Starting phenix.real_space_refine on Sat Aug 23 15:30:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gui_34274/08_2025/8gui_34274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gui_34274/08_2025/8gui_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_2025/8gui_34274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2025/8gui_34274.map" model { file = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2025/8gui_34274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gui_34274/08_2025/8gui_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.25, per 1000 atoms: 0.24 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: 1.03 Conformation dependent library (CDL) restraints added in 385.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.10 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: 2.84 Time building geometry restraints manager: 1.35 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' DA I 131 " pdb=" O3' DA I 131 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.35e+00 bond pdb=" C3' DA I 41 " pdb=" O3' DA I 41 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 14175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 19490 1.28 - 2.57: 812 2.57 - 3.85: 63 3.85 - 5.13: 14 5.13 - 6.42: 7 Bond angle restraints: 20386 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C3' DA I 131 " pdb=" O3' DA I 131 " pdb=" P DG I 132 " ideal model delta sigma weight residual 120.20 123.60 -3.40 1.50e+00 4.44e-01 5.15e+00 angle pdb=" N MET K 927 " pdb=" CA MET K 927 " pdb=" C MET K 927 " ideal model delta sigma weight residual 114.64 111.22 3.42 1.52e+00 4.33e-01 5.07e+00 angle pdb=" C3' DA I 41 " pdb=" O3' DA I 41 " pdb=" P DC I 42 " ideal model delta sigma weight residual 120.20 123.49 -3.29 1.50e+00 4.44e-01 4.80e+00 angle pdb=" C4' DA I 41 " pdb=" C3' DA I 41 " pdb=" C2' DA I 41 " ideal model delta sigma weight residual 102.40 105.62 -3.22 1.50e+00 4.44e-01 4.60e+00 ... (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 - 0.037: 1709 0.037 - 0.075: 490 0.075 - 0.112: 84 0.112 - 0.149: 19 0.149 - 0.187: 3 Chirality restraints: 2305 Sorted by residual: 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=" CG LEU B 62 " pdb=" CB LEU B 62 " pdb=" CD1 LEU B 62 " pdb=" CD2 LEU B 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 0.046 14196 Z= 0.172 Angle : 0.611 15.036 20404 Z= 0.344 Chirality : 0.036 0.187 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 aren 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 covalent geometry : bond 0.00384 (14180) covalent geometry : angle 0.57575 (20386) hydrogen bonds : bond 0.10628 ( 831) hydrogen bonds : angle 3.72738 ( 2089) metal coordination : bond 0.01096 ( 16) metal coordination : angle 6.94348 ( 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 : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8140 (m-30) cc_final: 0.7825 (m-30) REVERT: C 73 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8668 (t160) REVERT: H 71 GLU cc_start: 0.7765 (tp30) cc_final: 0.7495 (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: 0.7467 time to fit residues: 165.4308 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 : 0.346 ------------------------------------------------------------------------------- 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: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.117889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.089545 restraints weight = 24960.690| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.42 r_work: 0.3236 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 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 = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14196 Z= 0.206 Angle : 0.631 17.082 20404 Z= 0.354 Chirality : 0.037 0.145 2305 Planarity : 0.005 0.084 1563 Dihedral : 31.202 176.676 4241 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.48 % Allowed : 13.43 % Favored : 84.09 % 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 aren not related in a simple way. whole: 2.02 (0.27), residues: 900 helix: 1.94 (0.21), residues: 605 sheet: None (None), residues: 0 loop : 0.17 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.022 0.002 TYR H 40 PHE 0.011 0.001 PHE A 78 HIS 0.008 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00463 (14180) covalent geometry : angle 0.59764 (20386) hydrogen bonds : bond 0.04288 ( 831) hydrogen bonds : angle 3.14653 ( 2089) metal coordination : bond 0.00635 ( 16) metal coordination : angle 6.89074 ( 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 210 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8584 (tt0) cc_final: 0.8369 (tt0) REVERT: C 73 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8679 (t0) REVERT: C 95 LYS cc_start: 0.9066 (ptmm) cc_final: 0.8845 (ttpp) REVERT: D 93 GLU cc_start: 0.8681 (mp0) cc_final: 0.8476 (mp0) REVERT: K 941 PHE cc_start: 0.9025 (m-80) cc_final: 0.8799 (m-80) REVERT: K 943 PHE cc_start: 0.8844 (t80) cc_final: 0.7340 (t80) REVERT: K 954 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8490 (tp40) REVERT: K 970 HIS cc_start: 0.8701 (p-80) cc_final: 0.8470 (p90) REVERT: L 982 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7465 (mmmt) REVERT: L 985 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: L 996 HIS cc_start: 0.7759 (t-90) cc_final: 0.7404 (t-90) outliers start: 19 outliers final: 7 residues processed: 194 average time/residue: 0.6906 time to fit residues: 142.8829 Evaluate side-chains 192 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN 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 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 936 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.114337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.086252 restraints weight = 23209.780| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.39 r_work: 0.3215 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14196 Z= 0.172 Angle : 0.597 15.246 20404 Z= 0.341 Chirality : 0.036 0.145 2305 Planarity : 0.004 0.055 1563 Dihedral : 31.020 173.885 4237 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.48 % Allowed : 15.38 % 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 aren not related in a simple way. whole: 2.14 (0.28), residues: 900 helix: 2.15 (0.20), residues: 609 sheet: -2.05 (1.52), residues: 10 loop : -0.02 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 975 TYR 0.020 0.001 TYR H 40 PHE 0.011 0.001 PHE A 78 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00380 (14180) covalent geometry : angle 0.57113 (20386) hydrogen bonds : bond 0.03875 ( 831) hydrogen bonds : angle 2.97727 ( 2089) metal coordination : bond 0.00545 ( 16) metal coordination : angle 5.88807 ( 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 209 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8673 (t0) REVERT: D 93 GLU cc_start: 0.8722 (mp0) cc_final: 0.8470 (mp0) REVERT: D 99 ARG cc_start: 0.8548 (mtt-85) cc_final: 0.8322 (mtt90) REVERT: E 59 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: E 81 ASP cc_start: 0.8036 (t0) cc_final: 0.7814 (t0) REVERT: E 122 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8717 (ptpp) REVERT: H 108 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8529 (tmtt) REVERT: K 928 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6928 (pmt100) REVERT: K 954 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8458 (tp40) REVERT: K 970 HIS cc_start: 0.8585 (p-80) cc_final: 0.8320 (p90) REVERT: L 985 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8425 (ttmm) outliers start: 19 outliers final: 9 residues processed: 197 average time/residue: 0.6489 time to fit residues: 136.3545 Evaluate side-chains 193 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN 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 122 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 928 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.114983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.086959 restraints weight = 23328.155| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.38 r_work: 0.3228 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14196 Z= 0.165 Angle : 0.588 12.922 20404 Z= 0.338 Chirality : 0.035 0.145 2305 Planarity : 0.004 0.056 1563 Dihedral : 30.984 174.225 4237 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.26 % Allowed : 16.30 % 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 aren not related in a simple way. whole: 2.31 (0.28), residues: 900 helix: 2.32 (0.20), residues: 603 sheet: -1.93 (1.54), residues: 10 loop : -0.02 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 971 TYR 0.022 0.001 TYR H 40 PHE 0.013 0.002 PHE L 995 HIS 0.007 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00365 (14180) covalent geometry : angle 0.56513 (20386) hydrogen bonds : bond 0.03748 ( 831) hydrogen bonds : angle 2.90904 ( 2089) metal coordination : bond 0.00538 ( 16) metal coordination : angle 5.46030 ( 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 211 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8715 (t0) REVERT: D 93 GLU cc_start: 0.8735 (mp0) cc_final: 0.8400 (mp0) REVERT: D 99 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.8335 (mtt90) REVERT: E 59 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: H 105 GLU cc_start: 0.7779 (tp30) cc_final: 0.7557 (tp30) REVERT: K 954 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8406 (tp40) REVERT: K 970 HIS cc_start: 0.8739 (p-80) cc_final: 0.8450 (p90) REVERT: L 982 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7836 (mmmm) REVERT: L 985 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8423 (ttmm) outliers start: 25 outliers final: 16 residues processed: 194 average time/residue: 0.7378 time to fit residues: 152.5280 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 : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 73 ASN Chi-restraints excluded: chain C residue 75 LYS 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 K residue 928 ARG Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.115222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.086968 restraints weight = 23110.362| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.39 r_work: 0.3229 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14196 Z= 0.166 Angle : 0.580 10.838 20404 Z= 0.338 Chirality : 0.035 0.146 2305 Planarity : 0.004 0.054 1563 Dihedral : 30.982 174.562 4237 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.74 % Allowed : 17.73 % Favored : 79.53 % 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 aren not related in a simple way. whole: 2.31 (0.28), residues: 900 helix: 2.35 (0.20), residues: 603 sheet: -2.28 (1.43), residues: 10 loop : -0.07 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 975 TYR 0.022 0.001 TYR H 40 PHE 0.013 0.001 PHE A 78 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00368 (14180) covalent geometry : angle 0.56791 (20386) hydrogen bonds : bond 0.03744 ( 831) hydrogen bonds : angle 2.88945 ( 2089) metal coordination : bond 0.00570 ( 16) metal coordination : angle 4.08134 ( 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 210 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8731 (t0) REVERT: E 59 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: G 92 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: K 931 ASP cc_start: 0.8781 (p0) cc_final: 0.8547 (p0) REVERT: K 938 PHE cc_start: 0.8299 (m-80) cc_final: 0.8012 (m-80) REVERT: K 954 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8417 (tp40) REVERT: K 970 HIS cc_start: 0.8722 (p-80) cc_final: 0.8418 (p90) REVERT: L 982 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7782 (mmmm) REVERT: L 985 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8413 (ttmm) REVERT: L 996 HIS cc_start: 0.8279 (t-90) cc_final: 0.8068 (t-90) outliers start: 21 outliers final: 14 residues processed: 196 average time/residue: 0.8103 time to fit residues: 168.6847 Evaluate side-chains 197 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN 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 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain K residue 928 ARG Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.0670 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 961 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.114663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086375 restraints weight = 22955.714| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.39 r_work: 0.3216 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14196 Z= 0.180 Angle : 0.601 15.517 20404 Z= 0.343 Chirality : 0.036 0.153 2305 Planarity : 0.004 0.053 1563 Dihedral : 31.036 174.776 4237 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.74 % Allowed : 18.38 % 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 aren not related in a simple way. whole: 2.27 (0.28), residues: 900 helix: 2.32 (0.21), residues: 603 sheet: -2.61 (1.31), residues: 10 loop : -0.07 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 955 TYR 0.024 0.001 TYR H 40 PHE 0.014 0.001 PHE A 78 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00402 (14180) covalent geometry : angle 0.58265 (20386) hydrogen bonds : bond 0.03831 ( 831) hydrogen bonds : angle 2.91031 ( 2089) metal coordination : bond 0.00805 ( 16) metal coordination : angle 5.04366 ( 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 200 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8096 (pp30) cc_final: 0.7719 (pp30) REVERT: C 73 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8749 (t160) REVERT: D 57 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8693 (mmtm) REVERT: D 99 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.8342 (mtt90) REVERT: E 59 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: H 34 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8350 (pmtt) REVERT: K 928 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7298 (pmt170) REVERT: K 938 PHE cc_start: 0.8225 (m-80) cc_final: 0.7684 (m-80) REVERT: K 954 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8312 (tp40) REVERT: K 955 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8468 (mtm110) REVERT: K 970 HIS cc_start: 0.8723 (p-80) cc_final: 0.8370 (p90) REVERT: L 996 HIS cc_start: 0.8152 (t-90) cc_final: 0.7662 (t-90) REVERT: L 997 ARG cc_start: 0.7619 (tmm160) cc_final: 0.7404 (tmm160) outliers start: 21 outliers final: 13 residues processed: 187 average time/residue: 0.6749 time to fit residues: 134.5427 Evaluate side-chains 192 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN 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 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain K residue 928 ARG Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 961 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.109530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080716 restraints weight = 22868.356| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.41 r_work: 0.3141 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14196 Z= 0.312 Angle : 0.674 14.541 20404 Z= 0.384 Chirality : 0.042 0.167 2305 Planarity : 0.005 0.053 1563 Dihedral : 31.569 175.090 4237 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.39 % Allowed : 17.99 % Favored : 78.62 % 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 aren not related in a simple way. whole: 1.87 (0.27), residues: 900 helix: 2.00 (0.20), residues: 602 sheet: -2.39 (1.27), residues: 10 loop : -0.22 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 971 TYR 0.027 0.002 TYR H 40 PHE 0.024 0.002 PHE A 78 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00710 (14180) covalent geometry : angle 0.65748 (20386) hydrogen bonds : bond 0.04839 ( 831) hydrogen bonds : angle 3.16622 ( 2089) metal coordination : bond 0.01273 ( 16) metal coordination : angle 5.06806 ( 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 207 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8751 (t0) REVERT: D 57 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8636 (mmtm) REVERT: E 59 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: E 133 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: H 34 LYS cc_start: 0.8618 (ptpp) cc_final: 0.8407 (pmtt) REVERT: H 85 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8724 (mptp) REVERT: K 950 TYR cc_start: 0.8742 (t80) cc_final: 0.8465 (t80) REVERT: K 954 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8444 (tp40) REVERT: K 970 HIS cc_start: 0.8742 (p-80) cc_final: 0.8348 (p90) REVERT: L 996 HIS cc_start: 0.8181 (t-90) cc_final: 0.7758 (t-90) outliers start: 26 outliers final: 14 residues processed: 190 average time/residue: 0.6856 time to fit residues: 138.7927 Evaluate side-chains 187 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 73 ASN 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 E residue 133 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain K residue 928 ARG Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 104 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 961 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 = 0.111878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083373 restraints weight = 22640.812| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.37 r_work: 0.3205 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14196 Z= 0.185 Angle : 0.655 19.466 20404 Z= 0.370 Chirality : 0.038 0.154 2305 Planarity : 0.006 0.102 1563 Dihedral : 31.534 173.719 4237 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.48 % Allowed : 20.21 % Favored : 77.31 % 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 aren not related in a simple way. whole: 1.97 (0.27), residues: 900 helix: 2.01 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 955 TYR 0.029 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 covalent geometry : bond 0.00410 (14180) covalent geometry : angle 0.62857 (20386) hydrogen bonds : bond 0.04190 ( 831) hydrogen bonds : angle 3.08728 ( 2089) metal coordination : bond 0.00960 ( 16) metal coordination : angle 6.19463 ( 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 195 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8215 (pp30) cc_final: 0.7991 (pp30) REVERT: C 73 ASN cc_start: 0.9164 (t0) cc_final: 0.8728 (t0) REVERT: D 57 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8591 (mmtm) REVERT: E 59 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: K 928 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7385 (pmt170) REVERT: K 950 TYR cc_start: 0.8697 (t80) cc_final: 0.8432 (t80) REVERT: K 954 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8402 (tp40) REVERT: K 970 HIS cc_start: 0.8720 (p-80) cc_final: 0.8322 (p90) REVERT: L 996 HIS cc_start: 0.8353 (t-90) cc_final: 0.7943 (t-90) outliers start: 19 outliers final: 12 residues processed: 182 average time/residue: 0.8073 time to fit residues: 156.4565 Evaluate side-chains 185 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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 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 928 ARG Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN K 961 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084676 restraints weight = 23051.638| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.38 r_work: 0.3230 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14196 Z= 0.189 Angle : 0.633 15.395 20404 Z= 0.361 Chirality : 0.037 0.150 2305 Planarity : 0.005 0.083 1563 Dihedral : 31.180 173.246 4235 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.22 % Allowed : 21.25 % Favored : 76.53 % 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 aren not related in a simple way. whole: 2.15 (0.28), residues: 900 helix: 2.17 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.10 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 955 TYR 0.026 0.002 TYR H 40 PHE 0.013 0.002 PHE E 67 HIS 0.005 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00425 (14180) covalent geometry : angle 0.61526 (20386) hydrogen bonds : bond 0.03912 ( 831) hydrogen bonds : angle 3.02037 ( 2089) metal coordination : bond 0.00917 ( 16) metal coordination : angle 5.10451 ( 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 191 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8207 (pp30) cc_final: 0.7901 (pp30) REVERT: B 92 ARG cc_start: 0.8910 (ptm160) cc_final: 0.8701 (ptm160) REVERT: C 73 ASN cc_start: 0.9161 (t0) cc_final: 0.8730 (t0) REVERT: D 57 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8604 (mmtm) REVERT: E 59 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: G 15 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8071 (tmtt) REVERT: K 950 TYR cc_start: 0.8668 (t80) cc_final: 0.8351 (t80) REVERT: K 954 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8401 (tp-100) REVERT: K 970 HIS cc_start: 0.8712 (p-80) cc_final: 0.8306 (p90) REVERT: L 996 HIS cc_start: 0.8231 (t-90) cc_final: 0.7849 (t-90) outliers start: 17 outliers final: 11 residues processed: 180 average time/residue: 0.8259 time to fit residues: 158.2304 Evaluate side-chains 183 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 84 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN K 961 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084762 restraints weight = 22923.320| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.40 r_work: 0.3234 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14196 Z= 0.193 Angle : 0.637 15.504 20404 Z= 0.362 Chirality : 0.037 0.186 2305 Planarity : 0.005 0.063 1563 Dihedral : 31.157 173.536 4235 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.83 % Allowed : 21.64 % Favored : 76.53 % 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 aren not related in a simple way. whole: 2.15 (0.28), residues: 900 helix: 2.18 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 955 TYR 0.031 0.002 TYR H 40 PHE 0.013 0.002 PHE E 67 HIS 0.005 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00435 (14180) covalent geometry : angle 0.61931 (20386) hydrogen bonds : bond 0.03933 ( 831) hydrogen bonds : angle 3.01851 ( 2089) metal coordination : bond 0.00842 ( 16) metal coordination : angle 5.12845 ( 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 184 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8237 (pp30) cc_final: 0.7925 (pp30) REVERT: C 73 ASN cc_start: 0.9175 (t0) cc_final: 0.8741 (t0) REVERT: D 57 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8605 (mmtm) REVERT: E 59 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: K 950 TYR cc_start: 0.8683 (t80) cc_final: 0.8371 (t80) REVERT: K 954 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8467 (tp40) REVERT: K 970 HIS cc_start: 0.8729 (p-80) cc_final: 0.8357 (p90) REVERT: L 996 HIS cc_start: 0.8254 (t-90) cc_final: 0.7888 (t-90) outliers start: 14 outliers final: 11 residues processed: 176 average time/residue: 0.7726 time to fit residues: 144.3735 Evaluate side-chains 180 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN 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 L residue 945 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN K 961 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.112911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.084325 restraints weight = 22959.817| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.40 r_work: 0.3225 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14196 Z= 0.206 Angle : 0.637 15.615 20404 Z= 0.363 Chirality : 0.037 0.151 2305 Planarity : 0.005 0.057 1563 Dihedral : 31.180 173.963 4235 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.22 % Allowed : 21.51 % Favored : 76.27 % 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 aren not related in a simple way. whole: 2.08 (0.28), residues: 900 helix: 2.14 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.17 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 955 TYR 0.032 0.002 TYR H 40 PHE 0.013 0.002 PHE E 67 HIS 0.005 0.001 HIS K 970 Details of bonding type rmsd covalent geometry : bond 0.00464 (14180) covalent geometry : angle 0.62016 (20386) hydrogen bonds : bond 0.04030 ( 831) hydrogen bonds : angle 3.04108 ( 2089) metal coordination : bond 0.00931 ( 16) metal coordination : angle 4.94183 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4560.86 seconds wall clock time: 78 minutes 7.02 seconds (4687.02 seconds total)