc_final: 0.6881 (ppp) REVERT: A 484 TRP cc_start: 0.7155 (t60) cc_final: 0.6881 (t60) REVERT: A 788 MET cc_start: 0.4605 (ptp) cc_final: 0.4051 (mtt) REVERT: C 217 CYS cc_start: 0.8885 (m) cc_final: 0.8505 (m) REVERT: C 227 MET cc_start: 0.8474 (tpp) cc_final: 0.8224 (tpp) outliers start: 10 outliers final: 10 residues processed: 81 average time/residue: 0.0738 time to fit residues: 9.3865 Evaluate side-chains 79 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 40 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051115 restraints weight = 38531.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052963 restraints weight = 18691.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054170 restraints weight = 11561.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054950 restraints weight = 8340.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055489 restraints weight = 6690.186| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10329 Z= 0.137 Angle : 0.623 10.946 13954 Z= 0.297 Chirality : 0.040 0.188 1524 Planarity : 0.004 0.041 1777 Dihedral : 6.893 115.001 1387 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.93 % Allowed : 13.83 % Favored : 85.24 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1224 helix: 1.71 (0.22), residues: 604 sheet: 1.24 (0.40), residues: 155 loop : 0.20 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 343 TYR 0.012 0.001 TYR A 259 PHE 0.014 0.001 PHE B 12 TRP 0.014 0.001 TRP A 484 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10327) covalent geometry : angle 0.62294 / 0.30 (13948) hydrogen bonds : bond 0.03208 / 2.02 ( 510) hydrogen bonds : angle 4.60078 / 3.12 ( 1437) link_TRANS : bond 0.00123 / 0.06 ( 2) link_TRANS : angle 0.18846 / 0.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7768 (ppp) cc_final: 0.6816 (ppp) REVERT: A 484 TRP cc_start: 0.7127 (t60) cc_final: 0.6832 (t60) REVERT: A 500 GLU cc_start: 0.8313 (tt0) cc_final: 0.7918 (tm-30) REVERT: A 788 MET cc_start: 0.4586 (ptp) cc_final: 0.4038 (mtt) REVERT: C 217 CYS cc_start: 0.8909 (m) cc_final: 0.8569 (m) REVERT: C 227 MET cc_start: 0.8468 (tpp) cc_final: 0.8216 (tpp) outliers start: 10 outliers final: 10 residues processed: 79 average time/residue: 0.0579 time to fit residues: 7.3216 Evaluate side-chains 79 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051452 restraints weight = 38720.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.053318 restraints weight = 18660.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054536 restraints weight = 11526.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055362 restraints weight = 8300.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055886 restraints weight = 6633.203| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10329 Z= 0.123 Angle : 0.616 10.894 13954 Z= 0.293 Chirality : 0.040 0.188 1524 Planarity : 0.003 0.038 1777 Dihedral : 6.856 115.647 1387 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.93 % Allowed : 13.83 % Favored : 85.24 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1224 helix: 1.71 (0.22), residues: 604 sheet: 1.19 (0.40), residues: 157 loop : 0.22 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 343 TYR 0.010 0.001 TYR A 259 PHE 0.014 0.001 PHE B 12 TRP 0.013 0.001 TRP A 484 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10327) covalent geometry : angle 0.61576 / 0.29 (13948) hydrogen bonds : bond 0.03178 / 2.00 ( 510) hydrogen bonds : angle 4.58191 / 3.11 ( 1437) link_TRANS : bond 0.00098 / 0.05 ( 2) link_TRANS : angle 0.18753 / 0.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.61 seconds wall clock time: 31 minutes 22.73 seconds (1882.73 seconds total)