Starting phenix.real_space_refine on Thu Aug 6 02:24:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.map" model { file = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2026/8gui_34274.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 33 5.16 5 C 7467 2.51 5 N 2505 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s 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: 13348 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 862 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 590 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 595 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "K" 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} Chain: "L" 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 12430 SG CYS K 937 73.393 60.676 79.904 1.00109.17 S ATOM 12608 SG CYS K 957 74.505 58.912 76.711 1.00 98.43 S ATOM 12630 SG CYS K 960 74.436 57.059 79.742 1.00103.47 S ATOM 12316 SG CYS K 922 76.308 64.492 69.411 1.00129.40 S ATOM 12335 SG CYS K 925 77.446 65.863 66.094 1.00128.06 S ATOM 12475 SG CYS K 942 74.286 67.379 67.931 1.00117.74 S ATOM 12501 SG CYS K 945 74.011 64.345 66.214 1.00109.14 S ATOM 13024 SG CYS L 963 70.335 79.725 84.994 1.00140.01 S ATOM 13200 SG CYS L 983 72.002 82.530 86.878 1.00146.88 S ATOM 13222 SG CYS L 986 68.715 83.154 85.107 1.00146.57 S ATOM 12911 SG CYS L 948 81.094 80.332 87.061 1.00158.18 S ATOM 12930 SG CYS L 951 84.728 80.602 87.562 1.00158.61 S ATOM 13069 SG CYS L 968 82.695 77.429 89.070 1.00149.40 S ATOM 13095 SG CYS L 971 82.623 80.423 90.704 1.00149.73 S Time building chain proxies: 2.45, per 1000 atoms: 0.18 Number of scatterers: 13348 At special positions: 0 Unit cell: (115.5, 115.5, 120.75, 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 4 29.99 S 33 16.00 P 294 15.00 O 3045 8.00 N 2505 7.00 C 7467 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 252.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" ND1 HIS K 939 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 957 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 960 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 937 " pdb=" ZN K1002 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 945 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 942 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 922 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 925 " pdb=" ZN L1101 " pdb="ZN ZN L1101 " - pdb=" ND1 HIS L 965 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 983 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 963 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 986 " pdb=" ZN L1102 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 971 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 948 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 968 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 951 " Number of angles added : 18 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 66.1% alpha, 3.7% beta 147 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.519A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.602A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.661A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.181A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.645A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.742A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.698A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.234A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.557A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 905 through 920 removed outlier: 3.528A pdb=" N ILE K 913 " --> pdb=" O LEU K 909 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG K 919 " --> pdb=" O ASP K 915 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU K 920 " --> pdb=" O TYR K 916 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 952 Processing helix chain 'L' and resid 930 through 946 Processing helix chain 'L' and resid 968 through 978 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.555A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.257A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.025A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 940 through 941 Processing sheet with id=AB3, first strand: chain 'L' and resid 966 through 967 removed outlier: 3.550A pdb=" N HIS L 996 " --> pdb=" O VAL L 959 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2950 1.33 - 1.45: 4257 1.45 - 1.57: 6342 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 14180 Sorted by residual: bond pdb=" C3' DG J 137 " pdb=" C2' DG J 137 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA I 52 " pdb=" C2' DA I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 14175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 18577 1.28 - 2.57: 1593 2.57 - 3.85: 192 3.85 - 5.13: 17 5.13 - 6.42: 7 Bond angle restraints: 20386 Sorted by residual: angle pdb=" O4' DG I 100 " pdb=" C4' DG I 100 " pdb=" C3' DG I 100 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT J 17 " pdb=" C4 DT J 17 " pdb=" O4 DT J 17 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 117 " pdb=" C4 DT I 117 " pdb=" O4 DT I 117 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 24 " pdb=" C4 DT J 24 " pdb=" O4 DT J 24 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 20381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6402 35.66 - 71.33: 1375 71.33 - 106.99: 18 106.99 - 142.66: 1 142.66 - 178.32: 6 Dihedral angle restraints: 7802 sinusoidal: 5126 harmonic: 2676 Sorted by residual: dihedral pdb=" CA ARG L 954 " pdb=" C ARG L 954 " pdb=" N LYS L 955 " pdb=" CA LYS L 955 " ideal model delta harmonic sigma weight residual 180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual -140.00 38.32 -178.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " pdb=" P DG J 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.92 -173.92 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1548 0.040 - 0.081: 554 0.081 - 0.121: 182 0.121 - 0.162: 17 0.162 - 0.202: 4 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C3' DA I 41 " pdb=" C4' DA I 41 " pdb=" O3' DA I 41 " pdb=" C2' DA I 41 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C3' DA I 131 " pdb=" C4' DA I 131 " pdb=" O3' DA I 131 " pdb=" C2' DA I 131 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 2302 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 954 " 0.176 9.50e-02 1.11e+02 7.91e-02 3.92e+00 pdb=" NE ARG L 954 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG L 954 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG L 954 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 954 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO H 103 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 40 " -0.011 2.00e-02 2.50e+03 1.05e-02 2.22e+00 pdb=" CG TYR H 40 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR H 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 40 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 40 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 40 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 40 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 40 " 0.001 2.00e-02 2.50e+03 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 433 2.67 - 3.23: 11700 3.23 - 3.78: 26309 3.78 - 4.34: 33865 4.34 - 4.90: 47480 Nonbonded interactions: 119787 Sorted by model distance: nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 2.109 3.040 nonbonded pdb=" N2 DG I 132 " pdb=" O2 DC J 16 " model vdw 2.182 2.496 nonbonded pdb=" OE2 GLU D 105 " pdb=" OG1 THR K 952 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP F 68 " pdb=" NH2 ARG F 92 " model vdw 2.240 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.264 3.120 ... (remaining 119782 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 'A' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 9 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 through 120)) selection = (chain 'G' and (resid 9 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 98 or (resid 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 120)) } ncs_group { reference = (chain 'D' and resid 30 through 124) selection = (chain 'H' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 124)) } ncs_group { reference = (chain 'K' and (resid 906 through 909 or resid 911 through 914 or resid 916 thro \ ugh 926 or resid 928 through 946 or resid 949 through 950 or resid 953 through 9 \ 66 or resid 968 through 974 or resid 1001 through 1002)) selection = (chain 'L' and (resid 932 through 935 or resid 937 through 940 or resid 942 thro \ ugh 952 or resid 954 through 972 or resid 975 through 976 or resid 979 through 9 \ 92 or resid 994 through 1000 or resid 1101 through 1102)) } 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=0.27 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: 2.110 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 14196 Z= 0.495 Angle : 0.765 15.036 20404 Z= 0.645 Chirality : 0.045 0.202 2305 Planarity : 0.004 0.079 1563 Dihedral : 27.518 178.320 6072 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.74 % 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: 1.95 (0.28), residues: 900 helix: 1.94 (0.21), residues: 592 sheet: None (None), residues: 0 loop : 0.11 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.026 0.002 TYR H 40 PHE 0.010 0.001 PHE A 78 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.50 (14180) covalent geometry : angle 0.73654 / 0.64 (20386) hydrogen bonds : bond 0.10628 / 6.98 ( 831) hydrogen bonds : angle 3.72738 / 2.62 ( 2089) metal coordination : bond 0.01096 / 0.72 ( 16) metal coordination : angle 6.94348 / 4.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8140 (m-30) cc_final: 0.7826 (m-30) REVERT: C 73 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8668 (t160) REVERT: D 40 TYR cc_start: 0.8878 (m-80) cc_final: 0.8562 (m-80) REVERT: H 71 GLU cc_start: 0.7765 (tp30) cc_final: 0.7494 (mm-30) REVERT: K 938 PHE cc_start: 0.7614 (m-80) cc_final: 0.7114 (m-80) REVERT: K 943 PHE cc_start: 0.8515 (t80) cc_final: 0.7973 (t80) REVERT: K 955 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8073 (mtm110) outliers start: 1 outliers final: 2 residues processed: 208 average time/residue: 0.6536 time to fit residues: 145.3465 Evaluate side-chains 176 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain F residue 24 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.113004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.084868 restraints weight = 23029.433| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.37 r_work: 0.3192 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14196 Z= 0.189 Angle : 0.714 16.938 20404 Z= 0.396 Chirality : 0.048 0.364 2305 Planarity : 0.006 0.110 1563 Dihedral : 31.411 176.738 4241 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.35 % Allowed : 13.69 % Favored : 83.96 % 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: 1.89 (0.27), residues: 900 helix: 1.94 (0.20), residues: 597 sheet: -2.55 (1.54), residues: 10 loop : 0.06 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.023 0.002 TYR L 976 PHE 0.015 0.002 PHE A 78 HIS 0.009 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (14180) covalent geometry : angle 0.68343 / 0.39 (20386) hydrogen bonds : bond 0.05089 / 3.47 ( 831) hydrogen bonds : angle 3.29726 / 2.34 ( 2089) metal coordination : bond 0.00847 / 0.50 ( 16) metal coordination : angle 7.02638 / 4.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: D 93 GLU cc_start: 0.8708 (mp0) cc_final: 0.8474 (mp0) REVERT: K 943 PHE cc_start: 0.8772 (t80) cc_final: 0.8477 (t80) REVERT: L 982 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7518 (mmmt) REVERT: L 996 HIS cc_start: 0.7362 (t-90) cc_final: 0.7093 (t-90) outliers start: 18 outliers final: 6 residues processed: 192 average time/residue: 0.6809 time to fit residues: 139.9246 Evaluate side-chains 183 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.113064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085082 restraints weight = 23194.033| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.37 r_work: 0.3193 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14196 Z= 0.168 Angle : 0.680 14.075 20404 Z= 0.382 Chirality : 0.047 0.377 2305 Planarity : 0.005 0.077 1563 Dihedral : 31.423 175.173 4235 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.22 % Allowed : 15.65 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.03 (0.27), residues: 900 helix: 2.08 (0.20), residues: 599 sheet: -2.40 (1.53), residues: 10 loop : 0.01 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 971 TYR 0.018 0.002 TYR H 40 PHE 0.017 0.002 PHE K 941 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (14180) covalent geometry : angle 0.65599 / 0.38 (20386) hydrogen bonds : bond 0.04668 / 3.16 ( 831) hydrogen bonds : angle 3.16531 / 2.25 ( 2089) metal coordination : bond 0.00631 / 0.36 ( 16) metal coordination : angle 6.11704 / 3.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.294 Fit side-chains REVERT: D 93 GLU cc_start: 0.8674 (mp0) cc_final: 0.8462 (mp0) REVERT: E 59 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: K 943 PHE cc_start: 0.8822 (t80) cc_final: 0.7487 (t80) REVERT: K 954 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8429 (tp40) REVERT: L 976 TYR cc_start: 0.5994 (t80) cc_final: 0.5784 (t80) REVERT: L 985 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8453 (ttmm) outliers start: 17 outliers final: 7 residues processed: 190 average time/residue: 0.6222 time to fit residues: 126.5686 Evaluate side-chains 186 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 970 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088835 restraints weight = 24670.131| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.45 r_work: 0.3184 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14196 Z= 0.160 Angle : 0.673 13.084 20404 Z= 0.377 Chirality : 0.046 0.379 2305 Planarity : 0.005 0.061 1563 Dihedral : 31.463 173.298 4235 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.00 % Allowed : 16.56 % Favored : 80.44 % 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: 2.18 (0.27), residues: 900 helix: 2.13 (0.20), residues: 599 sheet: None (None), residues: 0 loop : 0.10 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG K 971 TYR 0.021 0.002 TYR H 40 PHE 0.026 0.002 PHE L 969 HIS 0.007 0.001 HIS L 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (14180) covalent geometry : angle 0.64865 / 0.38 (20386) hydrogen bonds : bond 0.04478 / 3.02 ( 831) hydrogen bonds : angle 3.10691 / 2.22 ( 2089) metal coordination : bond 0.00553 / 0.30 ( 16) metal coordination : angle 6.11267 / 3.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.9113 (ptmm) cc_final: 0.8762 (ttpt) REVERT: D 93 GLU cc_start: 0.8780 (mp0) cc_final: 0.8480 (mp0) REVERT: D 99 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.8378 (mtt90) REVERT: E 59 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: E 120 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7892 (mtt) REVERT: E 122 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8688 (ptpp) REVERT: G 39 TYR cc_start: 0.9157 (m-80) cc_final: 0.8889 (m-80) REVERT: H 71 GLU cc_start: 0.8529 (tp30) cc_final: 0.8261 (mm-30) REVERT: K 954 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8441 (tp40) REVERT: L 985 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8424 (ttmm) outliers start: 23 outliers final: 9 residues processed: 196 average time/residue: 0.6615 time to fit residues: 138.5795 Evaluate side-chains 189 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.112623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084157 restraints weight = 23225.096| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.41 r_work: 0.3171 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14196 Z= 0.176 Angle : 0.685 19.384 20404 Z= 0.378 Chirality : 0.046 0.386 2305 Planarity : 0.005 0.061 1563 Dihedral : 31.510 172.203 4235 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.87 % Allowed : 17.08 % Favored : 80.05 % 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: 2.14 (0.27), residues: 900 helix: 2.12 (0.20), residues: 602 sheet: None (None), residues: 0 loop : 0.00 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 973 TYR 0.021 0.002 TYR H 40 PHE 0.018 0.002 PHE A 78 HIS 0.005 0.001 HIS L 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 (14180) covalent geometry : angle 0.65192 / 0.38 (20386) hydrogen bonds : bond 0.04532 / 3.06 ( 831) hydrogen bonds : angle 3.10315 / 2.22 ( 2089) metal coordination : bond 0.01102 / 0.74 ( 16) metal coordination : angle 7.12356 / 4.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8959 (mtp-110) REVERT: D 93 GLU cc_start: 0.8785 (mp0) cc_final: 0.8457 (mp0) REVERT: D 99 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8355 (mtt90) REVERT: E 59 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: E 120 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7817 (mtt) REVERT: K 928 ARG cc_start: 0.7197 (pmt100) cc_final: 0.6848 (pmt170) REVERT: K 954 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8385 (tp40) REVERT: L 985 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8483 (ttmm) outliers start: 22 outliers final: 11 residues processed: 192 average time/residue: 0.6605 time to fit residues: 135.2797 Evaluate side-chains 195 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088610 restraints weight = 24941.528| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.46 r_work: 0.3220 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14196 Z= 0.159 Angle : 0.674 18.259 20404 Z= 0.375 Chirality : 0.046 0.385 2305 Planarity : 0.005 0.104 1563 Dihedral : 31.507 170.666 4235 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.26 % Allowed : 16.82 % Favored : 79.92 % 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: 2.10 (0.28), residues: 900 helix: 2.16 (0.20), residues: 603 sheet: -2.77 (1.48), residues: 10 loop : -0.06 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 955 TYR 0.023 0.002 TYR H 40 PHE 0.017 0.002 PHE L 969 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (14180) covalent geometry : angle 0.64698 / 0.37 (20386) hydrogen bonds : bond 0.04358 / 2.93 ( 831) hydrogen bonds : angle 3.07301 / 2.20 ( 2089) metal coordination : bond 0.00701 / 0.40 ( 16) metal coordination : angle 6.33609 / 3.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8948 (mtp-110) REVERT: C 95 LYS cc_start: 0.9174 (ptmm) cc_final: 0.8873 (ttpp) REVERT: D 93 GLU cc_start: 0.8780 (mp0) cc_final: 0.8461 (mp0) REVERT: D 99 ARG cc_start: 0.8602 (mtt-85) cc_final: 0.8383 (mtt90) REVERT: E 59 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: E 120 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7906 (mtt) REVERT: K 928 ARG cc_start: 0.7173 (pmt100) cc_final: 0.6917 (pmm-80) REVERT: K 938 PHE cc_start: 0.8259 (m-80) cc_final: 0.7678 (m-80) REVERT: K 954 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8404 (tp40) REVERT: L 985 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8442 (ttmm) REVERT: L 996 HIS cc_start: 0.8071 (t-90) cc_final: 0.7593 (t-90) outliers start: 25 outliers final: 16 residues processed: 189 average time/residue: 0.6692 time to fit residues: 135.1017 Evaluate side-chains 198 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 60 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.113316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.084794 restraints weight = 23188.697| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.41 r_work: 0.3221 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14196 Z= 0.158 Angle : 0.668 16.470 20404 Z= 0.374 Chirality : 0.046 0.384 2305 Planarity : 0.005 0.085 1563 Dihedral : 31.488 170.390 4235 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.52 % Allowed : 17.60 % Favored : 78.88 % 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: 2.15 (0.28), residues: 900 helix: 2.20 (0.20), residues: 603 sheet: -2.91 (1.45), residues: 10 loop : -0.05 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 955 TYR 0.023 0.002 TYR H 40 PHE 0.019 0.002 PHE L 969 HIS 0.004 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (14180) covalent geometry : angle 0.64506 / 0.37 (20386) hydrogen bonds : bond 0.04342 / 2.92 ( 831) hydrogen bonds : angle 3.07193 / 2.20 ( 2089) metal coordination : bond 0.00729 / 0.44 ( 16) metal coordination : angle 5.84340 / 3.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8109 (pp30) cc_final: 0.7845 (pp30) REVERT: C 95 LYS cc_start: 0.9189 (ptmm) cc_final: 0.8879 (ttpp) REVERT: D 93 GLU cc_start: 0.8807 (mp0) cc_final: 0.8478 (mp0) REVERT: D 99 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.8379 (mtt90) REVERT: E 59 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: E 120 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7859 (mtt) REVERT: H 108 LYS cc_start: 0.8684 (tmtt) cc_final: 0.8404 (ttmm) REVERT: K 938 PHE cc_start: 0.8308 (m-80) cc_final: 0.7867 (m-80) REVERT: K 954 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8436 (tp40) REVERT: L 985 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: L 996 HIS cc_start: 0.8312 (t-90) cc_final: 0.7960 (t-90) outliers start: 27 outliers final: 16 residues processed: 192 average time/residue: 0.6567 time to fit residues: 134.5608 Evaluate side-chains 201 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.110510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081810 restraints weight = 22932.875| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.40 r_work: 0.3159 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14196 Z= 0.239 Angle : 0.725 12.552 20404 Z= 0.400 Chirality : 0.049 0.407 2305 Planarity : 0.006 0.101 1563 Dihedral : 31.659 168.764 4235 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.65 % Allowed : 18.25 % Favored : 78.10 % 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: 1.88 (0.28), residues: 900 helix: 2.01 (0.20), residues: 601 sheet: -3.13 (1.32), residues: 10 loop : -0.19 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 955 TYR 0.028 0.002 TYR H 40 PHE 0.018 0.002 PHE L 969 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.24 (14180) covalent geometry : angle 0.70847 / 0.40 (20386) hydrogen bonds : bond 0.05245 / 3.55 ( 831) hydrogen bonds : angle 3.19828 / 2.28 ( 2089) metal coordination : bond 0.01202 / 0.70 ( 16) metal coordination : angle 5.15622 / 2.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9302 (mtpp) cc_final: 0.9096 (mtmm) REVERT: C 95 LYS cc_start: 0.9214 (ptmm) cc_final: 0.8904 (ttpp) REVERT: D 57 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8609 (mmtm) REVERT: D 93 GLU cc_start: 0.8854 (mp0) cc_final: 0.8416 (mp0) REVERT: D 99 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8354 (mtt90) REVERT: E 59 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: G 74 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8616 (mtmm) REVERT: H 108 LYS cc_start: 0.8762 (tmtt) cc_final: 0.8483 (ttmm) REVERT: K 928 ARG cc_start: 0.7202 (pmt100) cc_final: 0.6893 (pmt170) REVERT: K 938 PHE cc_start: 0.8303 (m-80) cc_final: 0.7920 (m-80) REVERT: K 954 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8474 (tp40) REVERT: L 985 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8380 (ttmm) REVERT: L 996 HIS cc_start: 0.8329 (t-90) cc_final: 0.7988 (t-90) outliers start: 28 outliers final: 16 residues processed: 188 average time/residue: 0.6663 time to fit residues: 133.5960 Evaluate side-chains 195 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain K residue 973 TYR Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.112036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083381 restraints weight = 23275.708| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.41 r_work: 0.3192 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14196 Z= 0.159 Angle : 0.695 12.750 20404 Z= 0.386 Chirality : 0.047 0.396 2305 Planarity : 0.005 0.079 1563 Dihedral : 31.649 169.717 4235 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.00 % Allowed : 19.95 % Favored : 77.05 % 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: 1.98 (0.28), residues: 900 helix: 2.08 (0.20), residues: 602 sheet: -3.07 (1.32), residues: 10 loop : -0.11 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG L 973 TYR 0.028 0.002 TYR H 40 PHE 0.018 0.002 PHE L 969 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (14180) covalent geometry : angle 0.67872 / 0.39 (20386) hydrogen bonds : bond 0.04486 / 3.01 ( 831) hydrogen bonds : angle 3.13702 / 2.24 ( 2089) metal coordination : bond 0.00946 / 0.55 ( 16) metal coordination : angle 5.03174 / 2.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.9191 (ptmm) cc_final: 0.8900 (ttpp) REVERT: D 93 GLU cc_start: 0.8817 (mp0) cc_final: 0.8416 (mp0) REVERT: D 99 ARG cc_start: 0.8548 (mtt-85) cc_final: 0.8324 (mtt90) REVERT: E 59 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: H 108 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8427 (ttmm) REVERT: K 938 PHE cc_start: 0.8282 (m-80) cc_final: 0.7927 (m-80) REVERT: K 954 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8452 (tp40) REVERT: L 985 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8392 (ttmm) REVERT: L 996 HIS cc_start: 0.8350 (t-90) cc_final: 0.8031 (t-90) outliers start: 23 outliers final: 16 residues processed: 185 average time/residue: 0.7163 time to fit residues: 141.0809 Evaluate side-chains 193 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 0.0000 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.112791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084196 restraints weight = 23187.362| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.41 r_work: 0.3171 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14196 Z= 0.156 Angle : 0.692 13.227 20404 Z= 0.385 Chirality : 0.047 0.392 2305 Planarity : 0.005 0.088 1563 Dihedral : 31.588 170.104 4235 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.74 % Allowed : 20.34 % Favored : 76.92 % 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: 2.07 (0.28), residues: 900 helix: 2.16 (0.20), residues: 602 sheet: -3.01 (1.29), residues: 10 loop : -0.11 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 955 TYR 0.029 0.002 TYR H 40 PHE 0.013 0.002 PHE A 67 HIS 0.007 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (14180) covalent geometry : angle 0.67449 / 0.38 (20386) hydrogen bonds : bond 0.04343 / 2.90 ( 831) hydrogen bonds : angle 3.11095 / 2.22 ( 2089) metal coordination : bond 0.00880 / 0.52 ( 16) metal coordination : angle 5.20171 / 2.75 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.9176 (ptmm) cc_final: 0.8891 (ttpp) REVERT: D 93 GLU cc_start: 0.8785 (mp0) cc_final: 0.8427 (mp0) REVERT: D 99 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8356 (mtt90) REVERT: E 59 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: H 108 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8464 (ttmm) REVERT: K 938 PHE cc_start: 0.8300 (m-80) cc_final: 0.8019 (m-80) REVERT: K 954 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8421 (tp40) REVERT: L 985 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: L 996 HIS cc_start: 0.8307 (t-90) cc_final: 0.8009 (t-90) outliers start: 21 outliers final: 16 residues processed: 185 average time/residue: 0.6494 time to fit residues: 128.1699 Evaluate side-chains 194 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 61 optimal weight: 0.0000 chunk 31 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.113306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084672 restraints weight = 23256.853| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.43 r_work: 0.3179 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14196 Z= 0.158 Angle : 0.691 14.016 20404 Z= 0.385 Chirality : 0.046 0.387 2305 Planarity : 0.005 0.084 1563 Dihedral : 31.531 170.339 4235 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.00 % Allowed : 20.21 % Favored : 76.79 % 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: 2.09 (0.28), residues: 900 helix: 2.17 (0.20), residues: 602 sheet: -3.04 (1.23), residues: 10 loop : -0.09 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 973 TYR 0.029 0.002 TYR H 40 PHE 0.012 0.001 PHE E 67 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (14180) covalent geometry : angle 0.67480 / 0.38 (20386) hydrogen bonds : bond 0.04290 / 2.88 ( 831) hydrogen bonds : angle 3.10143 / 2.22 ( 2089) metal coordination : bond 0.00874 / 0.54 ( 16) metal coordination : angle 5.05303 / 2.72 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4297.30 seconds wall clock time: 73 minutes 38.06 seconds (4418.06 seconds total)