Starting phenix.real_space_refine on Wed Aug 5 12:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibx_35348/08_2026/8ibx_35348.cif" } resolution = 3.74 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= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 108 5.49 5 S 38 5.16 5 C 5584 2.51 5 N 1815 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9502 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 7250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7250 Classifications: {'peptide': 922} Link IDs: {'PTRANS': 44, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 730 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 687 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 833 Classifications: {'RNAv2': 39} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain breaks: 2 Chain: "C" 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 31 SG CYS C 114 16.419 86.790 77.796 1.00120.15 S ATOM 57 SG CYS C 117 17.245 85.475 81.375 1.00125.02 S ATOM 5880 SG CYS C 934 54.317 47.378 120.733 1.00132.83 S ATOM 5906 SG CYS C 938 57.626 46.389 122.449 1.00138.77 S Time building chain proxies: 2.11, per 1000 atoms: 0.22 Number of scatterers: 9502 At special positions: 0 Unit cell: (106.496, 121.867, 136.14, 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 38 16.00 P 108 15.00 O 1955 8.00 N 1815 7.00 C 5584 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: 0.70 Conformation dependent library (CDL) restraints added in 193.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 135 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 130 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 114 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 117 " pdb=" ZN C1202 " pdb="ZN ZN C1202 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 934 " Number of angles added : 2 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 60.2% alpha, 7.2% beta 42 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 135 through 143 Processing helix chain 'C' and resid 153 through 172 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.871A pdb=" N GLY C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.574A pdb=" N LYS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.524A pdb=" N ALA C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 365 through 374 removed outlier: 3.538A pdb=" N ARG C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 413 through 420 removed outlier: 3.566A pdb=" N TRP C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.789A pdb=" N ARG C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 439 through 444' Processing helix chain 'C' and resid 458 through 462 removed outlier: 3.821A pdb=" N TYR C 462 " --> pdb=" O PRO C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.737A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 520 Processing helix chain 'C' and resid 532 through 537 removed outlier: 3.578A pdb=" N THR C 536 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 537 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 550 Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 606 removed outlier: 3.625A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 744 through 756 removed outlier: 3.508A pdb=" N ARG C 748 " --> pdb=" O HIS C 744 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS C 751 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 752 " --> pdb=" O ARG C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 779 Processing helix chain 'C' and resid 786 through 791 removed outlier: 4.229A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 817 Proline residue: C 808 - end of helix removed outlier: 4.327A pdb=" N GLY C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 831 Processing helix chain 'C' and resid 832 through 849 Processing helix chain 'C' and resid 861 through 872 Processing helix chain 'C' and resid 873 through 879 removed outlier: 3.562A pdb=" N ARG C 876 " --> pdb=" O VAL C 873 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU C 877 " --> pdb=" O ASP C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 889 removed outlier: 3.538A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 928 through 932 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 951 through 953 No H-bonds generated for 'chain 'C' and resid 951 through 953' Processing helix chain 'C' and resid 954 through 976 Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.855A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1045 Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1080 through 1085 removed outlier: 3.662A pdb=" N LEU C1084 " --> pdb=" O ARG C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1086 through 1105 Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.768A pdb=" N TRP C 112 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 465 through 467 removed outlier: 3.505A pdb=" N ILE C 467 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 446 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS C 445 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 626 Processing sheet with id=AA4, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AA5, first strand: chain 'C' and resid 668 through 671 removed outlier: 3.629A pdb=" N HIS C 678 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 686 through 687 Processing sheet with id=AA7, first strand: chain 'C' and resid 700 through 703 Processing sheet with id=AA8, first strand: chain 'C' and resid 851 through 852 removed outlier: 3.519A pdb=" N ARG C 851 " --> pdb=" O SER C 860 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 860 " --> pdb=" O ARG C 851 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 981 through 982 removed outlier: 3.797A pdb=" N GLU C 981 " --> pdb=" O ILE C 998 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 998 " --> pdb=" O GLU C 981 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY C1005 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR C1055 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 986 through 987 removed outlier: 4.484A pdb=" N LEU C 986 " --> pdb=" O ARG C 993 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 993 " --> pdb=" O LEU C 986 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 386 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2777 1.34 - 1.46: 2189 1.46 - 1.58: 4684 1.58 - 1.70: 211 1.70 - 1.82: 54 Bond restraints: 9915 Sorted by residual: bond pdb=" C1' DT A 28 " pdb=" N1 DT A 28 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" CA GLU C 575 " pdb=" C GLU C 575 " ideal model delta sigma weight residual 1.530 1.498 0.032 1.08e-02 8.57e+03 8.91e+00 bond pdb=" C3' DC B 42 " pdb=" C2' DC B 42 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.16e+00 bond pdb=" C3' DT B 35 " pdb=" O3' DT B 35 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 7.04e+00 bond pdb=" C3' DT B 36 " pdb=" O3' DT B 36 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.91e+00 ... (remaining 9910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 12897 1.21 - 2.43: 686 2.43 - 3.64: 238 3.64 - 4.86: 42 4.86 - 6.07: 10 Bond angle restraints: 13873 Sorted by residual: angle pdb=" N3 DT A 28 " pdb=" C4 DT A 28 " pdb=" O4 DT A 28 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT B 47 " pdb=" C4 DT B 47 " pdb=" O4 DT B 47 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT A 30 " pdb=" C4 DT A 30 " pdb=" O4 DT A 30 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT B 58 " pdb=" C4 DT B 58 " pdb=" O4 DT B 58 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT A 11 " pdb=" C4 DT A 11 " pdb=" O4 DT A 11 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 13868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 5206 35.16 - 70.32: 480 70.32 - 105.48: 23 105.48 - 140.64: 1 140.64 - 175.80: 2 Dihedral angle restraints: 5712 sinusoidal: 3080 harmonic: 2632 Sorted by residual: dihedral pdb=" C4' U D 129 " pdb=" C3' U D 129 " pdb=" C2' U D 129 " pdb=" C1' U D 129 " ideal model delta sinusoidal sigma weight residual 36.35 -36.65 72.99 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' G D 38 " pdb=" C3' G D 38 " pdb=" C2' G D 38 " pdb=" C1' G D 38 " ideal model delta sinusoidal sigma weight residual 36.35 -36.20 72.54 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" C4' A D 247 " pdb=" C3' A D 247 " pdb=" C2' A D 247 " pdb=" C1' A D 247 " ideal model delta sinusoidal sigma weight residual 36.34 -35.83 72.17 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 5709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1260 0.057 - 0.114: 173 0.114 - 0.171: 73 0.171 - 0.228: 23 0.228 - 0.285: 36 Chirality restraints: 1565 Sorted by residual: chirality pdb=" C2' U D 31 " pdb=" C3' U D 31 " pdb=" O2' U D 31 " pdb=" C1' U D 31 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' G D 244 " pdb=" C3' G D 244 " pdb=" O2' G D 244 " pdb=" C1' G D 244 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' G D 38 " pdb=" C3' G D 38 " pdb=" O2' G D 38 " pdb=" C1' G D 38 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1562 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 242 " -0.024 2.00e-02 2.50e+03 1.06e-02 3.08e+00 pdb=" N9 A D 242 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A D 242 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A D 242 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 242 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 242 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A D 242 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A D 242 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 242 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A D 242 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A D 242 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 669 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 670 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 670 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 670 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 593 " 0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 594 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 594 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 594 " 0.021 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 106 2.57 - 3.15: 8089 3.15 - 3.73: 16648 3.73 - 4.32: 20668 4.32 - 4.90: 32567 Nonbonded interactions: 78078 Sorted by model distance: nonbonded pdb=" OG SER C 175 " pdb=" OP2 DG A 8 " model vdw 1.982 3.040 nonbonded pdb=" NH1 ARG C 473 " pdb=" OP1 A D 247 " model vdw 2.080 3.120 nonbonded pdb=" OG SER C 406 " pdb=" OP1 A D 246 " model vdw 2.107 3.040 nonbonded pdb=" OD1 ASN C1028 " pdb=" N LYS C1029 " model vdw 2.128 3.120 nonbonded pdb=" NH1 ARG C 848 " pdb=" OP1 DT A 30 " model vdw 2.137 3.120 ... (remaining 78073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9922 Z= 0.317 Angle : 0.706 6.072 13875 Z= 0.455 Chirality : 0.064 0.285 1565 Planarity : 0.003 0.038 1402 Dihedral : 21.857 175.797 4014 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.81 % Favored : 94.97 % Rotamer: Outliers : 0.79 % Allowed : 25.13 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 914 helix: 1.57 (0.23), residues: 497 sheet: -0.68 (0.61), residues: 66 loop : -0.55 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 549 TYR 0.011 0.001 TYR C 628 PHE 0.010 0.001 PHE C 116 TRP 0.007 0.001 TRP C 701 HIS 0.003 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.32 ( 9915) covalent geometry : angle 0.70609 / 0.45 (13873) hydrogen bonds : bond 0.13936 / 9.66 ( 497) hydrogen bonds : angle 5.42580 / 4.02 ( 1323) metal coordination : bond 0.00619 / 0.39 ( 7) metal coordination : angle 1.02882 / 0.36 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 573 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7914 (m-40) outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 0.0735 time to fit residues: 7.2507 Evaluate side-chains 61 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 575 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 196 GLN C 694 GLN C1096 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.102179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.075521 restraints weight = 31406.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.077593 restraints weight = 17327.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.078874 restraints weight = 12458.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.079621 restraints weight = 10399.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080013 restraints weight = 9439.540| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9922 Z= 0.293 Angle : 0.893 18.340 13875 Z= 0.433 Chirality : 0.068 0.936 1565 Planarity : 0.005 0.040 1402 Dihedral : 22.089 178.942 2254 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 2.76 % Allowed : 23.55 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.28), residues: 914 helix: 1.29 (0.23), residues: 509 sheet: -0.76 (0.62), residues: 66 loop : -0.55 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 435 TYR 0.011 0.002 TYR C 628 PHE 0.017 0.002 PHE C 597 TRP 0.011 0.002 TRP C 777 HIS 0.006 0.002 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.29 ( 9915) covalent geometry : angle 0.89284 / 0.43 (13873) hydrogen bonds : bond 0.05386 / 3.77 ( 497) hydrogen bonds : angle 4.76532 / 3.48 ( 1323) metal coordination : bond 0.01241 / 0.83 ( 7) metal coordination : angle 2.41451 / 0.83 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 573 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8591 (m-40) outliers start: 21 outliers final: 14 residues processed: 73 average time/residue: 0.0699 time to fit residues: 7.9043 Evaluate side-chains 67 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 811 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 895 CYS Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.104493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.077967 restraints weight = 31155.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.080130 restraints weight = 16832.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081480 restraints weight = 11951.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082240 restraints weight = 9908.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.082689 restraints weight = 8985.631| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9922 Z= 0.155 Angle : 0.710 14.248 13875 Z= 0.353 Chirality : 0.053 0.645 1565 Planarity : 0.004 0.029 1402 Dihedral : 22.004 178.861 2251 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 3.16 % Allowed : 22.63 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.28), residues: 914 helix: 1.48 (0.23), residues: 509 sheet: -0.82 (0.62), residues: 66 loop : -0.55 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 547 TYR 0.010 0.002 TYR C 202 PHE 0.015 0.001 PHE C 116 TRP 0.010 0.001 TRP C 978 HIS 0.005 0.001 HIS C 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 ( 9915) covalent geometry : angle 0.70953 / 0.35 (13873) hydrogen bonds : bond 0.04384 / 3.05 ( 497) hydrogen bonds : angle 4.39863 / 3.19 ( 1323) metal coordination : bond 0.00984 / 0.59 ( 7) metal coordination : angle 2.73173 / 0.96 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: C 433 MET cc_start: 0.8826 (mmm) cc_final: 0.8579 (mmm) outliers start: 24 outliers final: 12 residues processed: 79 average time/residue: 0.0693 time to fit residues: 8.3707 Evaluate side-chains 68 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 811 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 0.0970 chunk 82 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 653 GLN C1098 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.104117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077606 restraints weight = 31431.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.079771 restraints weight = 16862.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.081119 restraints weight = 11951.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.081864 restraints weight = 9901.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082235 restraints weight = 8970.479| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9922 Z= 0.159 Angle : 0.690 10.336 13875 Z= 0.344 Chirality : 0.051 0.401 1565 Planarity : 0.004 0.027 1402 Dihedral : 21.920 177.992 2246 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 3.95 % Allowed : 22.63 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.29), residues: 914 helix: 1.65 (0.23), residues: 503 sheet: -0.81 (0.62), residues: 66 loop : -0.54 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1027 TYR 0.010 0.002 TYR C 202 PHE 0.013 0.001 PHE C 597 TRP 0.009 0.001 TRP C 978 HIS 0.004 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 9915) covalent geometry : angle 0.68932 / 0.34 (13873) hydrogen bonds : bond 0.04123 / 2.86 ( 497) hydrogen bonds : angle 4.27511 / 3.09 ( 1323) metal coordination : bond 0.00804 / 0.50 ( 7) metal coordination : angle 1.66046 / 0.57 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: C 433 MET cc_start: 0.8866 (mmm) cc_final: 0.8616 (mmm) REVERT: C 836 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8510 (ttp-110) outliers start: 30 outliers final: 24 residues processed: 82 average time/residue: 0.0799 time to fit residues: 9.9511 Evaluate side-chains 79 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 0.0050 chunk 69 optimal weight: 3.9990 overall best weight: 2.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.103039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.076166 restraints weight = 31075.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078293 restraints weight = 16941.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.079585 restraints weight = 12105.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.080354 restraints weight = 10093.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.080676 restraints weight = 9150.246| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9922 Z= 0.185 Angle : 0.698 13.854 13875 Z= 0.345 Chirality : 0.050 0.401 1565 Planarity : 0.004 0.027 1402 Dihedral : 21.923 177.963 2246 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 5.13 % Allowed : 22.37 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.91 (0.29), residues: 914 helix: 1.56 (0.23), residues: 509 sheet: -0.74 (0.63), residues: 66 loop : -0.52 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 547 TYR 0.011 0.002 TYR C 202 PHE 0.014 0.001 PHE C 597 TRP 0.008 0.001 TRP C 978 HIS 0.005 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 9915) covalent geometry : angle 0.69803 / 0.35 (13873) hydrogen bonds : bond 0.04159 / 2.88 ( 497) hydrogen bonds : angle 4.23500 / 3.06 ( 1323) metal coordination : bond 0.00959 / 0.59 ( 7) metal coordination : angle 1.71482 / 0.59 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 433 MET cc_start: 0.8896 (mmm) cc_final: 0.8693 (mmm) REVERT: C 836 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8500 (mtm-85) outliers start: 39 outliers final: 32 residues processed: 88 average time/residue: 0.0869 time to fit residues: 11.2225 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 811 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 895 CYS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1064 VAL Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.0970 chunk 78 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.105502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.079386 restraints weight = 31115.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.081540 restraints weight = 16794.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.082865 restraints weight = 11943.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.083639 restraints weight = 9936.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.084046 restraints weight = 9002.956| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9922 Z= 0.127 Angle : 0.660 9.178 13875 Z= 0.329 Chirality : 0.048 0.353 1565 Planarity : 0.004 0.043 1402 Dihedral : 21.834 176.214 2246 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % Rotamer: Outliers : 4.08 % Allowed : 23.29 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.29), residues: 914 helix: 1.69 (0.23), residues: 503 sheet: -0.66 (0.64), residues: 66 loop : -0.53 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 941 TYR 0.011 0.002 TYR C1070 PHE 0.011 0.001 PHE C 116 TRP 0.011 0.001 TRP C 978 HIS 0.004 0.001 HIS C 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 ( 9915) covalent geometry : angle 0.65967 / 0.33 (13873) hydrogen bonds : bond 0.03801 / 2.64 ( 497) hydrogen bonds : angle 4.14452 / 2.99 ( 1323) metal coordination : bond 0.00599 / 0.32 ( 7) metal coordination : angle 2.51238 / 0.87 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: C 186 PHE cc_start: 0.8897 (t80) cc_final: 0.8542 (t80) REVERT: C 575 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: C 836 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8446 (mtm-85) outliers start: 31 outliers final: 22 residues processed: 87 average time/residue: 0.0809 time to fit residues: 10.5185 Evaluate side-chains 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 40.0000 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.104209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.077874 restraints weight = 31116.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.080016 restraints weight = 16790.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081326 restraints weight = 11925.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.082111 restraints weight = 9892.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.082547 restraints weight = 8941.438| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9922 Z= 0.167 Angle : 0.687 10.283 13875 Z= 0.341 Chirality : 0.049 0.343 1565 Planarity : 0.004 0.046 1402 Dihedral : 21.851 175.935 2246 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 4.87 % Allowed : 23.82 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 914 helix: 1.74 (0.24), residues: 503 sheet: -0.68 (0.63), residues: 66 loop : -0.54 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 133 TYR 0.013 0.002 TYR C 202 PHE 0.013 0.001 PHE C 597 TRP 0.009 0.001 TRP C 978 HIS 0.005 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 9915) covalent geometry : angle 0.68605 / 0.34 (13873) hydrogen bonds : bond 0.03944 / 2.73 ( 497) hydrogen bonds : angle 4.16310 / 3.02 ( 1323) metal coordination : bond 0.00812 / 0.48 ( 7) metal coordination : angle 2.33231 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 575 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: C 836 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8442 (mtm-85) outliers start: 37 outliers final: 29 residues processed: 87 average time/residue: 0.0731 time to fit residues: 9.3119 Evaluate side-chains 86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 765 MET Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1064 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 50 optimal weight: 0.0870 chunk 94 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.105273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.079116 restraints weight = 30878.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081288 restraints weight = 16565.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.082631 restraints weight = 11694.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083407 restraints weight = 9661.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083870 restraints weight = 8738.357| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9922 Z= 0.128 Angle : 0.661 9.983 13875 Z= 0.330 Chirality : 0.048 0.321 1565 Planarity : 0.004 0.047 1402 Dihedral : 21.790 175.742 2245 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 4.47 % Allowed : 23.55 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 914 helix: 1.77 (0.23), residues: 503 sheet: -0.50 (0.64), residues: 66 loop : -0.56 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 133 TYR 0.014 0.002 TYR C1070 PHE 0.010 0.001 PHE C 597 TRP 0.012 0.001 TRP C 978 HIS 0.004 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 9915) covalent geometry : angle 0.66085 / 0.33 (13873) hydrogen bonds : bond 0.03760 / 2.62 ( 497) hydrogen bonds : angle 4.11493 / 2.98 ( 1323) metal coordination : bond 0.00597 / 0.32 ( 7) metal coordination : angle 2.26711 / 0.78 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 186 PHE cc_start: 0.8898 (t80) cc_final: 0.8504 (t80) REVERT: C 575 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: C 836 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8422 (mtm-85) outliers start: 34 outliers final: 27 residues processed: 87 average time/residue: 0.0688 time to fit residues: 9.0723 Evaluate side-chains 87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.103743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.077456 restraints weight = 31011.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.079566 restraints weight = 16837.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.080866 restraints weight = 11972.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.081615 restraints weight = 9941.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.081883 restraints weight = 9007.396| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9922 Z= 0.172 Angle : 0.685 10.173 13875 Z= 0.341 Chirality : 0.049 0.312 1565 Planarity : 0.004 0.030 1402 Dihedral : 21.806 176.716 2245 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 4.74 % Allowed : 23.29 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.29), residues: 914 helix: 1.82 (0.24), residues: 503 sheet: -0.49 (0.64), residues: 66 loop : -0.57 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1027 TYR 0.013 0.002 TYR C1070 PHE 0.015 0.001 PHE C 597 TRP 0.016 0.001 TRP C1099 HIS 0.006 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9915) covalent geometry : angle 0.68532 / 0.34 (13873) hydrogen bonds : bond 0.04000 / 2.76 ( 497) hydrogen bonds : angle 4.14306 / 3.00 ( 1323) metal coordination : bond 0.00846 / 0.52 ( 7) metal coordination : angle 1.36376 / 0.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 575 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: C 836 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8409 (mtm-85) outliers start: 36 outliers final: 31 residues processed: 86 average time/residue: 0.0783 time to fit residues: 9.7710 Evaluate side-chains 90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1064 VAL Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 96 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.101969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075267 restraints weight = 30619.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.077344 restraints weight = 16839.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.078596 restraints weight = 12109.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.079333 restraints weight = 10119.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.079510 restraints weight = 9191.111| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9922 Z= 0.219 Angle : 0.744 14.665 13875 Z= 0.366 Chirality : 0.051 0.342 1565 Planarity : 0.004 0.047 1402 Dihedral : 21.830 178.201 2245 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 4.74 % Allowed : 23.82 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.29), residues: 914 helix: 1.56 (0.23), residues: 510 sheet: -0.65 (0.64), residues: 67 loop : -0.62 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1027 TYR 0.012 0.002 TYR C1070 PHE 0.018 0.002 PHE C 597 TRP 0.009 0.001 TRP C 152 HIS 0.007 0.001 HIS C1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 9915) covalent geometry : angle 0.74391 / 0.37 (13873) hydrogen bonds : bond 0.04334 / 2.98 ( 497) hydrogen bonds : angle 4.26410 / 3.10 ( 1323) metal coordination : bond 0.01186 / 0.73 ( 7) metal coordination : angle 1.88469 / 0.69 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 57 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 561 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7850 (t-170) REVERT: C 575 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: C 836 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8436 (mtm-85) outliers start: 36 outliers final: 30 residues processed: 84 average time/residue: 0.0857 time to fit residues: 10.5240 Evaluate side-chains 86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1064 VAL Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.104016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.077593 restraints weight = 30408.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.079719 restraints weight = 16410.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.081036 restraints weight = 11645.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081804 restraints weight = 9658.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082158 restraints weight = 8740.801| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9922 Z= 0.130 Angle : 0.664 10.296 13875 Z= 0.331 Chirality : 0.048 0.312 1565 Planarity : 0.004 0.031 1402 Dihedral : 21.738 177.271 2245 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 3.68 % Allowed : 24.34 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.29), residues: 914 helix: 1.72 (0.23), residues: 504 sheet: -0.48 (0.65), residues: 67 loop : -0.64 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1027 TYR 0.015 0.002 TYR C1070 PHE 0.011 0.001 PHE C 597 TRP 0.014 0.001 TRP C 978 HIS 0.004 0.001 HIS C 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 9915) covalent geometry : angle 0.66328 / 0.33 (13873) hydrogen bonds : bond 0.03880 / 2.67 ( 497) hydrogen bonds : angle 4.14022 / 3.00 ( 1323) metal coordination : bond 0.00795 / 0.45 ( 7) metal coordination : angle 3.06747 / 1.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1435.50 seconds wall clock time: 25 minutes 24.27 seconds (1524.27 seconds total)