Starting phenix.real_space_refine on Thu Jun 12 18:50:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z90_39852/06_2025/8z90_39852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z90_39852/06_2025/8z90_39852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z90_39852/06_2025/8z90_39852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z90_39852/06_2025/8z90_39852.map" model { file = "/net/cci-nas-00/data/ceres_data/8z90_39852/06_2025/8z90_39852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z90_39852/06_2025/8z90_39852.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 77 5.16 5 C 8402 2.51 5 N 2345 2.21 5 O 2621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13481 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5014 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 588} Chain: "B" Number of atoms: 5710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5710 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 39, 'TRANS': 670} Chain: "C" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1986 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 16, 'TRANS': 228} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.36, per 1000 atoms: 0.62 Number of scatterers: 13481 At special positions: 0 Unit cell: (103.323, 106.018, 137.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 36 15.00 O 2621 8.00 N 2345 7.00 C 8402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.7 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3006 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 48.9% alpha, 10.5% beta 8 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.665A pdb=" N THR A 24 " --> pdb=" O ASP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.515A pdb=" N ASP A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 154 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.553A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 335 through 344 removed outlier: 4.122A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.505A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.596A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.601A pdb=" N ASN A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.553A pdb=" N ILE A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.590A pdb=" N ARG A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.760A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.640A pdb=" N THR B 5 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 removed outlier: 4.271A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.545A pdb=" N ILE B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.579A pdb=" N LYS B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.681A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.544A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.606A pdb=" N LYS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.727A pdb=" N LEU B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.661A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.599A pdb=" N MET B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.705A pdb=" N VAL B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.730A pdb=" N VAL B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.517A pdb=" N THR B 485 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 647 through 662 Processing helix chain 'B' and resid 679 through 695 Processing helix chain 'B' and resid 698 through 709 removed outlier: 3.601A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.674A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.783A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.587A pdb=" N VAL C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.888A pdb=" N GLN C 173 " --> pdb=" O HIS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 192 through 201 removed outlier: 3.573A pdb=" N LEU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.673A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.745A pdb=" N CYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.590A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 5.358A pdb=" N PHE A 425 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 416 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 427 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.972A pdb=" N LEU B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 531 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB2, first strand: chain 'B' and resid 188 through 191 removed outlier: 3.948A pdb=" N GLN B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 246 removed outlier: 6.954A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB5, first strand: chain 'B' and resid 608 through 611 Processing sheet with id=AB6, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.619A pdb=" N ILE C 67 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG C 98 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.542A pdb=" N ARG C 142 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.743A pdb=" N LYS C 151 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 227 " --> pdb=" O LYS C 151 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4319 1.34 - 1.47: 3350 1.47 - 1.60: 6019 1.60 - 1.72: 37 1.72 - 1.85: 128 Bond restraints: 13853 Sorted by residual: bond pdb=" CB PRO A 55 " pdb=" CG PRO A 55 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.32e+00 bond pdb=" CA ARG B 323 " pdb=" C ARG B 323 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.40e-02 5.10e+03 2.53e+00 bond pdb=" C ARG B 96 " pdb=" N PRO B 97 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.98e+00 bond pdb=" C ILE C 167 " pdb=" N PRO C 168 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.65e+00 bond pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.50e+00 ... (remaining 13848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 18243 1.56 - 3.11: 570 3.11 - 4.67: 99 4.67 - 6.22: 14 6.22 - 7.78: 4 Bond angle restraints: 18930 Sorted by residual: angle pdb=" CA PRO A 55 " pdb=" N PRO A 55 " pdb=" CD PRO A 55 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N SER A 616 " pdb=" CA SER A 616 " pdb=" C SER A 616 " ideal model delta sigma weight residual 114.09 107.18 6.91 1.55e+00 4.16e-01 1.99e+01 angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 111.48 107.72 3.76 9.40e-01 1.13e+00 1.60e+01 angle pdb=" N VAL B 669 " pdb=" CA VAL B 669 " pdb=" C VAL B 669 " ideal model delta sigma weight residual 112.83 108.96 3.87 9.90e-01 1.02e+00 1.53e+01 angle pdb=" C THR C 40 " pdb=" N PHE C 41 " pdb=" CA PHE C 41 " ideal model delta sigma weight residual 122.65 116.46 6.19 1.60e+00 3.91e-01 1.50e+01 ... (remaining 18925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 8316 34.36 - 68.71: 181 68.71 - 103.07: 21 103.07 - 137.43: 1 137.43 - 171.79: 2 Dihedral angle restraints: 8521 sinusoidal: 3892 harmonic: 4629 Sorted by residual: dihedral pdb=" CA MET A 538 " pdb=" C MET A 538 " pdb=" N THR A 539 " pdb=" CA THR A 539 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA HIS C 233 " pdb=" C HIS C 233 " pdb=" N THR C 234 " pdb=" CA THR C 234 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sinusoidal sigma weight residual -110.00 61.79 -171.79 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1561 0.043 - 0.086: 441 0.086 - 0.129: 107 0.129 - 0.172: 12 0.172 - 0.215: 2 Chirality restraints: 2123 Sorted by residual: chirality pdb=" CB VAL A 132 " pdb=" CA VAL A 132 " pdb=" CG1 VAL A 132 " pdb=" CG2 VAL A 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' A E 2 " pdb=" C4' A E 2 " pdb=" O3' A E 2 " pdb=" C2' A E 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" C3' C E 7 " pdb=" C4' C E 7 " pdb=" O3' C E 7 " pdb=" C2' C E 7 " both_signs ideal model delta sigma weight residual False -2.48 -2.33 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 2120 not shown) Planarity restraints: 2301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 54 " -0.067 5.00e-02 4.00e+02 9.89e-02 1.56e+01 pdb=" N PRO A 55 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 643 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO B 644 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B 97 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.039 5.00e-02 4.00e+02 ... (remaining 2298 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 294 2.67 - 3.23: 13017 3.23 - 3.79: 21822 3.79 - 4.34: 31033 4.34 - 4.90: 49500 Nonbonded interactions: 115666 Sorted by model distance: nonbonded pdb=" OD1 ASN B 306 " pdb=" O2' G2P B 801 " model vdw 2.113 3.040 nonbonded pdb=" OG SER A 318 " pdb=" OE1 GLU A 320 " model vdw 2.138 3.040 nonbonded pdb=" OD2 ASP A 21 " pdb=" OG1 THR A 24 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR C 229 " pdb=" O VAL C 231 " model vdw 2.188 3.040 nonbonded pdb=" O ALA B 404 " pdb=" OG SER B 407 " model vdw 2.211 3.040 ... (remaining 115661 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.520 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:15.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.003 0.091 13853 Z= 0.143 Angle : 0.666 7.780 18930 Z= 0.392 Chirality : 0.042 0.215 2123 Planarity : 0.006 0.099 2301 Dihedral : 14.444 171.787 5515 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1569 helix: 0.55 (0.21), residues: 678 sheet: -0.86 (0.38), residues: 180 loop : -1.37 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 13 HIS 0.007 0.001 HIS C 233 PHE 0.034 0.002 PHE C 149 TYR 0.018 0.001 TYR A 96 ARG 0.008 0.001 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.18644 ( 588) hydrogen bonds : angle 6.87606 ( 1608) covalent geometry : bond 0.00290 (13853) covalent geometry : angle 0.66602 (18930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.9008 (mp) cc_final: 0.8800 (mp) REVERT: B 167 ASP cc_start: 0.7999 (m-30) cc_final: 0.7713 (m-30) REVERT: B 673 GLU cc_start: 0.7688 (mp0) cc_final: 0.7462 (mp0) REVERT: B 701 ARG cc_start: 0.7909 (mmp80) cc_final: 0.7173 (mmp80) REVERT: B 704 ARG cc_start: 0.8443 (ttt90) cc_final: 0.8133 (mtp85) REVERT: C 146 MET cc_start: 0.7917 (mmp) cc_final: 0.7645 (mpm) outliers start: 0 outliers final: 1 residues processed: 261 average time/residue: 1.9628 time to fit residues: 551.0498 Evaluate side-chains 181 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 424 GLN A 535 GLN B 148 GLN B 429 ASN B 650 ASN C 51 HIS C 233 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088439 restraints weight = 20528.155| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.93 r_work: 0.2988 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13853 Z= 0.241 Angle : 0.675 9.030 18930 Z= 0.351 Chirality : 0.046 0.224 2123 Planarity : 0.006 0.063 2301 Dihedral : 13.914 164.394 2293 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.84 % Allowed : 9.68 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1569 helix: 0.73 (0.21), residues: 685 sheet: -0.69 (0.37), residues: 179 loop : -1.38 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.039 0.002 PHE C 41 TYR 0.017 0.002 TYR B 537 ARG 0.014 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 588) hydrogen bonds : angle 4.91798 ( 1608) covalent geometry : bond 0.00567 (13853) covalent geometry : angle 0.67516 (18930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8583 (p) cc_final: 0.8126 (m) REVERT: A 133 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 149 LEU cc_start: 0.9065 (mp) cc_final: 0.8840 (mp) REVERT: B 167 ASP cc_start: 0.8581 (m-30) cc_final: 0.8282 (m-30) REVERT: B 588 GLU cc_start: 0.7028 (pm20) cc_final: 0.6822 (pm20) REVERT: B 603 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7023 (pt0) REVERT: B 689 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 701 ARG cc_start: 0.7973 (mmp80) cc_final: 0.7706 (mmp80) REVERT: C 146 MET cc_start: 0.8315 (mmp) cc_final: 0.8018 (mpm) REVERT: C 186 ARG cc_start: 0.9157 (mtm180) cc_final: 0.8750 (mtp180) outliers start: 26 outliers final: 9 residues processed: 196 average time/residue: 1.9265 time to fit residues: 406.2293 Evaluate side-chains 177 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 7 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 90 ASN B 148 GLN C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092142 restraints weight = 20401.690| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.92 r_work: 0.3050 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13853 Z= 0.118 Angle : 0.569 6.451 18930 Z= 0.297 Chirality : 0.041 0.190 2123 Planarity : 0.005 0.057 2301 Dihedral : 13.756 165.307 2291 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.70 % Allowed : 11.17 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1569 helix: 0.99 (0.21), residues: 683 sheet: -0.53 (0.38), residues: 181 loop : -1.24 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.007 0.001 HIS A 49 PHE 0.031 0.001 PHE C 41 TYR 0.014 0.001 TYR B 533 ARG 0.012 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 588) hydrogen bonds : angle 4.56845 ( 1608) covalent geometry : bond 0.00261 (13853) covalent geometry : angle 0.56926 (18930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8105 (m90) cc_final: 0.7758 (m170) REVERT: A 92 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8127 (ttm110) REVERT: A 139 GLN cc_start: 0.8477 (mm110) cc_final: 0.8206 (mm-40) REVERT: A 156 ASN cc_start: 0.8772 (t0) cc_final: 0.8483 (t0) REVERT: B 332 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9039 (mtp) REVERT: B 588 GLU cc_start: 0.7045 (pm20) cc_final: 0.6687 (pm20) REVERT: B 603 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6891 (pt0) REVERT: B 686 ARG cc_start: 0.8524 (mmp80) cc_final: 0.8211 (mmp80) REVERT: B 689 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7915 (mt-10) REVERT: B 701 ARG cc_start: 0.7939 (mmp80) cc_final: 0.7149 (mmp80) REVERT: B 704 ARG cc_start: 0.8663 (ttt90) cc_final: 0.8329 (mtp85) REVERT: C 142 ARG cc_start: 0.7839 (ppt-90) cc_final: 0.7619 (mtm-85) REVERT: C 146 MET cc_start: 0.8283 (mmp) cc_final: 0.8015 (mpm) outliers start: 24 outliers final: 9 residues processed: 203 average time/residue: 1.6831 time to fit residues: 369.1239 Evaluate side-chains 176 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087344 restraints weight = 20482.574| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.00 r_work: 0.2975 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13853 Z= 0.191 Angle : 0.607 6.589 18930 Z= 0.314 Chirality : 0.044 0.193 2123 Planarity : 0.005 0.053 2301 Dihedral : 13.757 164.685 2291 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.70 % Allowed : 11.80 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1569 helix: 1.01 (0.21), residues: 682 sheet: -0.51 (0.38), residues: 183 loop : -1.18 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS A 49 PHE 0.030 0.002 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.013 0.001 ARG B 708 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 588) hydrogen bonds : angle 4.45017 ( 1608) covalent geometry : bond 0.00447 (13853) covalent geometry : angle 0.60661 (18930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8568 (mm110) cc_final: 0.8296 (mm-40) REVERT: A 156 ASN cc_start: 0.8760 (t0) cc_final: 0.8483 (t0) REVERT: A 619 ASN cc_start: 0.8642 (p0) cc_final: 0.8405 (p0) REVERT: B 332 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9065 (mtp) REVERT: B 588 GLU cc_start: 0.7066 (pm20) cc_final: 0.6823 (pm20) REVERT: B 603 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6865 (pt0) REVERT: B 633 THR cc_start: 0.8790 (p) cc_final: 0.8487 (p) REVERT: B 686 ARG cc_start: 0.8530 (mmp80) cc_final: 0.8300 (mmp80) REVERT: B 689 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 701 ARG cc_start: 0.7948 (mmp80) cc_final: 0.7710 (mmp80) REVERT: C 146 MET cc_start: 0.8363 (mmp) cc_final: 0.8040 (mpm) outliers start: 24 outliers final: 9 residues processed: 191 average time/residue: 1.5450 time to fit residues: 317.2620 Evaluate side-chains 174 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 660 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN B 641 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.084107 restraints weight = 21107.616| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.15 r_work: 0.2904 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13853 Z= 0.131 Angle : 0.566 8.277 18930 Z= 0.293 Chirality : 0.041 0.182 2123 Planarity : 0.005 0.060 2301 Dihedral : 13.706 164.369 2291 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.05 % Allowed : 12.58 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1569 helix: 1.11 (0.21), residues: 682 sheet: -0.43 (0.38), residues: 178 loop : -1.08 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.009 0.001 HIS A 49 PHE 0.029 0.001 PHE C 41 TYR 0.014 0.001 TYR B 533 ARG 0.012 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 588) hydrogen bonds : angle 4.32564 ( 1608) covalent geometry : bond 0.00301 (13853) covalent geometry : angle 0.56638 (18930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8595 (mm110) cc_final: 0.8289 (mm-40) REVERT: A 156 ASN cc_start: 0.8761 (t0) cc_final: 0.8461 (t0) REVERT: A 619 ASN cc_start: 0.8641 (p0) cc_final: 0.8345 (p0) REVERT: B 332 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.9053 (mtp) REVERT: B 588 GLU cc_start: 0.7034 (pm20) cc_final: 0.6754 (pm20) REVERT: B 603 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6815 (pt0) REVERT: B 633 THR cc_start: 0.8766 (p) cc_final: 0.8447 (p) REVERT: B 686 ARG cc_start: 0.8501 (mmp80) cc_final: 0.8221 (mmp80) REVERT: B 689 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 701 ARG cc_start: 0.7949 (mmp80) cc_final: 0.7615 (mmp80) REVERT: C 69 MET cc_start: 0.9308 (ttp) cc_final: 0.8893 (ttp) REVERT: C 146 MET cc_start: 0.8403 (mmp) cc_final: 0.7887 (mpm) outliers start: 29 outliers final: 10 residues processed: 199 average time/residue: 1.5749 time to fit residues: 337.7044 Evaluate side-chains 173 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN C 163 ASN C 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083143 restraints weight = 21320.027| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.16 r_work: 0.2879 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13853 Z= 0.157 Angle : 0.591 8.881 18930 Z= 0.304 Chirality : 0.042 0.187 2123 Planarity : 0.005 0.065 2301 Dihedral : 13.701 164.102 2291 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.70 % Allowed : 13.78 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1569 helix: 1.20 (0.21), residues: 682 sheet: -0.51 (0.38), residues: 180 loop : -1.02 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.012 0.001 HIS A 49 PHE 0.029 0.002 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.015 0.001 ARG B 708 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 588) hydrogen bonds : angle 4.25707 ( 1608) covalent geometry : bond 0.00369 (13853) covalent geometry : angle 0.59121 (18930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8649 (mm110) cc_final: 0.8327 (mm-40) REVERT: A 156 ASN cc_start: 0.8784 (t0) cc_final: 0.8468 (t0) REVERT: A 619 ASN cc_start: 0.8669 (p0) cc_final: 0.8368 (p0) REVERT: B 332 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9020 (mtp) REVERT: B 588 GLU cc_start: 0.7028 (pm20) cc_final: 0.6769 (pm20) REVERT: B 686 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8230 (mmp80) REVERT: B 689 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 701 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7592 (mmp80) REVERT: B 708 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8531 (tpp80) REVERT: C 69 MET cc_start: 0.9312 (ttp) cc_final: 0.8804 (ptm) REVERT: C 146 MET cc_start: 0.8405 (mmp) cc_final: 0.7855 (mpm) outliers start: 24 outliers final: 12 residues processed: 184 average time/residue: 1.5789 time to fit residues: 313.3983 Evaluate side-chains 173 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 603 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083732 restraints weight = 21050.036| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.14 r_work: 0.2896 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13853 Z= 0.139 Angle : 0.583 10.095 18930 Z= 0.301 Chirality : 0.042 0.183 2123 Planarity : 0.005 0.075 2301 Dihedral : 13.682 163.881 2291 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.48 % Allowed : 14.63 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1569 helix: 1.26 (0.21), residues: 682 sheet: -0.48 (0.38), residues: 180 loop : -0.96 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.013 0.001 HIS A 51 PHE 0.028 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.017 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 588) hydrogen bonds : angle 4.22019 ( 1608) covalent geometry : bond 0.00325 (13853) covalent geometry : angle 0.58302 (18930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8190 (tp) cc_final: 0.7747 (tt) REVERT: A 120 ASN cc_start: 0.8019 (p0) cc_final: 0.7432 (t0) REVERT: A 139 GLN cc_start: 0.8673 (mm110) cc_final: 0.8333 (mm-40) REVERT: A 147 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: A 156 ASN cc_start: 0.8818 (t0) cc_final: 0.8505 (t0) REVERT: A 619 ASN cc_start: 0.8673 (p0) cc_final: 0.8368 (p0) REVERT: B 55 GLN cc_start: 0.9135 (mm110) cc_final: 0.8933 (mm-40) REVERT: B 144 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8043 (tm-30) REVERT: B 202 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.8134 (ptm-80) REVERT: B 332 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9000 (mtp) REVERT: B 588 GLU cc_start: 0.7010 (pm20) cc_final: 0.6747 (pm20) REVERT: B 686 ARG cc_start: 0.8512 (mmp80) cc_final: 0.8251 (mmp80) REVERT: B 689 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 701 ARG cc_start: 0.7807 (mmp80) cc_final: 0.6987 (mmp80) REVERT: B 704 ARG cc_start: 0.8974 (ttt90) cc_final: 0.8408 (mtp85) REVERT: B 708 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8547 (tpp80) REVERT: C 146 MET cc_start: 0.8405 (mmp) cc_final: 0.7869 (mpm) outliers start: 21 outliers final: 11 residues processed: 180 average time/residue: 1.6430 time to fit residues: 317.8991 Evaluate side-chains 172 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.084107 restraints weight = 21180.678| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.16 r_work: 0.2900 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13853 Z= 0.130 Angle : 0.583 10.830 18930 Z= 0.298 Chirality : 0.041 0.179 2123 Planarity : 0.005 0.072 2301 Dihedral : 13.653 163.576 2291 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.77 % Allowed : 14.56 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1569 helix: 1.34 (0.21), residues: 682 sheet: -0.42 (0.38), residues: 175 loop : -0.92 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.008 0.001 HIS A 51 PHE 0.028 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.017 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 588) hydrogen bonds : angle 4.18689 ( 1608) covalent geometry : bond 0.00303 (13853) covalent geometry : angle 0.58252 (18930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8178 (tp) cc_final: 0.7646 (tt) REVERT: A 139 GLN cc_start: 0.8697 (mm110) cc_final: 0.8347 (mm-40) REVERT: A 147 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7609 (mtm-85) REVERT: A 156 ASN cc_start: 0.8875 (t0) cc_final: 0.8613 (t0) REVERT: A 263 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 619 ASN cc_start: 0.8684 (p0) cc_final: 0.8386 (p0) REVERT: B 55 GLN cc_start: 0.9116 (mm110) cc_final: 0.8911 (mm-40) REVERT: B 202 ARG cc_start: 0.8397 (ptm-80) cc_final: 0.8126 (ptm-80) REVERT: B 588 GLU cc_start: 0.6983 (pm20) cc_final: 0.6674 (pm20) REVERT: B 686 ARG cc_start: 0.8513 (mmp80) cc_final: 0.8206 (tpp-160) REVERT: B 701 ARG cc_start: 0.7816 (mmp80) cc_final: 0.7481 (mmp80) REVERT: B 708 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8541 (tpp80) REVERT: C 69 MET cc_start: 0.9289 (ttp) cc_final: 0.8904 (ptm) REVERT: C 140 GLU cc_start: 0.7317 (pp20) cc_final: 0.7103 (pp20) REVERT: C 146 MET cc_start: 0.8408 (mmp) cc_final: 0.7891 (mpm) outliers start: 25 outliers final: 13 residues processed: 188 average time/residue: 1.6547 time to fit residues: 333.8270 Evaluate side-chains 176 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 35 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 100 optimal weight: 0.0000 chunk 6 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 45 optimal weight: 0.7980 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.086439 restraints weight = 20862.614| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.15 r_work: 0.2946 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13853 Z= 0.120 Angle : 0.594 11.193 18930 Z= 0.306 Chirality : 0.041 0.248 2123 Planarity : 0.005 0.080 2301 Dihedral : 13.616 163.209 2291 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.27 % Allowed : 15.34 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1569 helix: 1.45 (0.21), residues: 682 sheet: -0.45 (0.37), residues: 176 loop : -0.85 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.008 0.001 HIS C 233 PHE 0.027 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.019 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 588) hydrogen bonds : angle 4.13062 ( 1608) covalent geometry : bond 0.00271 (13853) covalent geometry : angle 0.59369 (18930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7970 (tp) cc_final: 0.7534 (tt) REVERT: A 120 ASN cc_start: 0.8098 (p0) cc_final: 0.7134 (t0) REVERT: A 139 GLN cc_start: 0.8652 (mm110) cc_final: 0.8368 (mm-40) REVERT: A 147 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7668 (mtm-85) REVERT: A 149 LEU cc_start: 0.8901 (mp) cc_final: 0.8684 (mp) REVERT: A 156 ASN cc_start: 0.8898 (t0) cc_final: 0.8624 (t0) REVERT: A 263 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 393 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8828 (mp) REVERT: A 619 ASN cc_start: 0.8651 (p0) cc_final: 0.8352 (p0) REVERT: B 55 GLN cc_start: 0.9111 (mm110) cc_final: 0.8909 (mm-40) REVERT: B 202 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8159 (ptm-80) REVERT: B 588 GLU cc_start: 0.6973 (pm20) cc_final: 0.6697 (pm20) REVERT: B 686 ARG cc_start: 0.8473 (mmp80) cc_final: 0.8114 (tpp-160) REVERT: B 689 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7728 (mt-10) REVERT: B 704 ARG cc_start: 0.8779 (ttt90) cc_final: 0.8381 (ptm160) REVERT: B 708 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8529 (tpp80) REVERT: C 55 MET cc_start: 0.9173 (mmt) cc_final: 0.8948 (tpp) REVERT: C 146 MET cc_start: 0.8368 (mmp) cc_final: 0.7854 (mpm) outliers start: 18 outliers final: 11 residues processed: 180 average time/residue: 1.5798 time to fit residues: 307.2584 Evaluate side-chains 173 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.086349 restraints weight = 20765.368| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.13 r_work: 0.2929 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13853 Z= 0.121 Angle : 0.592 12.086 18930 Z= 0.304 Chirality : 0.041 0.249 2123 Planarity : 0.005 0.084 2301 Dihedral : 13.593 162.933 2291 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.99 % Allowed : 16.25 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1569 helix: 1.45 (0.21), residues: 682 sheet: -0.28 (0.38), residues: 165 loop : -0.81 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 543 HIS 0.007 0.001 HIS C 233 PHE 0.027 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.020 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 588) hydrogen bonds : angle 4.08616 ( 1608) covalent geometry : bond 0.00280 (13853) covalent geometry : angle 0.59190 (18930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7967 (tp) cc_final: 0.7532 (tt) REVERT: A 120 ASN cc_start: 0.8050 (p0) cc_final: 0.7353 (t0) REVERT: A 139 GLN cc_start: 0.8660 (mm110) cc_final: 0.8371 (mm-40) REVERT: A 149 LEU cc_start: 0.8892 (mp) cc_final: 0.8677 (mp) REVERT: A 156 ASN cc_start: 0.8928 (t0) cc_final: 0.8665 (t0) REVERT: A 196 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7777 (mmm160) REVERT: A 263 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 393 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8815 (mp) REVERT: A 619 ASN cc_start: 0.8651 (p0) cc_final: 0.8356 (p0) REVERT: B 55 GLN cc_start: 0.9077 (mm110) cc_final: 0.8875 (mm-40) REVERT: B 202 ARG cc_start: 0.8432 (ptm-80) cc_final: 0.8135 (ptm-80) REVERT: B 588 GLU cc_start: 0.6885 (pm20) cc_final: 0.6655 (pm20) REVERT: B 686 ARG cc_start: 0.8504 (mmp80) cc_final: 0.8248 (mmp80) REVERT: B 689 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7773 (mt-10) REVERT: B 704 ARG cc_start: 0.8886 (ttt90) cc_final: 0.8387 (ptm160) REVERT: B 708 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8511 (tpp80) REVERT: C 140 GLU cc_start: 0.7285 (pp20) cc_final: 0.6873 (pp20) REVERT: C 146 MET cc_start: 0.8347 (mmp) cc_final: 0.7803 (mpm) outliers start: 14 outliers final: 9 residues processed: 171 average time/residue: 1.7428 time to fit residues: 320.0239 Evaluate side-chains 165 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 0.0770 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 0.0270 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087756 restraints weight = 20837.924| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.15 r_work: 0.2954 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13853 Z= 0.113 Angle : 0.585 11.981 18930 Z= 0.298 Chirality : 0.041 0.230 2123 Planarity : 0.005 0.077 2301 Dihedral : 13.562 162.578 2291 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.06 % Allowed : 16.33 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1569 helix: 1.48 (0.21), residues: 683 sheet: -0.19 (0.38), residues: 165 loop : -0.75 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.007 0.001 HIS C 233 PHE 0.027 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.018 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 588) hydrogen bonds : angle 4.03323 ( 1608) covalent geometry : bond 0.00260 (13853) covalent geometry : angle 0.58489 (18930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10869.92 seconds wall clock time: 190 minutes 27.11 seconds (11427.11 seconds total)