Starting phenix.real_space_refine on Fri Sep 11 20:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yyt_11007/09_2026/6yyt_11007_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yyt_11007/09_2026/6yyt_11007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yyt_11007/09_2026/6yyt_11007_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yyt_11007/09_2026/6yyt_11007_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yyt_11007/09_2026/6yyt_11007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yyt_11007/09_2026/6yyt_11007.map" } resolution = 2.9 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= 0.016 sd= 0.974 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 54 5.49 5 S 77 5.16 5 C 7014 2.51 5 N 1926 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11375 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6880 Classifications: {'peptide': 853} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 824} Chain breaks: 2 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1393 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1391 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} Chain: "Q" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna3p': 11} Chain: "U" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1864 SG CYS A 301 92.661 65.587 45.161 1.00 25.99 S ATOM 1905 SG CYS A 306 92.937 64.791 41.187 1.00 25.44 S ATOM 1937 SG CYS A 310 95.767 64.736 44.077 1.00 24.45 S ATOM 3345 SG CYS A 487 75.166 60.156 53.972 1.00 21.81 S ATOM 4598 SG CYS A 645 73.794 60.060 50.132 1.00 27.45 S ATOM 4604 SG CYS A 646 77.157 61.975 51.989 1.00 24.88 S Time building chain proxies: 2.58, per 1000 atoms: 0.23 Number of scatterers: 11375 At special positions: 0 Unit cell: (140.112, 92.574, 127.602, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 77 16.00 P 54 15.00 O 2302 8.00 N 1926 7.00 C 7014 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: 0.64 Conformation dependent library (CDL) restraints added in 425.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 57.6% alpha, 10.2% beta 22 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 198 removed outlier: 4.013A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.553A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 3.710A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.251A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.712A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.606A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.685A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.514A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.768A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.542A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.927A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.879A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.740A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.555A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 847 through 852 removed outlier: 4.152A pdb=" N ASP A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 removed outlier: 4.058A pdb=" N ARG A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.555A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.914A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.767A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.322A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.817A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 98 removed outlier: 3.560A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.700A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.905A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.621A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.230A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.713A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.299A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.601A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.051A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.040A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.111A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA6, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.735A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3189 1.33 - 1.45: 2214 1.45 - 1.57: 6087 1.57 - 1.69: 102 1.69 - 1.81: 122 Bond restraints: 11714 Sorted by residual: bond pdb=" O3' G T 13 " pdb=" P C T 14 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.20e-02 6.94e+03 1.08e+01 bond pdb=" O3' A P 17 " pdb=" P G P 18 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.20e-02 6.94e+03 9.92e+00 bond pdb=" O3' C T 14 " pdb=" P G T 15 " ideal model delta sigma weight residual 1.607 1.574 0.033 1.20e-02 6.94e+03 7.72e+00 bond pdb=" O3' U P 16 " pdb=" P A P 17 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.20e-02 6.94e+03 6.86e+00 bond pdb=" O3' G P 15 " pdb=" P U P 16 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.20e-02 6.94e+03 5.14e+00 ... (remaining 11709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15813 1.55 - 3.10: 277 3.10 - 4.65: 44 4.65 - 6.21: 3 6.21 - 7.76: 1 Bond angle restraints: 16138 Sorted by residual: angle pdb=" O5' G U 15 " pdb=" C5' G U 15 " pdb=" C4' G U 15 " ideal model delta sigma weight residual 109.40 111.82 -2.42 8.00e-01 1.56e+00 9.14e+00 angle pdb=" O5' C U 5 " pdb=" C5' C U 5 " pdb=" C4' C U 5 " ideal model delta sigma weight residual 109.40 111.79 -2.39 8.00e-01 1.56e+00 8.91e+00 angle pdb=" O5' U Q 16 " pdb=" C5' U Q 16 " pdb=" C4' U Q 16 " ideal model delta sigma weight residual 109.40 111.78 -2.38 8.00e-01 1.56e+00 8.86e+00 angle pdb=" O5' C U 14 " pdb=" C5' C U 14 " pdb=" C4' C U 14 " ideal model delta sigma weight residual 109.40 111.78 -2.38 8.00e-01 1.56e+00 8.82e+00 angle pdb=" O5' C Q 12 " pdb=" C5' C Q 12 " pdb=" C4' C Q 12 " ideal model delta sigma weight residual 109.40 111.76 -2.36 8.00e-01 1.56e+00 8.72e+00 ... (remaining 16133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6178 17.91 - 35.82: 660 35.82 - 53.73: 191 53.73 - 71.63: 67 71.63 - 89.54: 21 Dihedral angle restraints: 7117 sinusoidal: 3260 harmonic: 3857 Sorted by residual: dihedral pdb=" C5' G P 18 " pdb=" C4' G P 18 " pdb=" C3' G P 18 " pdb=" O3' G P 18 " ideal model delta sinusoidal sigma weight residual 147.00 125.28 21.72 1 8.00e+00 1.56e-02 1.07e+01 dihedral pdb=" CB GLU B 48 " pdb=" CG GLU B 48 " pdb=" CD GLU B 48 " pdb=" OE1 GLU B 48 " ideal model delta sinusoidal sigma weight residual 0.00 89.54 -89.54 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 640 " pdb=" CD ARG A 640 " pdb=" NE ARG A 640 " pdb=" CZ ARG A 640 " ideal model delta sinusoidal sigma weight residual 90.00 131.86 -41.86 2 1.50e+01 4.44e-03 9.50e+00 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1570 0.048 - 0.096: 202 0.096 - 0.145: 96 0.145 - 0.193: 6 0.193 - 0.241: 3 Chirality restraints: 1877 Sorted by residual: chirality pdb=" C3' G P 8 " pdb=" C4' G P 8 " pdb=" O3' G P 8 " pdb=" C2' G P 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' G P 18 " pdb=" C4' G P 18 " pdb=" O3' G P 18 " pdb=" C2' G P 18 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' G T 18 " pdb=" C4' G T 18 " pdb=" O3' G T 18 " pdb=" C2' G T 18 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1874 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G T 13 " -0.019 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 G T 13 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G T 13 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G T 13 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G T 13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G T 13 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G T 13 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G T 13 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G T 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G P 18 " 0.022 2.00e-02 2.50e+03 9.04e-03 2.45e+00 pdb=" N9 G P 18 " -0.017 2.00e-02 2.50e+03 pdb=" C8 G P 18 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G P 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G P 18 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G P 18 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G P 18 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G P 18 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G P 18 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G P 18 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G P 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G P 18 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C P 12 " 0.019 2.00e-02 2.50e+03 9.49e-03 2.03e+00 pdb=" N1 C P 12 " -0.018 2.00e-02 2.50e+03 pdb=" C2 C P 12 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C P 12 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C P 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C P 12 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C P 12 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C P 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C P 12 " -0.007 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2698 2.79 - 3.31: 10547 3.31 - 3.84: 19707 3.84 - 4.37: 23335 4.37 - 4.90: 38279 Nonbonded interactions: 94566 Sorted by model distance: nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.258 3.040 nonbonded pdb=" O GLY A 852 " pdb=" OG1 THR A 853 " model vdw 2.275 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.347 3.040 nonbonded pdb=" O ASN A 705 " pdb=" OG SER A 709 " model vdw 2.365 3.040 nonbonded pdb=" O ALA A 448 " pdb=" OG SER A 451 " model vdw 2.372 3.040 ... (remaining 94561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 18 or (resid 19 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 191)) } ncs_group { reference = (chain 'P' and resid 7 through 18) selection = (chain 'Q' and resid 7 through 18) selection = chain 'T' selection = (chain 'U' and resid 7 through 18) } 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: 0.920 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.000 Find NCS groups from input model: 0.110 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 0.236 11722 Z= 0.181 Angle : 0.583 25.705 16144 Z= 0.312 Chirality : 0.041 0.241 1877 Planarity : 0.002 0.033 1862 Dihedral : 16.992 89.542 4617 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.36 % Allowed : 6.14 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.98 (0.21), residues: 1286 helix: -0.06 (0.19), residues: 652 sheet: -0.62 (0.47), residues: 108 loop : -1.31 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 836 TYR 0.013 0.001 TYR A 788 PHE 0.010 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.18 (11714) covalent geometry : angle 0.48650 / 0.30 (16138) hydrogen bonds : bond 0.13011 / 8.65 ( 627) hydrogen bonds : angle 5.22944 / 3.69 ( 1726) metal coordination : bond 0.08428 / 2.62 ( 8) metal coordination : angle 16.70365 / 9.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.274 Fit side-chains REVERT: B 79 LYS cc_start: 0.6908 (mmtp) cc_final: 0.6415 (ptpt) REVERT: B 85 SER cc_start: 0.8006 (p) cc_final: 0.7791 (t) outliers start: 4 outliers final: 1 residues processed: 178 average time/residue: 0.4545 time to fit residues: 88.9585 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 177 ASN A 347 HIS A 439 HIS A 570 GLN B 88 GLN B 140 ASN D 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.141457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097632 restraints weight = 16371.985| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.23 r_work: 0.3136 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11722 Z= 0.238 Angle : 0.572 6.413 16144 Z= 0.306 Chirality : 0.043 0.215 1877 Planarity : 0.004 0.065 1862 Dihedral : 14.145 74.820 2251 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.62 % Allowed : 13.45 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.08 (0.22), residues: 1286 helix: 0.99 (0.20), residues: 664 sheet: -0.30 (0.48), residues: 110 loop : -1.08 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 111 TYR 0.023 0.002 TYR B 135 PHE 0.023 0.002 PHE A 920 TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (11714) covalent geometry : angle 0.57093 / 0.31 (16138) hydrogen bonds : bond 0.04080 / 2.60 ( 627) hydrogen bonds : angle 3.90734 / 2.80 ( 1726) metal coordination : bond 0.01167 / 0.53 ( 8) metal coordination : angle 1.79127 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.458 Fit side-chains REVERT: A 33 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6731 (mtm110) REVERT: A 284 ASP cc_start: 0.8510 (m-30) cc_final: 0.8242 (t0) REVERT: A 418 ASP cc_start: 0.8682 (m-30) cc_final: 0.8442 (t0) REVERT: A 722 ASN cc_start: 0.7844 (m110) cc_final: 0.7558 (m-40) REVERT: A 899 MET cc_start: 0.7594 (mmm) cc_final: 0.7032 (mmt) REVERT: B 79 LYS cc_start: 0.6194 (mmtp) cc_final: 0.5418 (ptpt) REVERT: C 34 GLN cc_start: 0.8239 (tp40) cc_final: 0.7973 (tp40) REVERT: D 189 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8847 (mm) outliers start: 29 outliers final: 14 residues processed: 159 average time/residue: 0.5308 time to fit residues: 92.4561 Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 ASN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.140153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095750 restraints weight = 16495.623| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.20 r_work: 0.3114 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11722 Z= 0.193 Angle : 0.509 6.117 16144 Z= 0.269 Chirality : 0.040 0.160 1877 Planarity : 0.004 0.054 1862 Dihedral : 14.118 74.638 2249 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.16 % Allowed : 16.16 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.45 (0.22), residues: 1286 helix: 1.38 (0.20), residues: 661 sheet: -0.22 (0.53), residues: 95 loop : -0.97 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 51 TYR 0.014 0.002 TYR A 149 PHE 0.019 0.002 PHE A 920 TRP 0.014 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (11714) covalent geometry : angle 0.50646 / 0.27 (16138) hydrogen bonds : bond 0.03927 / 2.52 ( 627) hydrogen bonds : angle 3.77159 / 2.68 ( 1726) metal coordination : bond 0.00593 / 0.37 ( 8) metal coordination : angle 2.43898 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.438 Fit side-chains REVERT: A 33 ARG cc_start: 0.6919 (mtm110) cc_final: 0.6687 (mtm110) REVERT: A 260 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7597 (t0) REVERT: A 284 ASP cc_start: 0.8516 (m-30) cc_final: 0.8283 (t0) REVERT: A 418 ASP cc_start: 0.8654 (m-30) cc_final: 0.8446 (t0) REVERT: A 899 MET cc_start: 0.7652 (mmm) cc_final: 0.7147 (mmt) REVERT: B 79 LYS cc_start: 0.6284 (mmtp) cc_final: 0.5467 (ptpt) REVERT: B 85 SER cc_start: 0.7742 (t) cc_final: 0.7390 (p) REVERT: C 34 GLN cc_start: 0.8353 (tp40) cc_final: 0.8114 (tp40) REVERT: D 62 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8052 (mmm) outliers start: 35 outliers final: 16 residues processed: 162 average time/residue: 0.4959 time to fit residues: 88.3505 Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 187 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 85 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099766 restraints weight = 16487.652| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.82 r_work: 0.3151 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11722 Z= 0.113 Angle : 0.475 7.964 16144 Z= 0.250 Chirality : 0.038 0.157 1877 Planarity : 0.003 0.049 1862 Dihedral : 14.119 74.308 2249 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.71 % Allowed : 18.32 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.81 (0.23), residues: 1286 helix: 1.63 (0.20), residues: 660 sheet: -0.25 (0.49), residues: 105 loop : -0.69 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.014 0.001 TYR A 217 PHE 0.019 0.001 PHE A 920 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11714) covalent geometry : angle 0.47424 / 0.25 (16138) hydrogen bonds : bond 0.03350 / 2.15 ( 627) hydrogen bonds : angle 3.62770 / 2.57 ( 1726) metal coordination : bond 0.00516 / 0.32 ( 8) metal coordination : angle 1.78200 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.434 Fit side-chains REVERT: A 260 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7527 (t0) REVERT: A 284 ASP cc_start: 0.8543 (m-30) cc_final: 0.8311 (t0) REVERT: B 79 LYS cc_start: 0.6152 (mmtp) cc_final: 0.5368 (ptpt) REVERT: B 85 SER cc_start: 0.7726 (t) cc_final: 0.7363 (p) REVERT: C 34 GLN cc_start: 0.8336 (tp40) cc_final: 0.8087 (tp40) outliers start: 30 outliers final: 10 residues processed: 156 average time/residue: 0.5353 time to fit residues: 91.6312 Evaluate side-chains 148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 4 optimal weight: 0.0000 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093983 restraints weight = 16320.150| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.99 r_work: 0.3153 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11722 Z= 0.112 Angle : 0.464 8.942 16144 Z= 0.243 Chirality : 0.037 0.166 1877 Planarity : 0.003 0.044 1862 Dihedral : 14.093 74.195 2249 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.62 % Allowed : 18.68 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.96 (0.23), residues: 1286 helix: 1.75 (0.20), residues: 661 sheet: -0.07 (0.52), residues: 95 loop : -0.64 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.014 0.001 TYR A 217 PHE 0.017 0.001 PHE A 920 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11714) covalent geometry : angle 0.46295 / 0.24 (16138) hydrogen bonds : bond 0.03259 / 2.09 ( 627) hydrogen bonds : angle 3.56065 / 2.53 ( 1726) metal coordination : bond 0.00451 / 0.28 ( 8) metal coordination : angle 1.63220 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.463 Fit side-chains REVERT: A 284 ASP cc_start: 0.8586 (m-30) cc_final: 0.8363 (t0) REVERT: B 79 LYS cc_start: 0.6167 (mmtp) cc_final: 0.5392 (ptpt) REVERT: C 34 GLN cc_start: 0.8395 (tp40) cc_final: 0.8150 (tp40) outliers start: 29 outliers final: 20 residues processed: 160 average time/residue: 0.4926 time to fit residues: 86.5814 Evaluate side-chains 158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 3 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 overall best weight: 1.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.141210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098580 restraints weight = 16317.762| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.98 r_work: 0.3120 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11722 Z= 0.133 Angle : 0.481 8.931 16144 Z= 0.251 Chirality : 0.038 0.174 1877 Planarity : 0.003 0.045 1862 Dihedral : 14.083 74.286 2249 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.07 % Allowed : 19.22 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.03 (0.23), residues: 1286 helix: 1.79 (0.20), residues: 663 sheet: -0.25 (0.49), residues: 105 loop : -0.54 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.014 0.001 TYR A 217 PHE 0.016 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11714) covalent geometry : angle 0.47999 / 0.25 (16138) hydrogen bonds : bond 0.03359 / 2.15 ( 627) hydrogen bonds : angle 3.58171 / 2.54 ( 1726) metal coordination : bond 0.00480 / 0.30 ( 8) metal coordination : angle 1.56470 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.433 Fit side-chains REVERT: A 260 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7596 (t0) REVERT: A 284 ASP cc_start: 0.8587 (m-30) cc_final: 0.8349 (t0) REVERT: B 79 LYS cc_start: 0.6169 (mmtp) cc_final: 0.5440 (ptpt) REVERT: C 34 GLN cc_start: 0.8353 (tp40) cc_final: 0.8090 (tp40) outliers start: 34 outliers final: 22 residues processed: 163 average time/residue: 0.4825 time to fit residues: 86.5434 Evaluate side-chains 160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.137722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093089 restraints weight = 16455.651| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.44 r_work: 0.3059 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11722 Z= 0.262 Angle : 0.576 9.895 16144 Z= 0.301 Chirality : 0.043 0.172 1877 Planarity : 0.004 0.056 1862 Dihedral : 14.101 74.842 2249 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.79 % Allowed : 19.40 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.67 (0.23), residues: 1286 helix: 1.42 (0.20), residues: 683 sheet: -0.11 (0.53), residues: 97 loop : -0.76 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.018 0.002 TYR A 149 PHE 0.018 0.002 PHE A 440 TRP 0.012 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (11714) covalent geometry : angle 0.57571 / 0.30 (16138) hydrogen bonds : bond 0.04251 / 2.73 ( 627) hydrogen bonds : angle 3.81251 / 2.68 ( 1726) metal coordination : bond 0.00911 / 0.50 ( 8) metal coordination : angle 1.47788 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.464 Fit side-chains REVERT: A 761 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: A 899 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7202 (mmt) REVERT: B 79 LYS cc_start: 0.6261 (mmtp) cc_final: 0.5457 (ptpt) REVERT: C 18 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8939 (tm-30) REVERT: C 34 GLN cc_start: 0.8501 (tp40) cc_final: 0.8265 (tp40) outliers start: 42 outliers final: 23 residues processed: 164 average time/residue: 0.5179 time to fit residues: 93.1904 Evaluate side-chains 157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 88 optimal weight: 50.0000 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 88 GLN ** D 158 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 = 0.3939 r_free = 0.3939 target = 0.140640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095879 restraints weight = 16344.575| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.47 r_work: 0.3111 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11722 Z= 0.110 Angle : 0.506 11.697 16144 Z= 0.264 Chirality : 0.038 0.189 1877 Planarity : 0.003 0.043 1862 Dihedral : 14.139 74.256 2249 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.35 % Allowed : 20.85 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.05 (0.23), residues: 1286 helix: 1.77 (0.20), residues: 671 sheet: -0.16 (0.52), residues: 95 loop : -0.52 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.016 0.001 TYR B 135 PHE 0.016 0.001 PHE A 920 TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11714) covalent geometry : angle 0.50525 / 0.26 (16138) hydrogen bonds : bond 0.03342 / 2.14 ( 627) hydrogen bonds : angle 3.61918 / 2.55 ( 1726) metal coordination : bond 0.00391 / 0.24 ( 8) metal coordination : angle 1.76857 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.434 Fit side-chains REVERT: A 899 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7083 (mmt) REVERT: B 79 LYS cc_start: 0.6130 (mmtp) cc_final: 0.5360 (ptpt) REVERT: B 85 SER cc_start: 0.7710 (t) cc_final: 0.7354 (p) REVERT: C 18 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8881 (tm-30) REVERT: C 34 GLN cc_start: 0.8387 (tp40) cc_final: 0.8103 (tp40) REVERT: D 142 CYS cc_start: 0.6784 (m) cc_final: 0.6569 (m) outliers start: 26 outliers final: 15 residues processed: 150 average time/residue: 0.5361 time to fit residues: 87.8091 Evaluate side-chains 146 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 128 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 88 GLN ** D 158 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 = 0.3906 r_free = 0.3906 target = 0.137911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093783 restraints weight = 16284.470| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.97 r_work: 0.3069 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11722 Z= 0.240 Angle : 0.576 12.037 16144 Z= 0.298 Chirality : 0.042 0.185 1877 Planarity : 0.004 0.051 1862 Dihedral : 14.107 74.682 2249 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.26 % Allowed : 21.48 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.77 (0.23), residues: 1286 helix: 1.53 (0.20), residues: 680 sheet: -0.23 (0.51), residues: 97 loop : -0.71 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.018 0.002 TYR A 149 PHE 0.017 0.002 PHE A 440 TRP 0.013 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (11714) covalent geometry : angle 0.57591 / 0.30 (16138) hydrogen bonds : bond 0.04097 / 2.63 ( 627) hydrogen bonds : angle 3.78611 / 2.66 ( 1726) metal coordination : bond 0.00851 / 0.46 ( 8) metal coordination : angle 1.40332 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.422 Fit side-chains REVERT: A 899 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7170 (mmt) REVERT: B 79 LYS cc_start: 0.6189 (mmtp) cc_final: 0.5375 (ptpt) REVERT: C 18 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8887 (tm-30) REVERT: C 34 GLN cc_start: 0.8445 (tp40) cc_final: 0.8150 (tp40) REVERT: D 164 SER cc_start: 0.8895 (m) cc_final: 0.8620 (p) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 0.5496 time to fit residues: 89.4247 Evaluate side-chains 149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 121 optimal weight: 0.0040 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 88 GLN ** D 158 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 = 0.3938 r_free = 0.3938 target = 0.140535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096670 restraints weight = 16481.136| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.99 r_work: 0.3113 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11722 Z= 0.114 Angle : 0.515 11.684 16144 Z= 0.269 Chirality : 0.038 0.196 1877 Planarity : 0.003 0.041 1862 Dihedral : 14.145 74.278 2249 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.26 % Allowed : 21.75 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.04 (0.23), residues: 1286 helix: 1.69 (0.20), residues: 681 sheet: -0.42 (0.48), residues: 107 loop : -0.41 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 111 TYR 0.015 0.001 TYR B 135 PHE 0.017 0.001 PHE A 920 TRP 0.014 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11714) covalent geometry : angle 0.51405 / 0.27 (16138) hydrogen bonds : bond 0.03325 / 2.12 ( 627) hydrogen bonds : angle 3.64435 / 2.56 ( 1726) metal coordination : bond 0.00413 / 0.26 ( 8) metal coordination : angle 1.72880 / 0.97 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.437 Fit side-chains REVERT: A 119 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6132 (tp) REVERT: A 551 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8644 (mttm) REVERT: A 556 THR cc_start: 0.8974 (p) cc_final: 0.8671 (p) REVERT: A 899 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7165 (mmt) REVERT: B 79 LYS cc_start: 0.6247 (mmtp) cc_final: 0.5464 (ptpt) REVERT: C 18 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8901 (tm-30) REVERT: C 34 GLN cc_start: 0.8390 (tp40) cc_final: 0.8119 (tp40) REVERT: D 164 SER cc_start: 0.8910 (m) cc_final: 0.8630 (p) outliers start: 25 outliers final: 16 residues processed: 151 average time/residue: 0.5341 time to fit residues: 88.0075 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 50.0000 chunk 124 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.138376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096313 restraints weight = 16415.983| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.96 r_work: 0.3072 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11722 Z= 0.219 Angle : 0.791 41.594 16144 Z= 0.377 Chirality : 0.041 0.184 1877 Planarity : 0.004 0.054 1862 Dihedral : 14.105 74.560 2249 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.62 % Allowed : 21.21 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.78 (0.23), residues: 1286 helix: 1.49 (0.20), residues: 687 sheet: -0.30 (0.50), residues: 97 loop : -0.63 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.041 0.002 TYR D 138 PHE 0.017 0.002 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (11714) covalent geometry : angle 0.79089 / 0.38 (16138) hydrogen bonds : bond 0.03895 / 2.49 ( 627) hydrogen bonds : angle 3.75710 / 2.64 ( 1726) metal coordination : bond 0.00700 / 0.39 ( 8) metal coordination : angle 1.38128 / 0.77 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4553.30 seconds wall clock time: 78 minutes 18.25 seconds (4698.25 seconds total)