Starting phenix.real_space_refine on Mon Jun 16 08:33:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qeb_18350/06_2025/8qeb_18350_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qeb_18350/06_2025/8qeb_18350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qeb_18350/06_2025/8qeb_18350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qeb_18350/06_2025/8qeb_18350.map" model { file = "/net/cci-nas-00/data/ceres_data/8qeb_18350/06_2025/8qeb_18350_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qeb_18350/06_2025/8qeb_18350_trim.cif" } resolution = 3.3 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= 0.039 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5863 2.51 5 N 1400 2.21 5 O 1651 1.98 5 H 8700 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17671 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 17485 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 47, 'TRANS': 1050} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'ERG': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 9.16, per 1000 atoms: 0.52 Number of scatterers: 17671 At special positions: 0 Unit cell: (84.11, 102.226, 161.75, 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 57 16.00 O 1651 8.00 N 1400 7.00 C 5863 6.00 H 8700 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 41 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 868 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 869 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 879 " - pdb=" SG CYS A 888 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 1 " - " ASN A 940 " " NAG C 1 " - " ASN A 900 " " NAG D 1 " - " ASN A 401 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 61.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.759A pdb=" N ALA A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.823A pdb=" N PHE A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.739A pdb=" N PHE A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 121' Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.613A pdb=" N LEU A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 4.109A pdb=" N GLY A 194 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.639A pdb=" N GLU A 210 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 318 through 337 removed outlier: 4.074A pdb=" N ALA A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.876A pdb=" N THR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 408 through 423 removed outlier: 3.520A pdb=" N ASP A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.642A pdb=" N LEU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 4.686A pdb=" N PHE A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.567A pdb=" N LEU A 481 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.705A pdb=" N LEU A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 532 removed outlier: 3.725A pdb=" N ARG A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 4.183A pdb=" N LEU A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 removed outlier: 7.449A pdb=" N ASN A 556 " --> pdb=" O ASN A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 557 through 576 removed outlier: 3.581A pdb=" N TRP A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 608 removed outlier: 3.764A pdb=" N ILE A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 645 removed outlier: 3.602A pdb=" N ILE A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Proline residue: A 622 - end of helix removed outlier: 3.782A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 632 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 682 removed outlier: 3.553A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Proline residue: A 665 - end of helix removed outlier: 3.688A pdb=" N ALA A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.675A pdb=" N THR A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 701 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.018A pdb=" N THR A 747 " --> pdb=" O LYS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.515A pdb=" N ILE A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 770 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.893A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 786 through 794 removed outlier: 3.924A pdb=" N ASP A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 908 through 919 removed outlier: 4.259A pdb=" N ILE A 916 " --> pdb=" O GLU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 976 removed outlier: 3.862A pdb=" N PHE A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 995 removed outlier: 4.358A pdb=" N GLN A 993 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 994 " --> pdb=" O PHE A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1021 removed outlier: 3.580A pdb=" N LEU A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1047 removed outlier: 3.523A pdb=" N ILE A1037 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A1045 " --> pdb=" O GLY A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1079 removed outlier: 3.568A pdb=" N ASN A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1100 Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1106 through 1119 removed outlier: 3.710A pdb=" N VAL A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1130 Processing helix chain 'A' and resid 1136 through 1147 removed outlier: 3.525A pdb=" N ALA A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1155 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 4.214A pdb=" N CYS A 41 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 6.689A pdb=" N GLU A 139 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 127 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 137 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS A 129 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASP A 135 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 199 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.604A pdb=" N VAL A 252 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 255 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AA6, first strand: chain 'A' and resid 937 through 939 removed outlier: 4.304A pdb=" N ASP A 980 " --> pdb=" O LYS A 808 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8690 1.03 - 1.23: 43 1.23 - 1.43: 3849 1.43 - 1.62: 5240 1.62 - 1.82: 76 Bond restraints: 17898 Sorted by residual: bond pdb=" N ALA A 21 " pdb=" CA ALA A 21 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C6 ERG A1201 " pdb=" C7 ERG A1201 " ideal model delta sigma weight residual 1.452 1.419 0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" N ALA A 21 " pdb=" H ALA A 21 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 17893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 30143 1.04 - 2.09: 2003 2.09 - 3.13: 87 3.13 - 4.18: 34 4.18 - 5.22: 10 Bond angle restraints: 32277 Sorted by residual: angle pdb=" N VAL A 335 " pdb=" CA VAL A 335 " pdb=" C VAL A 335 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" CB ARG A 886 " pdb=" CG ARG A 886 " pdb=" CD ARG A 886 " ideal model delta sigma weight residual 111.30 116.52 -5.22 2.30e+00 1.89e-01 5.16e+00 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" C PRO A 955 " ideal model delta sigma weight residual 112.47 116.93 -4.46 2.06e+00 2.36e-01 4.70e+00 angle pdb=" CA VAL A 335 " pdb=" C VAL A 335 " pdb=" N GLU A 336 " ideal model delta sigma weight residual 118.65 116.67 1.98 1.07e+00 8.73e-01 3.42e+00 angle pdb=" C HIS A 954 " pdb=" CA HIS A 954 " pdb=" CB HIS A 954 " ideal model delta sigma weight residual 109.96 112.73 -2.77 1.50e+00 4.44e-01 3.41e+00 ... (remaining 32272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 8127 23.57 - 47.14: 507 47.14 - 70.70: 111 70.70 - 94.27: 25 94.27 - 117.84: 6 Dihedral angle restraints: 8776 sinusoidal: 4793 harmonic: 3983 Sorted by residual: dihedral pdb=" CB CYS A 869 " pdb=" SG CYS A 869 " pdb=" SG CYS A 891 " pdb=" CB CYS A 891 " ideal model delta sinusoidal sigma weight residual 93.00 143.15 -50.15 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS A 822 " pdb=" SG CYS A 822 " pdb=" SG CYS A 828 " pdb=" CB CYS A 828 " ideal model delta sinusoidal sigma weight residual -86.00 -40.98 -45.02 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS A 223 " pdb=" SG CYS A 223 " pdb=" SG CYS A 235 " pdb=" CB CYS A 235 " ideal model delta sinusoidal sigma weight residual 93.00 49.27 43.73 1 1.00e+01 1.00e-02 2.66e+01 ... (remaining 8773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1179 0.047 - 0.094: 203 0.094 - 0.141: 46 0.141 - 0.187: 3 0.187 - 0.234: 2 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 940 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 900 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PRO A 955 " pdb=" N PRO A 955 " pdb=" C PRO A 955 " pdb=" CB PRO A 955 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1430 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 886 " 0.090 9.50e-02 1.11e+02 3.04e-02 1.25e+00 pdb=" NE ARG A 886 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 886 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 886 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 886 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 886 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 886 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 886 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 886 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 43 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 44 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 39 " 0.016 5.00e-02 4.00e+02 2.48e-02 9.87e-01 pdb=" N PRO A 40 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 40 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 40 " 0.014 5.00e-02 4.00e+02 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1516 2.22 - 2.82: 38461 2.82 - 3.41: 47331 3.41 - 4.01: 63495 4.01 - 4.60: 97283 Nonbonded interactions: 248086 Sorted by model distance: nonbonded pdb=" O LEU A 493 " pdb=" H VAL A 506 " model vdw 1.629 2.450 nonbonded pdb=" O GLY A 969 " pdb=" HG SER A 973 " model vdw 1.637 2.450 nonbonded pdb=" HG SER A 547 " pdb=" OH TYR A 785 " model vdw 1.643 2.450 nonbonded pdb=" OD1 ASP A 154 " pdb=" HZ1 LYS A 157 " model vdw 1.664 2.450 nonbonded pdb=" O ALA A 83 " pdb="HD22 ASN A 87 " model vdw 1.681 2.450 ... (remaining 248081 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' selection = chain 'C' selection = chain 'D' } 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 41.970 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 0.033 9218 Z= 0.144 Angle : 0.494 7.910 12549 Z= 0.247 Chirality : 0.038 0.234 1433 Planarity : 0.003 0.040 1558 Dihedral : 17.617 117.838 3575 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.41 % Allowed : 15.03 % Favored : 84.57 % 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: -0.18 (0.26), residues: 1092 helix: 0.35 (0.23), residues: 570 sheet: -0.87 (0.67), residues: 68 loop : -0.46 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.005 0.001 HIS A 954 PHE 0.017 0.001 PHE A 265 TYR 0.006 0.001 TYR A 711 ARG 0.009 0.000 ARG A 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 3) link_NAG-ASN : angle 0.56858 ( 9) link_BETA1-4 : bond 0.00508 ( 3) link_BETA1-4 : angle 3.11355 ( 9) hydrogen bonds : bond 0.27352 ( 432) hydrogen bonds : angle 9.33595 ( 1242) SS BOND : bond 0.00201 ( 14) SS BOND : angle 0.70327 ( 28) covalent geometry : bond 0.00323 ( 9198) covalent geometry : angle 0.48665 (12503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.329 Fit side-chains REVERT: A 805 MET cc_start: 0.9368 (mmt) cc_final: 0.9019 (mmm) outliers start: 4 outliers final: 3 residues processed: 89 average time/residue: 0.4633 time to fit residues: 58.3823 Evaluate side-chains 89 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 ASN A 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.182183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138838 restraints weight = 29695.650| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.05 r_work: 0.3236 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9218 Z= 0.180 Angle : 0.583 8.955 12549 Z= 0.311 Chirality : 0.040 0.184 1433 Planarity : 0.004 0.039 1558 Dihedral : 9.146 99.124 1512 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.73 % Allowed : 13.71 % Favored : 84.57 % 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: -0.47 (0.25), residues: 1092 helix: 0.14 (0.21), residues: 604 sheet: -1.11 (0.66), residues: 67 loop : -0.66 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 466 HIS 0.004 0.001 HIS A 954 PHE 0.021 0.001 PHE A 505 TYR 0.016 0.001 TYR A 711 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 0.85282 ( 9) link_BETA1-4 : bond 0.00443 ( 3) link_BETA1-4 : angle 2.21973 ( 9) hydrogen bonds : bond 0.06345 ( 432) hydrogen bonds : angle 6.21021 ( 1242) SS BOND : bond 0.00195 ( 14) SS BOND : angle 0.86321 ( 28) covalent geometry : bond 0.00396 ( 9198) covalent geometry : angle 0.57891 (12503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.464 Fit side-chains REVERT: A 25 MET cc_start: 0.6877 (tmm) cc_final: 0.6301 (tmm) REVERT: A 47 PHE cc_start: 0.5018 (OUTLIER) cc_final: 0.4502 (p90) REVERT: A 92 GLN cc_start: 0.7573 (tt0) cc_final: 0.7062 (tt0) REVERT: A 522 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: A 570 LEU cc_start: 0.8254 (tp) cc_final: 0.8044 (tt) REVERT: A 589 ILE cc_start: 0.8044 (mm) cc_final: 0.7590 (mt) REVERT: A 805 MET cc_start: 0.9179 (mmt) cc_final: 0.8822 (mmm) outliers start: 17 outliers final: 10 residues processed: 113 average time/residue: 0.4227 time to fit residues: 69.1002 Evaluate side-chains 103 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.183580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139138 restraints weight = 29519.215| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.08 r_work: 0.3310 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9218 Z= 0.122 Angle : 0.514 8.884 12549 Z= 0.266 Chirality : 0.038 0.178 1433 Planarity : 0.003 0.037 1558 Dihedral : 7.883 83.346 1510 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.93 % Allowed : 14.31 % Favored : 83.76 % 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: -0.37 (0.25), residues: 1092 helix: 0.27 (0.21), residues: 607 sheet: -1.19 (0.67), residues: 67 loop : -0.67 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.015 0.001 PHE A 569 TYR 0.012 0.001 TYR A 711 ARG 0.006 0.000 ARG A 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 3) link_NAG-ASN : angle 1.09362 ( 9) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.88755 ( 9) hydrogen bonds : bond 0.05404 ( 432) hydrogen bonds : angle 5.61261 ( 1242) SS BOND : bond 0.00288 ( 14) SS BOND : angle 0.86815 ( 28) covalent geometry : bond 0.00265 ( 9198) covalent geometry : angle 0.50998 (12503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6748 (tmm) cc_final: 0.6383 (tmm) REVERT: A 47 PHE cc_start: 0.5059 (OUTLIER) cc_final: 0.4547 (p90) REVERT: A 92 GLN cc_start: 0.7546 (tt0) cc_final: 0.6986 (tt0) REVERT: A 589 ILE cc_start: 0.8121 (mm) cc_final: 0.7725 (mt) REVERT: A 805 MET cc_start: 0.9116 (mmt) cc_final: 0.8714 (mmm) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 0.3774 time to fit residues: 62.4400 Evaluate side-chains 107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.180475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135973 restraints weight = 29706.274| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.00 r_work: 0.3319 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9218 Z= 0.190 Angle : 0.548 7.062 12549 Z= 0.288 Chirality : 0.040 0.190 1433 Planarity : 0.004 0.038 1558 Dihedral : 7.600 65.266 1510 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 2.54 % Allowed : 14.21 % Favored : 83.25 % 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: -0.59 (0.25), residues: 1092 helix: 0.14 (0.21), residues: 606 sheet: -1.40 (0.66), residues: 65 loop : -0.86 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 415 HIS 0.005 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.015 0.001 TYR A 857 ARG 0.002 0.000 ARG A 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 3) link_NAG-ASN : angle 0.93236 ( 9) link_BETA1-4 : bond 0.00365 ( 3) link_BETA1-4 : angle 1.95031 ( 9) hydrogen bonds : bond 0.04814 ( 432) hydrogen bonds : angle 5.41525 ( 1242) SS BOND : bond 0.00254 ( 14) SS BOND : angle 0.97400 ( 28) covalent geometry : bond 0.00439 ( 9198) covalent geometry : angle 0.54415 (12503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5097 (OUTLIER) cc_final: 0.4600 (p90) REVERT: A 589 ILE cc_start: 0.8131 (mm) cc_final: 0.7722 (mt) REVERT: A 778 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7487 (pp) REVERT: A 805 MET cc_start: 0.9134 (mmt) cc_final: 0.8734 (mmm) outliers start: 25 outliers final: 17 residues processed: 112 average time/residue: 0.4070 time to fit residues: 67.4460 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.183267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138740 restraints weight = 29916.104| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.03 r_work: 0.3344 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9218 Z= 0.126 Angle : 0.511 6.409 12549 Z= 0.264 Chirality : 0.038 0.182 1433 Planarity : 0.003 0.037 1558 Dihedral : 7.105 59.478 1510 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.13 % Allowed : 14.62 % Favored : 83.25 % 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 (0.25), residues: 1092 helix: 0.33 (0.21), residues: 607 sheet: -1.31 (0.67), residues: 65 loop : -0.73 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.019 0.001 PHE A 569 TYR 0.013 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 3) link_NAG-ASN : angle 0.90443 ( 9) link_BETA1-4 : bond 0.00346 ( 3) link_BETA1-4 : angle 1.86060 ( 9) hydrogen bonds : bond 0.04416 ( 432) hydrogen bonds : angle 5.21521 ( 1242) SS BOND : bond 0.00177 ( 14) SS BOND : angle 0.79615 ( 28) covalent geometry : bond 0.00285 ( 9198) covalent geometry : angle 0.50743 (12503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.295 Fit side-chains REVERT: A 47 PHE cc_start: 0.5087 (OUTLIER) cc_final: 0.4515 (p90) REVERT: A 89 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: A 140 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7264 (pp) REVERT: A 570 LEU cc_start: 0.8212 (tt) cc_final: 0.7988 (tp) REVERT: A 589 ILE cc_start: 0.8109 (mm) cc_final: 0.7690 (mt) REVERT: A 805 MET cc_start: 0.9150 (mmt) cc_final: 0.8752 (mmm) outliers start: 21 outliers final: 16 residues processed: 109 average time/residue: 0.3705 time to fit residues: 60.5038 Evaluate side-chains 105 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.182645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138277 restraints weight = 29623.870| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.02 r_work: 0.3344 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9218 Z= 0.126 Angle : 0.504 6.581 12549 Z= 0.262 Chirality : 0.038 0.176 1433 Planarity : 0.003 0.036 1558 Dihedral : 6.998 57.449 1510 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 2.34 % Allowed : 14.72 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1092 helix: 0.41 (0.21), residues: 606 sheet: -1.39 (0.67), residues: 65 loop : -0.69 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.020 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 3) link_NAG-ASN : angle 0.87140 ( 9) link_BETA1-4 : bond 0.00300 ( 3) link_BETA1-4 : angle 1.77722 ( 9) hydrogen bonds : bond 0.04163 ( 432) hydrogen bonds : angle 5.07173 ( 1242) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.79219 ( 28) covalent geometry : bond 0.00287 ( 9198) covalent geometry : angle 0.50063 (12503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.809 Fit side-chains REVERT: A 47 PHE cc_start: 0.5113 (OUTLIER) cc_final: 0.4554 (p90) REVERT: A 89 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7887 (mm-40) REVERT: A 140 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7242 (pp) REVERT: A 589 ILE cc_start: 0.8210 (mm) cc_final: 0.7730 (mt) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.3810 time to fit residues: 65.2094 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.182533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138167 restraints weight = 29475.122| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.01 r_work: 0.3345 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9218 Z= 0.131 Angle : 0.500 5.231 12549 Z= 0.261 Chirality : 0.038 0.181 1433 Planarity : 0.003 0.037 1558 Dihedral : 6.967 58.596 1510 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 2.34 % Allowed : 14.82 % Favored : 82.84 % 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: -0.20 (0.26), residues: 1092 helix: 0.50 (0.22), residues: 606 sheet: -1.50 (0.64), residues: 68 loop : -0.69 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 3) link_NAG-ASN : angle 0.90233 ( 9) link_BETA1-4 : bond 0.00345 ( 3) link_BETA1-4 : angle 1.74231 ( 9) hydrogen bonds : bond 0.04067 ( 432) hydrogen bonds : angle 4.97030 ( 1242) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.80503 ( 28) covalent geometry : bond 0.00302 ( 9198) covalent geometry : angle 0.49670 (12503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.495 Fit side-chains REVERT: A 47 PHE cc_start: 0.5118 (OUTLIER) cc_final: 0.4572 (p90) REVERT: A 89 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7884 (mm-40) REVERT: A 140 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7232 (pp) REVERT: A 421 PHE cc_start: 0.8201 (t80) cc_final: 0.7987 (t80) REVERT: A 570 LEU cc_start: 0.8232 (tp) cc_final: 0.8015 (tt) REVERT: A 589 ILE cc_start: 0.8103 (mm) cc_final: 0.7697 (mt) REVERT: A 778 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7442 (pp) outliers start: 23 outliers final: 16 residues processed: 113 average time/residue: 0.4211 time to fit residues: 73.6196 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.179807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134867 restraints weight = 29628.651| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.99 r_work: 0.3310 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9218 Z= 0.207 Angle : 0.549 5.650 12549 Z= 0.290 Chirality : 0.040 0.192 1433 Planarity : 0.004 0.040 1558 Dihedral : 7.174 56.907 1510 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.04 % Favored : 93.77 % Rotamer: Outliers : 2.23 % Allowed : 15.43 % Favored : 82.34 % 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: -0.46 (0.25), residues: 1092 helix: 0.31 (0.21), residues: 606 sheet: -1.71 (0.64), residues: 66 loop : -0.84 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.022 0.001 PHE A 569 TYR 0.017 0.001 TYR A 857 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 3) link_NAG-ASN : angle 0.99656 ( 9) link_BETA1-4 : bond 0.00275 ( 3) link_BETA1-4 : angle 1.79713 ( 9) hydrogen bonds : bond 0.04377 ( 432) hydrogen bonds : angle 5.06674 ( 1242) SS BOND : bond 0.00236 ( 14) SS BOND : angle 1.01011 ( 28) covalent geometry : bond 0.00488 ( 9198) covalent geometry : angle 0.54520 (12503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5175 (OUTLIER) cc_final: 0.4571 (p90) REVERT: A 89 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7837 (mm-40) REVERT: A 140 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6975 (pp) REVERT: A 570 LEU cc_start: 0.8296 (tp) cc_final: 0.8060 (tt) REVERT: A 589 ILE cc_start: 0.8118 (mm) cc_final: 0.7709 (mt) REVERT: A 778 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7431 (pp) outliers start: 22 outliers final: 17 residues processed: 112 average time/residue: 0.7642 time to fit residues: 135.5051 Evaluate side-chains 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.182433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137951 restraints weight = 29620.130| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.00 r_work: 0.3342 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9218 Z= 0.119 Angle : 0.497 5.302 12549 Z= 0.260 Chirality : 0.038 0.181 1433 Planarity : 0.003 0.039 1558 Dihedral : 6.941 57.620 1510 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 2.23 % Allowed : 15.43 % Favored : 82.34 % 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: -0.23 (0.26), residues: 1092 helix: 0.50 (0.22), residues: 606 sheet: -1.61 (0.64), residues: 68 loop : -0.72 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 3) link_NAG-ASN : angle 0.89443 ( 9) link_BETA1-4 : bond 0.00323 ( 3) link_BETA1-4 : angle 1.73389 ( 9) hydrogen bonds : bond 0.03961 ( 432) hydrogen bonds : angle 4.90881 ( 1242) SS BOND : bond 0.00160 ( 14) SS BOND : angle 0.77290 ( 28) covalent geometry : bond 0.00274 ( 9198) covalent geometry : angle 0.49405 (12503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.4571 (p90) REVERT: A 89 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: A 421 PHE cc_start: 0.8125 (t80) cc_final: 0.7908 (t80) REVERT: A 570 LEU cc_start: 0.8250 (tp) cc_final: 0.8025 (tt) REVERT: A 589 ILE cc_start: 0.8090 (mm) cc_final: 0.7678 (mt) REVERT: A 778 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7396 (pp) REVERT: A 805 MET cc_start: 0.9129 (mmt) cc_final: 0.8815 (mmt) outliers start: 22 outliers final: 16 residues processed: 112 average time/residue: 0.4451 time to fit residues: 72.0162 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.182119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137416 restraints weight = 29336.740| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.01 r_work: 0.3336 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9218 Z= 0.138 Angle : 0.509 5.205 12549 Z= 0.264 Chirality : 0.038 0.177 1433 Planarity : 0.003 0.041 1558 Dihedral : 6.935 57.533 1510 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.77 % Favored : 94.05 % Rotamer: Outliers : 1.83 % Allowed : 15.53 % Favored : 82.64 % 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 (0.26), residues: 1092 helix: 0.51 (0.22), residues: 607 sheet: -1.59 (0.64), residues: 68 loop : -0.71 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 3) link_NAG-ASN : angle 0.86964 ( 9) link_BETA1-4 : bond 0.00327 ( 3) link_BETA1-4 : angle 1.69904 ( 9) hydrogen bonds : bond 0.03955 ( 432) hydrogen bonds : angle 4.87983 ( 1242) SS BOND : bond 0.00168 ( 14) SS BOND : angle 0.83350 ( 28) covalent geometry : bond 0.00321 ( 9198) covalent geometry : angle 0.50567 (12503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5143 (OUTLIER) cc_final: 0.4529 (p90) REVERT: A 89 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7938 (mm-40) REVERT: A 570 LEU cc_start: 0.8274 (tp) cc_final: 0.8041 (tt) REVERT: A 589 ILE cc_start: 0.8098 (mm) cc_final: 0.7689 (mt) REVERT: A 778 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7430 (pp) REVERT: A 805 MET cc_start: 0.9137 (mmt) cc_final: 0.8816 (mmt) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 0.4322 time to fit residues: 68.5854 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.180980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136523 restraints weight = 29458.432| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.96 r_work: 0.3349 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 9218 Z= 0.126 Angle : 0.523 13.624 12549 Z= 0.274 Chirality : 0.038 0.175 1433 Planarity : 0.003 0.040 1558 Dihedral : 6.827 57.461 1509 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.31 % Favored : 94.41 % Rotamer: Outliers : 2.03 % Allowed : 15.74 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.15 (0.26), residues: 1092 helix: 0.58 (0.22), residues: 607 sheet: -1.54 (0.64), residues: 68 loop : -0.72 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 3) link_NAG-ASN : angle 0.88406 ( 9) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.67125 ( 9) hydrogen bonds : bond 0.03854 ( 432) hydrogen bonds : angle 4.82787 ( 1242) SS BOND : bond 0.00564 ( 14) SS BOND : angle 2.66164 ( 28) covalent geometry : bond 0.00293 ( 9198) covalent geometry : angle 0.50637 (12503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9871.87 seconds wall clock time: 173 minutes 22.93 seconds (10402.93 seconds total)