Starting phenix.real_space_refine on Thu Aug 6 07:06:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg1_43197/08_2026/8vg1_43197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg1_43197/08_2026/8vg1_43197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vg1_43197/08_2026/8vg1_43197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg1_43197/08_2026/8vg1_43197.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg1_43197/08_2026/8vg1_43197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg1_43197/08_2026/8vg1_43197.cif" } resolution = 2.48 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 1 6.06 5 P 342 5.49 5 S 27 5.16 5 C 8022 2.51 5 N 2688 2.21 5 O 3354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14434 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" 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: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} 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: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "T" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14039 SG CYS T 271 25.471 18.700 101.461 1.00183.13 S ATOM 14058 SG CYS T 274 24.780 19.674 105.145 1.00185.68 S ATOM 14201 SG CYS T 292 28.170 20.609 103.380 1.00170.07 S ATOM 14220 SG CYS T 295 27.451 17.231 104.344 1.00173.94 S Time building chain proxies: 2.65, per 1000 atoms: 0.18 Number of scatterers: 14434 At special positions: 0 Unit cell: (92.928, 122.496, 180.576, 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 1 29.99 S 27 16.00 P 342 15.00 O 3354 8.00 N 2688 7.00 C 8022 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: 1.11 Conformation dependent library (CDL) restraints added in 398.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 501 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 295 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 292 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 271 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 274 " Number of angles added : 6 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 66.6% alpha, 3.3% beta 171 base pairs and 317 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.967A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) 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: 3.739A 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: 3.657A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.308A 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 123 removed outlier: 3.624A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.573A 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: 3.955A 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 24 through 29 removed outlier: 3.585A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.720A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.527A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) 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 73 removed outlier: 4.276A 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: 3.729A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 186 removed outlier: 3.517A pdb=" N ALA O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.893A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 248 through 251 Processing helix chain 'T' and resid 292 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A 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: 6.646A 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: 7.137A 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 101 through 102 removed outlier: 6.729A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.136A 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: 7.091A 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 'O' and resid 191 through 192 removed outlier: 4.585A pdb=" N LEU O 191 " --> pdb=" O TRP O 244 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP O 244 " --> pdb=" O LEU O 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 283 through 284 450 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 317 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3009 1.33 - 1.45: 4676 1.45 - 1.57: 6991 1.57 - 1.69: 682 1.69 - 1.81: 43 Bond restraints: 15401 Sorted by residual: bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" C1' DT I 29 " pdb=" N1 DT I 29 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" C1' DC J 56 " pdb=" N1 DC J 56 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.18e+01 bond pdb=" C1' DT J 54 " pdb=" N1 DT J 54 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" C1' DC I 111 " pdb=" N1 DC I 111 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.99e+01 ... (remaining 15396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 19870 1.25 - 2.50: 1795 2.50 - 3.75: 544 3.75 - 5.01: 47 5.01 - 6.26: 5 Bond angle restraints: 22261 Sorted by residual: angle pdb=" O4' DA I 78 " pdb=" C1' DA I 78 " pdb=" N9 DA I 78 " ideal model delta sigma weight residual 108.00 111.32 -3.32 7.00e-01 2.04e+00 2.25e+01 angle pdb=" N3 DT I 71 " pdb=" C4 DT I 71 " pdb=" O4 DT I 71 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 121 " pdb=" C4 DT I 121 " pdb=" O4 DT I 121 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 123 " pdb=" C4 DT I 123 " pdb=" O4 DT I 123 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 153 " pdb=" C4 DT I 153 " pdb=" O4 DT I 153 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 22256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 6834 33.52 - 67.03: 1602 67.03 - 100.55: 31 100.55 - 134.07: 0 134.07 - 167.59: 2 Dihedral angle restraints: 8469 sinusoidal: 5771 harmonic: 2698 Sorted by residual: dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 52.41 167.59 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 63.87 156.13 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1696 0.039 - 0.079: 407 0.079 - 0.118: 137 0.118 - 0.158: 233 0.158 - 0.197: 34 Chirality restraints: 2507 Sorted by residual: chirality pdb=" C3' DT I 121 " pdb=" C4' DT I 121 " pdb=" O3' DT I 121 " pdb=" C2' DT I 121 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C3' DC I 111 " pdb=" C4' DC I 111 " pdb=" O3' DC I 111 " pdb=" C2' DC I 111 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C3' DA J 70 " pdb=" C4' DA J 70 " pdb=" O3' DA J 70 " pdb=" C2' DA J 70 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 2504 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO O 238 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " -0.035 2.00e-02 2.50e+03 1.45e-02 6.34e+00 pdb=" N9 DG I 131 " 0.031 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " 0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 138 " -0.027 2.00e-02 2.50e+03 1.16e-02 4.02e+00 pdb=" N9 DG I 138 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 138 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 138 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 138 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 138 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 138 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 138 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 138 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 138 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 138 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 138 " 0.008 2.00e-02 2.50e+03 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4211 2.86 - 3.37: 12501 3.37 - 3.88: 28858 3.88 - 4.39: 33533 4.39 - 4.90: 45718 Nonbonded interactions: 124821 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.351 3.040 nonbonded pdb=" OE2 GLU H 113 " pdb=" NH1 ARG T 320 " model vdw 2.371 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.375 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.377 3.040 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.407 3.120 ... (remaining 124816 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.270 Find NCS groups from input model: 0.080 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:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.007 0.073 15405 Z= 0.590 Angle : 0.831 8.079 22267 Z= 0.724 Chirality : 0.059 0.197 2507 Planarity : 0.005 0.064 1633 Dihedral : 26.205 167.585 6729 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.32 % Favored : 98.57 % Rotamer: Outliers : 0.51 % Allowed : 2.93 % Favored : 96.56 % 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: 2.20 (0.27), residues: 910 helix: 2.38 (0.21), residues: 588 sheet: -0.78 (1.29), residues: 12 loop : -0.25 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 49 TYR 0.010 0.001 TYR C 50 PHE 0.007 0.001 PHE F 61 TRP 0.014 0.001 TRP O 214 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.59 (15401) covalent geometry : angle 0.82772 / 0.72 (22261) hydrogen bonds : bond 0.09716 / 6.36 ( 867) hydrogen bonds : angle 3.37012 / 2.49 ( 2148) metal coordination : bond 0.01007 / 0.50 ( 4) metal coordination : angle 4.57506 / 2.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8408 (ttpt) REVERT: B 79 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8573 (mtmt) REVERT: C 99 ARG cc_start: 0.8284 (mmp80) cc_final: 0.7988 (mmm-85) REVERT: D 59 MET cc_start: 0.9329 (tpp) cc_final: 0.9115 (tpp) REVERT: D 105 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8321 (mm-30) REVERT: D 113 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8599 (mm-30) REVERT: E 79 LYS cc_start: 0.8704 (tttp) cc_final: 0.8479 (ttpt) REVERT: E 90 MET cc_start: 0.8888 (mmm) cc_final: 0.8667 (mmp) REVERT: G 41 GLU cc_start: 0.8520 (tt0) cc_final: 0.8239 (tt0) REVERT: G 95 LYS cc_start: 0.9240 (tmtm) cc_final: 0.9003 (tmtt) REVERT: H 37 TYR cc_start: 0.9482 (m-80) cc_final: 0.9217 (m-80) REVERT: H 47 GLN cc_start: 0.8712 (mt0) cc_final: 0.8420 (mt0) REVERT: H 59 MET cc_start: 0.9396 (tpp) cc_final: 0.9008 (tpp) REVERT: H 76 GLU cc_start: 0.8865 (tp30) cc_final: 0.8647 (tp30) REVERT: H 86 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.8222 (mmt90) REVERT: H 105 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8515 (mm-30) REVERT: H 108 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8233 (mttp) REVERT: O 181 MET cc_start: 0.8472 (tmm) cc_final: 0.8098 (ptt) REVERT: O 190 MET cc_start: 0.6002 (tpt) cc_final: 0.4846 (tpt) outliers start: 4 outliers final: 2 residues processed: 188 average time/residue: 0.7857 time to fit residues: 156.9781 Evaluate side-chains 163 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 63 ASN G 24 GLN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076450 restraints weight = 22521.471| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.54 r_work: 0.2760 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15405 Z= 0.215 Angle : 0.720 8.459 22267 Z= 0.412 Chirality : 0.050 0.291 2507 Planarity : 0.005 0.069 1633 Dihedral : 30.268 172.097 4863 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.32 % Favored : 98.57 % Rotamer: Outliers : 1.40 % Allowed : 10.33 % Favored : 88.27 % 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 are not related in a simple way. whole: 2.15 (0.27), residues: 910 helix: 2.23 (0.20), residues: 603 sheet: -1.73 (1.11), residues: 12 loop : -0.09 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 86 TYR 0.012 0.002 TYR F 51 PHE 0.008 0.002 PHE E 67 TRP 0.018 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (15401) covalent geometry : angle 0.71849 / 0.41 (22261) hydrogen bonds : bond 0.05406 / 3.56 ( 867) hydrogen bonds : angle 3.09527 / 2.24 ( 2148) metal coordination : bond 0.00711 / 0.35 ( 4) metal coordination : angle 3.02694 / 1.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8756 (mtmt) REVERT: C 99 ARG cc_start: 0.8519 (mmp80) cc_final: 0.8091 (mmm-85) REVERT: D 105 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8463 (mm-30) REVERT: E 90 MET cc_start: 0.8945 (mmm) cc_final: 0.8709 (mmt) REVERT: G 41 GLU cc_start: 0.8778 (tt0) cc_final: 0.8526 (tt0) REVERT: G 95 LYS cc_start: 0.9275 (tmtm) cc_final: 0.9035 (tmtt) REVERT: H 37 TYR cc_start: 0.9377 (m-80) cc_final: 0.9138 (m-80) REVERT: H 47 GLN cc_start: 0.8670 (mt0) cc_final: 0.8406 (mt0) REVERT: H 59 MET cc_start: 0.9286 (tpp) cc_final: 0.9032 (tpp) REVERT: H 83 TYR cc_start: 0.8873 (m-10) cc_final: 0.8645 (m-10) REVERT: H 86 ARG cc_start: 0.8626 (mmt-90) cc_final: 0.8270 (mmt90) REVERT: H 105 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8775 (mm-30) REVERT: H 108 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8278 (mttp) REVERT: O 190 MET cc_start: 0.6284 (tpt) cc_final: 0.4997 (tpt) outliers start: 11 outliers final: 4 residues processed: 166 average time/residue: 0.9186 time to fit residues: 161.7455 Evaluate side-chains 161 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 113 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN 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 = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077210 restraints weight = 22760.564| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.55 r_work: 0.2780 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15405 Z= 0.166 Angle : 0.669 7.729 22267 Z= 0.386 Chirality : 0.047 0.321 2507 Planarity : 0.004 0.070 1633 Dihedral : 30.563 166.180 4861 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.43 % Favored : 98.46 % Rotamer: Outliers : 1.66 % Allowed : 12.50 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.38 (0.27), residues: 910 helix: 2.40 (0.20), residues: 603 sheet: -1.55 (1.15), residues: 12 loop : -0.01 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 262 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE E 67 TRP 0.014 0.002 TRP O 214 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (15401) covalent geometry : angle 0.66746 / 0.39 (22261) hydrogen bonds : bond 0.04595 / 3.05 ( 867) hydrogen bonds : angle 2.91827 / 2.12 ( 2148) metal coordination : bond 0.00536 / 0.27 ( 4) metal coordination : angle 3.16180 / 1.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8743 (mtmt) REVERT: C 73 ASN cc_start: 0.8543 (m-40) cc_final: 0.8264 (t160) REVERT: C 99 ARG cc_start: 0.8517 (mmp80) cc_final: 0.8012 (mmm-85) REVERT: E 73 GLU cc_start: 0.9189 (tt0) cc_final: 0.8892 (tt0) REVERT: E 90 MET cc_start: 0.8965 (mmm) cc_final: 0.8724 (mmp) REVERT: F 25 ASN cc_start: 0.8770 (m110) cc_final: 0.8307 (m110) REVERT: G 95 LYS cc_start: 0.9285 (tmtm) cc_final: 0.9008 (tmtt) REVERT: H 33 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6992 (mtp-110) REVERT: H 37 TYR cc_start: 0.9368 (m-80) cc_final: 0.9138 (m-80) REVERT: H 47 GLN cc_start: 0.8673 (mt0) cc_final: 0.8423 (mt0) REVERT: H 59 MET cc_start: 0.9274 (tpp) cc_final: 0.9012 (tpp) REVERT: H 83 TYR cc_start: 0.8839 (m-10) cc_final: 0.8544 (m-10) REVERT: H 86 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.8276 (mmt90) REVERT: H 105 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8735 (mm-30) REVERT: H 108 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8242 (mttp) REVERT: O 190 MET cc_start: 0.6240 (tpt) cc_final: 0.4957 (tpt) REVERT: T 299 MET cc_start: 0.6772 (tpp) cc_final: 0.6540 (tmm) outliers start: 13 outliers final: 7 residues processed: 164 average time/residue: 0.9492 time to fit residues: 165.3171 Evaluate side-chains 164 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.126798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.076429 restraints weight = 22726.731| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.54 r_work: 0.2763 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15405 Z= 0.192 Angle : 0.679 7.925 22267 Z= 0.385 Chirality : 0.047 0.299 2507 Planarity : 0.005 0.071 1633 Dihedral : 30.687 159.813 4861 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.54 % Favored : 98.35 % Rotamer: Outliers : 1.53 % Allowed : 13.52 % Favored : 84.95 % 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: 2.40 (0.27), residues: 910 helix: 2.41 (0.20), residues: 602 sheet: -1.38 (1.30), residues: 12 loop : 0.03 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 262 TYR 0.012 0.001 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.014 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (15401) covalent geometry : angle 0.67731 / 0.38 (22261) hydrogen bonds : bond 0.04798 / 3.16 ( 867) hydrogen bonds : angle 2.92675 / 2.12 ( 2148) metal coordination : bond 0.00576 / 0.29 ( 4) metal coordination : angle 2.96159 / 1.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8736 (mtmt) REVERT: C 73 ASN cc_start: 0.8520 (m-40) cc_final: 0.8265 (t160) REVERT: C 99 ARG cc_start: 0.8582 (mmp80) cc_final: 0.8023 (mmm-85) REVERT: D 105 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8502 (mm-30) REVERT: E 73 GLU cc_start: 0.9206 (tt0) cc_final: 0.8966 (tt0) REVERT: E 90 MET cc_start: 0.8980 (mmm) cc_final: 0.8746 (mmt) REVERT: F 25 ASN cc_start: 0.8830 (m110) cc_final: 0.8426 (m110) REVERT: G 95 LYS cc_start: 0.9297 (tmtm) cc_final: 0.9045 (tmtt) REVERT: H 47 GLN cc_start: 0.8646 (mt0) cc_final: 0.8378 (mt0) REVERT: H 83 TYR cc_start: 0.8855 (m-10) cc_final: 0.8590 (m-10) REVERT: H 86 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.8295 (mmt90) REVERT: H 105 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8747 (mm-30) REVERT: H 108 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8269 (mttp) REVERT: O 190 MET cc_start: 0.6231 (tpt) cc_final: 0.4957 (tpt) REVERT: T 299 MET cc_start: 0.6793 (tpp) cc_final: 0.6552 (tmm) outliers start: 12 outliers final: 5 residues processed: 161 average time/residue: 0.8085 time to fit residues: 138.4372 Evaluate side-chains 158 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076904 restraints weight = 22700.347| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.54 r_work: 0.2777 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15405 Z= 0.151 Angle : 0.670 7.845 22267 Z= 0.380 Chirality : 0.046 0.299 2507 Planarity : 0.004 0.072 1633 Dihedral : 30.692 159.299 4861 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 1.53 % Allowed : 13.52 % Favored : 84.95 % 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: 2.49 (0.27), residues: 910 helix: 2.48 (0.21), residues: 602 sheet: -1.55 (1.29), residues: 12 loop : 0.06 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 208 TYR 0.011 0.001 TYR F 51 PHE 0.010 0.001 PHE E 67 TRP 0.013 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (15401) covalent geometry : angle 0.66836 / 0.38 (22261) hydrogen bonds : bond 0.04566 / 3.02 ( 867) hydrogen bonds : angle 2.90983 / 2.11 ( 2148) metal coordination : bond 0.00508 / 0.25 ( 4) metal coordination : angle 2.63566 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8744 (mtmt) REVERT: C 73 ASN cc_start: 0.8523 (m-40) cc_final: 0.8280 (t160) REVERT: C 99 ARG cc_start: 0.8568 (mmp80) cc_final: 0.8007 (mmm-85) REVERT: E 90 MET cc_start: 0.8982 (mmm) cc_final: 0.8758 (mmp) REVERT: G 95 LYS cc_start: 0.9295 (tmtm) cc_final: 0.9041 (tmtt) REVERT: H 33 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6985 (mtp-110) REVERT: H 47 GLN cc_start: 0.8653 (mt0) cc_final: 0.8395 (mt0) REVERT: H 83 TYR cc_start: 0.8849 (m-10) cc_final: 0.8581 (m-10) REVERT: H 86 ARG cc_start: 0.8642 (mmt-90) cc_final: 0.8298 (mmt90) REVERT: H 105 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8738 (mm-30) REVERT: H 108 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8266 (mttp) REVERT: O 190 MET cc_start: 0.6216 (tpt) cc_final: 0.4953 (tpt) REVERT: T 299 MET cc_start: 0.6786 (tpp) cc_final: 0.6549 (tmm) outliers start: 12 outliers final: 6 residues processed: 158 average time/residue: 0.8560 time to fit residues: 143.4533 Evaluate side-chains 163 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 106 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.126267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075815 restraints weight = 22573.923| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.53 r_work: 0.2754 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15405 Z= 0.192 Angle : 0.681 8.127 22267 Z= 0.382 Chirality : 0.047 0.251 2507 Planarity : 0.005 0.072 1633 Dihedral : 30.890 159.442 4861 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 12.63 % Favored : 84.95 % 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: 2.40 (0.27), residues: 910 helix: 2.40 (0.20), residues: 603 sheet: -1.72 (1.38), residues: 12 loop : 0.07 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.017 0.002 TYR B 88 PHE 0.010 0.001 PHE E 67 TRP 0.011 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (15401) covalent geometry : angle 0.67990 / 0.38 (22261) hydrogen bonds : bond 0.04876 / 3.23 ( 867) hydrogen bonds : angle 2.93630 / 2.14 ( 2148) metal coordination : bond 0.00622 / 0.31 ( 4) metal coordination : angle 2.91361 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8520 (mttm) REVERT: C 99 ARG cc_start: 0.8562 (mmp80) cc_final: 0.7942 (mmm-85) REVERT: D 105 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8528 (mm-30) REVERT: E 73 GLU cc_start: 0.9198 (tt0) cc_final: 0.8981 (tt0) REVERT: E 90 MET cc_start: 0.9015 (mmm) cc_final: 0.8752 (mmt) REVERT: F 92 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8312 (ttp80) REVERT: G 36 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8530 (mptm) REVERT: G 95 LYS cc_start: 0.9292 (tmtm) cc_final: 0.9016 (tmtt) REVERT: H 33 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6960 (mtp-110) REVERT: H 47 GLN cc_start: 0.8636 (mt0) cc_final: 0.8376 (mt0) REVERT: H 83 TYR cc_start: 0.8880 (m-10) cc_final: 0.8608 (m-10) REVERT: H 86 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.8315 (mmt90) REVERT: T 299 MET cc_start: 0.6817 (tpp) cc_final: 0.6579 (tmm) outliers start: 19 outliers final: 8 residues processed: 165 average time/residue: 0.9771 time to fit residues: 171.1012 Evaluate side-chains 164 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.0270 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN F 25 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076898 restraints weight = 22475.450| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.53 r_work: 0.2776 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 15405 Z= 0.133 Angle : 0.674 9.710 22267 Z= 0.378 Chirality : 0.046 0.251 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.884 159.252 4861 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.66 % Allowed : 14.29 % Favored : 84.06 % 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: 2.54 (0.28), residues: 910 helix: 2.50 (0.21), residues: 603 sheet: -1.65 (1.37), residues: 12 loop : 0.14 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 33 TYR 0.013 0.001 TYR B 88 PHE 0.011 0.001 PHE E 67 TRP 0.020 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (15401) covalent geometry : angle 0.67236 / 0.38 (22261) hydrogen bonds : bond 0.04399 / 2.91 ( 867) hydrogen bonds : angle 2.93079 / 2.13 ( 2148) metal coordination : bond 0.00489 / 0.24 ( 4) metal coordination : angle 2.54300 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8497 (mttm) REVERT: C 99 ARG cc_start: 0.8560 (mmp80) cc_final: 0.7929 (mmm-85) REVERT: D 105 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8549 (mm-30) REVERT: E 90 MET cc_start: 0.8981 (mmm) cc_final: 0.8770 (mmp) REVERT: F 92 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8284 (ttp80) REVERT: G 95 LYS cc_start: 0.9287 (tmtm) cc_final: 0.9015 (tmtt) REVERT: H 33 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6977 (mtp-110) REVERT: H 47 GLN cc_start: 0.8650 (mt0) cc_final: 0.8389 (mt0) REVERT: H 83 TYR cc_start: 0.8856 (m-10) cc_final: 0.8564 (m-10) REVERT: H 86 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8301 (mmt90) REVERT: H 108 LYS cc_start: 0.8583 (mtpm) cc_final: 0.8130 (mttp) REVERT: O 190 MET cc_start: 0.6406 (tpt) cc_final: 0.5271 (tpt) REVERT: T 299 MET cc_start: 0.6782 (tpp) cc_final: 0.6548 (tmm) outliers start: 13 outliers final: 8 residues processed: 160 average time/residue: 0.8948 time to fit residues: 152.2757 Evaluate side-chains 165 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 0.5980 chunk 74 optimal weight: 40.0000 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 114 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN 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 = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076811 restraints weight = 22480.308| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.54 r_work: 0.2773 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15405 Z= 0.144 Angle : 0.668 8.448 22267 Z= 0.375 Chirality : 0.046 0.249 2507 Planarity : 0.004 0.073 1633 Dihedral : 30.868 159.751 4861 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.79 % Allowed : 14.41 % Favored : 83.80 % 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: 2.54 (0.27), residues: 910 helix: 2.50 (0.21), residues: 603 sheet: -1.61 (1.39), residues: 12 loop : 0.14 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.014 0.001 TYR B 88 PHE 0.010 0.001 PHE E 67 TRP 0.017 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (15401) covalent geometry : angle 0.66639 / 0.38 (22261) hydrogen bonds : bond 0.04340 / 2.88 ( 867) hydrogen bonds : angle 2.91996 / 2.12 ( 2148) metal coordination : bond 0.00482 / 0.24 ( 4) metal coordination : angle 2.46674 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8486 (mttm) REVERT: C 99 ARG cc_start: 0.8555 (mmp80) cc_final: 0.7919 (mmm-85) REVERT: D 105 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8565 (mm-30) REVERT: E 90 MET cc_start: 0.8957 (mmm) cc_final: 0.8742 (mmp) REVERT: F 25 ASN cc_start: 0.8811 (m-40) cc_final: 0.8464 (m110) REVERT: F 92 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: G 95 LYS cc_start: 0.9295 (tmtm) cc_final: 0.9016 (tmtt) REVERT: H 33 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6964 (mtp-110) REVERT: H 47 GLN cc_start: 0.8647 (mt0) cc_final: 0.8384 (mt0) REVERT: H 83 TYR cc_start: 0.8847 (m-10) cc_final: 0.8545 (m-10) REVERT: H 86 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.8299 (mmt90) REVERT: H 108 LYS cc_start: 0.8585 (mtpm) cc_final: 0.8118 (mttp) REVERT: O 190 MET cc_start: 0.6424 (tpt) cc_final: 0.5335 (tpt) REVERT: T 299 MET cc_start: 0.6772 (tpp) cc_final: 0.6542 (tmm) outliers start: 14 outliers final: 10 residues processed: 161 average time/residue: 0.9200 time to fit residues: 157.4524 Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 90 optimal weight: 10.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN F 25 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075664 restraints weight = 22633.232| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.53 r_work: 0.2749 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15405 Z= 0.206 Angle : 0.696 10.523 22267 Z= 0.386 Chirality : 0.048 0.258 2507 Planarity : 0.005 0.072 1633 Dihedral : 30.961 159.836 4861 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 14.54 % Favored : 83.55 % 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: 2.35 (0.27), residues: 910 helix: 2.36 (0.20), residues: 603 sheet: -1.38 (1.48), residues: 12 loop : 0.04 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 33 TYR 0.017 0.002 TYR B 88 PHE 0.011 0.002 PHE O 204 TRP 0.011 0.001 TRP O 214 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (15401) covalent geometry : angle 0.69473 / 0.39 (22261) hydrogen bonds : bond 0.05022 / 3.32 ( 867) hydrogen bonds : angle 2.98018 / 2.16 ( 2148) metal coordination : bond 0.00640 / 0.32 ( 4) metal coordination : angle 2.70483 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8535 (mttm) REVERT: C 73 ASN cc_start: 0.8724 (t0) cc_final: 0.8520 (t160) REVERT: C 99 ARG cc_start: 0.8569 (mmp80) cc_final: 0.7973 (mmm-85) REVERT: D 105 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8562 (mm-30) REVERT: E 90 MET cc_start: 0.8992 (mmm) cc_final: 0.8744 (mmt) REVERT: F 92 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8297 (ttp80) REVERT: G 36 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8535 (mptm) REVERT: G 95 LYS cc_start: 0.9291 (tmtm) cc_final: 0.9016 (tmtt) REVERT: H 33 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6964 (mtp-110) REVERT: H 47 GLN cc_start: 0.8654 (mt0) cc_final: 0.8387 (mt0) REVERT: H 83 TYR cc_start: 0.8879 (m-10) cc_final: 0.8599 (m-10) REVERT: H 86 ARG cc_start: 0.8651 (mmt-90) cc_final: 0.8322 (mmt90) REVERT: H 108 LYS cc_start: 0.8653 (mtpm) cc_final: 0.8172 (mttp) REVERT: O 181 MET cc_start: 0.8595 (tmm) cc_final: 0.8186 (ptt) REVERT: O 190 MET cc_start: 0.6205 (tpt) cc_final: 0.5435 (tpt) outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 0.9592 time to fit residues: 161.8198 Evaluate side-chains 159 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 0.0070 chunk 104 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 overall best weight: 2.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN H 63 ASN 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 = 0.125265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074793 restraints weight = 22437.073| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.54 r_work: 0.2734 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15405 Z= 0.237 Angle : 0.722 9.896 22267 Z= 0.395 Chirality : 0.049 0.263 2507 Planarity : 0.005 0.072 1633 Dihedral : 31.138 159.965 4861 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.98 % Favored : 97.91 % Rotamer: Outliers : 1.79 % Allowed : 15.18 % Favored : 83.04 % 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: 2.19 (0.27), residues: 910 helix: 2.25 (0.20), residues: 603 sheet: -1.27 (1.50), residues: 12 loop : -0.07 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 33 TYR 0.017 0.002 TYR B 88 PHE 0.009 0.002 PHE A 67 TRP 0.010 0.002 TRP O 199 HIS 0.005 0.001 HIS T 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 (15401) covalent geometry : angle 0.72091 / 0.39 (22261) hydrogen bonds : bond 0.05177 / 3.44 ( 867) hydrogen bonds : angle 3.04861 / 2.22 ( 2148) metal coordination : bond 0.00884 / 0.44 ( 4) metal coordination : angle 2.44734 / 1.30 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8521 (mttm) REVERT: C 73 ASN cc_start: 0.8738 (t0) cc_final: 0.8537 (t160) REVERT: C 99 ARG cc_start: 0.8580 (mmp80) cc_final: 0.7975 (mmm-85) REVERT: D 105 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8504 (mm-30) REVERT: E 90 MET cc_start: 0.8987 (mmm) cc_final: 0.8736 (mmt) REVERT: F 92 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8296 (ttp80) REVERT: G 36 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8527 (mptm) REVERT: G 95 LYS cc_start: 0.9281 (tmtm) cc_final: 0.9020 (tmtt) REVERT: H 33 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.6968 (mtp-110) REVERT: H 47 GLN cc_start: 0.8579 (mt0) cc_final: 0.8320 (mt0) REVERT: H 83 TYR cc_start: 0.8858 (m-10) cc_final: 0.8555 (m-10) REVERT: H 86 ARG cc_start: 0.8657 (mmt-90) cc_final: 0.8334 (mmt90) REVERT: H 108 LYS cc_start: 0.8651 (mtpm) cc_final: 0.8169 (mttp) REVERT: O 181 MET cc_start: 0.8591 (tmm) cc_final: 0.8181 (ptt) REVERT: O 190 MET cc_start: 0.6249 (tpt) cc_final: 0.5144 (tpt) outliers start: 14 outliers final: 9 residues processed: 158 average time/residue: 0.9250 time to fit residues: 155.1093 Evaluate side-chains 164 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 216 ASN Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN F 25 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075316 restraints weight = 22583.496| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.54 r_work: 0.2745 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15405 Z= 0.175 Angle : 0.710 8.499 22267 Z= 0.390 Chirality : 0.047 0.263 2507 Planarity : 0.005 0.072 1633 Dihedral : 31.138 159.740 4861 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.98 % Favored : 97.91 % Rotamer: Outliers : 1.66 % Allowed : 15.56 % Favored : 82.78 % 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: 2.28 (0.27), residues: 910 helix: 2.33 (0.21), residues: 603 sheet: -1.28 (1.50), residues: 12 loop : -0.05 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.018 0.002 TYR B 88 PHE 0.010 0.002 PHE E 67 TRP 0.010 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (15401) covalent geometry : angle 0.70929 / 0.39 (22261) hydrogen bonds : bond 0.04935 / 3.28 ( 867) hydrogen bonds : angle 3.04110 / 2.22 ( 2148) metal coordination : bond 0.00653 / 0.32 ( 4) metal coordination : angle 2.51239 / 1.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6915.36 seconds wall clock time: 117 minutes 42.98 seconds (7062.98 seconds total)