Starting phenix.real_space_refine on Thu Mar 13 23:22:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ye4_10789/03_2025/6ye4_10789.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ye4_10789/03_2025/6ye4_10789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ye4_10789/03_2025/6ye4_10789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ye4_10789/03_2025/6ye4_10789.map" model { file = "/net/cci-nas-00/data/ceres_data/6ye4_10789/03_2025/6ye4_10789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ye4_10789/03_2025/6ye4_10789.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 25 5.16 5 C 5780 2.51 5 N 1645 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "B" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "C" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "D" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "E" Number of atoms: 1784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 236, 1776 Classifications: {'peptide': 236} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1792 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 10.82, per 1000 atoms: 1.18 Number of scatterers: 9140 At special positions: 0 Unit cell: (82.7, 82.7, 130.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 5 15.00 O 1685 8.00 N 1645 7.00 C 5780 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: 2.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.608A pdb=" N TYR A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 100 removed outlier: 4.515A pdb=" N SER A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 140 through 164 removed outlier: 3.800A pdb=" N GLY A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 199 Proline residue: A 178 - end of helix removed outlier: 3.643A pdb=" N SER A 199 " --> pdb=" O GLY A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 280 removed outlier: 4.316A pdb=" N VAL A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Proline residue: A 209 - end of helix Proline residue: A 227 - end of helix removed outlier: 4.530A pdb=" N HIS A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.589A pdb=" N TYR B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 100 removed outlier: 4.520A pdb=" N SER B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 120 through 135 Processing helix chain 'B' and resid 140 through 164 removed outlier: 3.779A pdb=" N GLY B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 199 Proline residue: B 178 - end of helix removed outlier: 3.640A pdb=" N SER B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 280 removed outlier: 4.328A pdb=" N VAL B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Proline residue: B 209 - end of helix Proline residue: B 227 - end of helix removed outlier: 4.412A pdb=" N HIS B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.583A pdb=" N TYR C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 100 removed outlier: 4.524A pdb=" N SER C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 140 through 164 removed outlier: 3.776A pdb=" N GLY C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 199 Proline residue: C 178 - end of helix removed outlier: 3.632A pdb=" N SER C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 280 removed outlier: 4.333A pdb=" N VAL C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Proline residue: C 209 - end of helix Proline residue: C 227 - end of helix removed outlier: 4.437A pdb=" N HIS C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 removed outlier: 3.602A pdb=" N TYR D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 100 removed outlier: 4.533A pdb=" N SER D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 120 through 135 Processing helix chain 'D' and resid 140 through 164 removed outlier: 3.799A pdb=" N GLY D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 199 Proline residue: D 178 - end of helix removed outlier: 3.630A pdb=" N SER D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 280 removed outlier: 4.336A pdb=" N VAL D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Proline residue: D 209 - end of helix Proline residue: D 227 - end of helix removed outlier: 4.516A pdb=" N HIS D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 55 removed outlier: 3.612A pdb=" N TYR E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 100 removed outlier: 4.519A pdb=" N SER E 83 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 94 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 120 through 135 Processing helix chain 'E' and resid 140 through 164 removed outlier: 3.779A pdb=" N GLY E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 199 Proline residue: E 178 - end of helix removed outlier: 3.626A pdb=" N SER E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 280 removed outlier: 4.326A pdb=" N VAL E 207 " --> pdb=" O ASN E 203 " (cutoff:3.500A) Proline residue: E 209 - end of helix Proline residue: E 227 - end of helix removed outlier: 4.418A pdb=" N HIS E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1505 1.29 - 1.41: 2321 1.41 - 1.54: 5343 1.54 - 1.66: 46 1.66 - 1.79: 50 Bond restraints: 9265 Sorted by residual: bond pdb=" CB VAL B 229 " pdb=" CG2 VAL B 229 " ideal model delta sigma weight residual 1.521 1.387 0.134 3.30e-02 9.18e+02 1.64e+01 bond pdb=" CB VAL E 229 " pdb=" CG2 VAL E 229 " ideal model delta sigma weight residual 1.521 1.388 0.133 3.30e-02 9.18e+02 1.63e+01 bond pdb=" CB VAL C 229 " pdb=" CG2 VAL C 229 " ideal model delta sigma weight residual 1.521 1.388 0.133 3.30e-02 9.18e+02 1.63e+01 bond pdb=" CB VAL D 229 " pdb=" CG2 VAL D 229 " ideal model delta sigma weight residual 1.521 1.389 0.132 3.30e-02 9.18e+02 1.60e+01 bond pdb=" CB VAL A 229 " pdb=" CG2 VAL A 229 " ideal model delta sigma weight residual 1.521 1.389 0.132 3.30e-02 9.18e+02 1.59e+01 ... (remaining 9260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 12039 3.90 - 7.81: 391 7.81 - 11.71: 57 11.71 - 15.61: 13 15.61 - 19.52: 5 Bond angle restraints: 12505 Sorted by residual: angle pdb=" O3P PGT B 301 " pdb=" P PGT B 301 " pdb=" O4P PGT B 301 " ideal model delta sigma weight residual 92.82 112.34 -19.52 3.00e+00 1.11e-01 4.23e+01 angle pdb=" O3P PGT A 301 " pdb=" P PGT A 301 " pdb=" O4P PGT A 301 " ideal model delta sigma weight residual 92.82 111.94 -19.12 3.00e+00 1.11e-01 4.06e+01 angle pdb=" O3P PGT D 301 " pdb=" P PGT D 301 " pdb=" O4P PGT D 301 " ideal model delta sigma weight residual 92.82 111.92 -19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" CA GLU B 137 " pdb=" CB GLU B 137 " pdb=" CG GLU B 137 " ideal model delta sigma weight residual 114.10 125.39 -11.29 2.00e+00 2.50e-01 3.18e+01 angle pdb=" CA GLU D 137 " pdb=" CB GLU D 137 " pdb=" CG GLU D 137 " ideal model delta sigma weight residual 114.10 125.35 -11.25 2.00e+00 2.50e-01 3.16e+01 ... (remaining 12500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 4844 15.81 - 31.63: 586 31.63 - 47.44: 141 47.44 - 63.26: 59 63.26 - 79.07: 5 Dihedral angle restraints: 5635 sinusoidal: 2265 harmonic: 3370 Sorted by residual: dihedral pdb=" N GLU B 137 " pdb=" C GLU B 137 " pdb=" CA GLU B 137 " pdb=" CB GLU B 137 " ideal model delta harmonic sigma weight residual 122.80 130.98 -8.18 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N GLU C 137 " pdb=" C GLU C 137 " pdb=" CA GLU C 137 " pdb=" CB GLU C 137 " ideal model delta harmonic sigma weight residual 122.80 130.97 -8.17 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CG ARG B 271 " pdb=" CD ARG B 271 " pdb=" NE ARG B 271 " pdb=" CZ ARG B 271 " ideal model delta sinusoidal sigma weight residual 90.00 134.45 -44.45 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 713 0.065 - 0.130: 449 0.130 - 0.195: 202 0.195 - 0.260: 65 0.260 - 0.325: 21 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CG LEU B 216 " pdb=" CB LEU B 216 " pdb=" CD1 LEU B 216 " pdb=" CD2 LEU B 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CG LEU D 216 " pdb=" CB LEU D 216 " pdb=" CD1 LEU D 216 " pdb=" CD2 LEU D 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU E 216 " pdb=" CB LEU E 216 " pdb=" CD1 LEU E 216 " pdb=" CD2 LEU E 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1447 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 255 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C LEU E 255 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU E 255 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU E 256 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 255 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C LEU A 255 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU A 255 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A 256 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 255 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C LEU D 255 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU D 255 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU D 256 " -0.024 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3333 2.88 - 3.38: 9023 3.38 - 3.89: 15032 3.89 - 4.39: 17315 4.39 - 4.90: 30078 Nonbonded interactions: 74781 Sorted by model distance: nonbonded pdb=" OD1 ASP A 248 " pdb=" NH1 ARG E 154 " model vdw 2.373 3.120 nonbonded pdb=" NH1 ARG B 154 " pdb=" OD1 ASP C 248 " model vdw 2.375 3.120 nonbonded pdb=" NH1 ARG D 154 " pdb=" OD1 ASP E 248 " model vdw 2.402 3.120 nonbonded pdb=" NH1 ARG C 154 " pdb=" OD1 ASP D 248 " model vdw 2.402 3.120 nonbonded pdb=" NH1 ARG A 154 " pdb=" OD1 ASP B 248 " model vdw 2.422 3.120 ... (remaining 74776 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.400 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 30.790 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.026 0.144 9265 Z= 1.753 Angle : 1.692 19.517 12505 Z= 0.828 Chirality : 0.103 0.325 1450 Planarity : 0.010 0.058 1605 Dihedral : 15.502 79.073 3465 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.18), residues: 1175 helix: -1.79 (0.11), residues: 1060 sheet: None (None), residues: 0 loop : -4.08 (0.44), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.006 TRP C 50 HIS 0.023 0.004 HIS D 242 PHE 0.041 0.008 PHE D 79 TYR 0.023 0.008 TYR C 53 ARG 0.016 0.002 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.940 Fit side-chains REVERT: A 52 MET cc_start: 0.8087 (mtp) cc_final: 0.7463 (mtt) REVERT: A 81 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8337 (tptt) REVERT: A 139 ASN cc_start: 0.7912 (m-40) cc_final: 0.7647 (p0) REVERT: B 81 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8376 (tttt) REVERT: C 81 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8355 (tttt) REVERT: C 126 ASN cc_start: 0.8013 (t0) cc_final: 0.7635 (m-40) REVERT: D 81 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8374 (tptt) REVERT: E 81 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8420 (tptt) REVERT: E 159 TYR cc_start: 0.8239 (t80) cc_final: 0.7969 (t80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1883 time to fit residues: 42.5200 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN B 191 ASN C 130 ASN D 130 ASN E 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110940 restraints weight = 40973.886| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.71 r_work: 0.2961 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9265 Z= 0.225 Angle : 0.526 6.528 12505 Z= 0.273 Chirality : 0.035 0.149 1450 Planarity : 0.005 0.036 1605 Dihedral : 11.626 74.502 1495 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.11 % Allowed : 12.00 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1175 helix: 0.95 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.82 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 50 HIS 0.003 0.001 HIS C 242 PHE 0.008 0.002 PHE B 179 TYR 0.009 0.002 TYR D 159 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.880 Fit side-chains REVERT: A 52 MET cc_start: 0.7307 (mtp) cc_final: 0.6642 (mtt) REVERT: A 81 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7672 (tptt) REVERT: A 96 GLN cc_start: 0.8702 (tt0) cc_final: 0.8452 (mt0) REVERT: A 133 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6470 (mt-10) REVERT: B 52 MET cc_start: 0.7503 (mtp) cc_final: 0.6709 (mtm) REVERT: B 81 LYS cc_start: 0.8324 (ttpp) cc_final: 0.7619 (tptt) REVERT: C 52 MET cc_start: 0.7329 (mtp) cc_final: 0.6518 (mtm) REVERT: C 81 LYS cc_start: 0.8444 (ttpp) cc_final: 0.7690 (tptt) REVERT: C 113 GLN cc_start: 0.8357 (tp40) cc_final: 0.8101 (tp40) REVERT: D 52 MET cc_start: 0.7432 (mtp) cc_final: 0.6747 (mtm) REVERT: D 81 LYS cc_start: 0.8404 (ttpp) cc_final: 0.7693 (tptt) REVERT: D 204 LEU cc_start: 0.7576 (tt) cc_final: 0.7218 (tt) REVERT: E 52 MET cc_start: 0.7371 (mtp) cc_final: 0.6763 (mtp) REVERT: E 81 LYS cc_start: 0.8484 (ttpp) cc_final: 0.7669 (tptt) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1869 time to fit residues: 30.1569 Evaluate side-chains 94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112673 restraints weight = 28057.293| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.13 r_work: 0.3000 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9265 Z= 0.212 Angle : 0.495 5.974 12505 Z= 0.259 Chirality : 0.035 0.141 1450 Planarity : 0.004 0.032 1605 Dihedral : 9.928 57.541 1495 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.67 % Allowed : 13.89 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1175 helix: 2.02 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.46 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 50 HIS 0.002 0.000 HIS C 242 PHE 0.007 0.001 PHE B 183 TYR 0.021 0.002 TYR A 159 ARG 0.003 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.103 Fit side-chains REVERT: A 52 MET cc_start: 0.7409 (mtp) cc_final: 0.6722 (mtt) REVERT: A 81 LYS cc_start: 0.8473 (ttpp) cc_final: 0.7695 (tptt) REVERT: A 96 GLN cc_start: 0.8692 (tt0) cc_final: 0.8445 (mt0) REVERT: A 133 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6465 (mt-10) REVERT: B 52 MET cc_start: 0.7506 (mtp) cc_final: 0.6752 (mtm) REVERT: B 81 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7617 (tptt) REVERT: C 52 MET cc_start: 0.7314 (mtp) cc_final: 0.6562 (mtm) REVERT: C 81 LYS cc_start: 0.8443 (ttpp) cc_final: 0.7682 (tptt) REVERT: C 113 GLN cc_start: 0.8388 (tp40) cc_final: 0.8131 (tp40) REVERT: D 52 MET cc_start: 0.7491 (mtp) cc_final: 0.6845 (mtm) REVERT: D 81 LYS cc_start: 0.8419 (ttpp) cc_final: 0.7662 (tptt) REVERT: D 126 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7357 (t0) REVERT: D 159 TYR cc_start: 0.7867 (t80) cc_final: 0.7636 (t80) REVERT: E 52 MET cc_start: 0.7366 (mtp) cc_final: 0.6726 (mtp) REVERT: E 81 LYS cc_start: 0.8454 (ttpp) cc_final: 0.7630 (tptt) REVERT: E 159 TYR cc_start: 0.7837 (t80) cc_final: 0.7507 (t80) outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.1924 time to fit residues: 26.9537 Evaluate side-chains 96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114255 restraints weight = 30023.862| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.25 r_work: 0.3025 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9265 Z= 0.162 Angle : 0.447 5.827 12505 Z= 0.232 Chirality : 0.034 0.124 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.742 51.023 1495 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.44 % Allowed : 14.78 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.25), residues: 1175 helix: 2.60 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.25 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 50 HIS 0.002 0.000 HIS D 242 PHE 0.005 0.001 PHE A 169 TYR 0.017 0.002 TYR B 159 ARG 0.001 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.895 Fit side-chains REVERT: A 52 MET cc_start: 0.7400 (mtp) cc_final: 0.6618 (mtm) REVERT: A 81 LYS cc_start: 0.8450 (ttpp) cc_final: 0.7796 (tptt) REVERT: A 96 GLN cc_start: 0.8661 (tt0) cc_final: 0.8455 (mt0) REVERT: A 159 TYR cc_start: 0.7900 (t80) cc_final: 0.7686 (t80) REVERT: B 52 MET cc_start: 0.7494 (mtp) cc_final: 0.6763 (mtm) REVERT: B 81 LYS cc_start: 0.8343 (ttpp) cc_final: 0.7654 (tptt) REVERT: C 52 MET cc_start: 0.7214 (mtp) cc_final: 0.6484 (mtm) REVERT: C 81 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7751 (tptt) REVERT: C 96 GLN cc_start: 0.8724 (mt0) cc_final: 0.8503 (mt0) REVERT: C 113 GLN cc_start: 0.8357 (tp40) cc_final: 0.8120 (tp40) REVERT: C 252 GLN cc_start: 0.8316 (tt0) cc_final: 0.7784 (tt0) REVERT: D 52 MET cc_start: 0.7452 (mtp) cc_final: 0.6804 (mtm) REVERT: D 81 LYS cc_start: 0.8398 (ttpp) cc_final: 0.7708 (tptt) REVERT: E 52 MET cc_start: 0.7346 (mtp) cc_final: 0.6629 (mtm) REVERT: E 81 LYS cc_start: 0.8434 (ttpp) cc_final: 0.7653 (tptt) REVERT: E 160 SER cc_start: 0.8792 (p) cc_final: 0.8500 (m) outliers start: 4 outliers final: 4 residues processed: 101 average time/residue: 0.1801 time to fit residues: 26.8717 Evaluate side-chains 93 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115358 restraints weight = 23268.876| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.83 r_work: 0.3046 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9265 Z= 0.180 Angle : 0.450 5.832 12505 Z= 0.233 Chirality : 0.034 0.118 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.644 52.985 1495 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.22 % Allowed : 14.67 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.25), residues: 1175 helix: 2.81 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.22 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 50 HIS 0.002 0.000 HIS E 242 PHE 0.006 0.001 PHE E 169 TYR 0.015 0.002 TYR D 159 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.090 Fit side-chains REVERT: A 52 MET cc_start: 0.7479 (mtp) cc_final: 0.6685 (mtm) REVERT: A 81 LYS cc_start: 0.8456 (ttpp) cc_final: 0.7743 (tptt) REVERT: A 96 GLN cc_start: 0.8641 (tt0) cc_final: 0.8419 (mt0) REVERT: B 52 MET cc_start: 0.7542 (mtp) cc_final: 0.6814 (mtm) REVERT: B 81 LYS cc_start: 0.8380 (ttpp) cc_final: 0.7688 (tptt) REVERT: B 159 TYR cc_start: 0.7751 (t80) cc_final: 0.7477 (t80) REVERT: C 52 MET cc_start: 0.7370 (mtp) cc_final: 0.6592 (mtm) REVERT: C 81 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7732 (tptt) REVERT: C 96 GLN cc_start: 0.8725 (mt0) cc_final: 0.8509 (mt0) REVERT: C 113 GLN cc_start: 0.8303 (tp40) cc_final: 0.8067 (tp40) REVERT: C 252 GLN cc_start: 0.8310 (tt0) cc_final: 0.7774 (tt0) REVERT: D 52 MET cc_start: 0.7512 (mtp) cc_final: 0.6846 (mtm) REVERT: D 81 LYS cc_start: 0.8407 (ttpp) cc_final: 0.7790 (tptt) REVERT: E 52 MET cc_start: 0.7428 (mtp) cc_final: 0.6756 (mtp) REVERT: E 81 LYS cc_start: 0.8442 (ttpp) cc_final: 0.7679 (tptt) REVERT: E 160 SER cc_start: 0.8760 (p) cc_final: 0.8526 (m) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 0.2335 time to fit residues: 33.3194 Evaluate side-chains 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112492 restraints weight = 32895.223| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.42 r_work: 0.2988 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9265 Z= 0.198 Angle : 0.453 5.865 12505 Z= 0.234 Chirality : 0.035 0.115 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.706 56.179 1495 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.78 % Allowed : 15.11 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.24), residues: 1175 helix: 2.87 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.21 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.002 0.000 HIS B 242 PHE 0.006 0.001 PHE B 183 TYR 0.015 0.002 TYR C 159 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.029 Fit side-chains REVERT: A 52 MET cc_start: 0.7442 (mtp) cc_final: 0.6628 (mtm) REVERT: A 81 LYS cc_start: 0.8500 (ttpp) cc_final: 0.7780 (tptt) REVERT: A 96 GLN cc_start: 0.8680 (tt0) cc_final: 0.8460 (mt0) REVERT: B 52 MET cc_start: 0.7520 (mtp) cc_final: 0.6754 (mtm) REVERT: B 81 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7670 (tptt) REVERT: B 159 TYR cc_start: 0.7815 (t80) cc_final: 0.7548 (t80) REVERT: C 52 MET cc_start: 0.7352 (mtp) cc_final: 0.6583 (mtm) REVERT: C 81 LYS cc_start: 0.8477 (ttpp) cc_final: 0.7745 (tptt) REVERT: C 113 GLN cc_start: 0.8297 (tp40) cc_final: 0.8069 (tp40) REVERT: C 252 GLN cc_start: 0.8352 (tt0) cc_final: 0.7814 (tt0) REVERT: D 52 MET cc_start: 0.7515 (mtp) cc_final: 0.6828 (mtm) REVERT: D 81 LYS cc_start: 0.8409 (ttpp) cc_final: 0.7778 (tptt) REVERT: D 113 GLN cc_start: 0.8295 (tp40) cc_final: 0.8054 (mm-40) REVERT: D 126 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7343 (t0) REVERT: E 52 MET cc_start: 0.7390 (mtp) cc_final: 0.6705 (mtp) REVERT: E 81 LYS cc_start: 0.8442 (ttpp) cc_final: 0.7684 (tptt) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.1884 time to fit residues: 25.8446 Evaluate side-chains 96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112825 restraints weight = 28879.135| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.16 r_work: 0.3006 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9265 Z= 0.202 Angle : 0.453 5.871 12505 Z= 0.234 Chirality : 0.035 0.114 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.766 59.196 1495 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.78 % Allowed : 15.44 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.24), residues: 1175 helix: 2.92 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.15 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.002 0.000 HIS B 242 PHE 0.006 0.001 PHE B 183 TYR 0.015 0.002 TYR A 159 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.970 Fit side-chains REVERT: A 52 MET cc_start: 0.7490 (mtp) cc_final: 0.6675 (mtm) REVERT: A 81 LYS cc_start: 0.8520 (ttpp) cc_final: 0.7812 (tptt) REVERT: A 96 GLN cc_start: 0.8707 (tt0) cc_final: 0.8476 (mt0) REVERT: B 52 MET cc_start: 0.7589 (mtp) cc_final: 0.6800 (mtm) REVERT: B 81 LYS cc_start: 0.8374 (ttpp) cc_final: 0.7696 (tptt) REVERT: B 159 TYR cc_start: 0.7859 (t80) cc_final: 0.7586 (t80) REVERT: C 52 MET cc_start: 0.7369 (mtp) cc_final: 0.6593 (mtm) REVERT: C 81 LYS cc_start: 0.8478 (ttpp) cc_final: 0.7762 (tptt) REVERT: C 113 GLN cc_start: 0.8289 (tp40) cc_final: 0.8061 (tp40) REVERT: C 252 GLN cc_start: 0.8327 (tt0) cc_final: 0.7782 (tt0) REVERT: D 52 MET cc_start: 0.7542 (mtp) cc_final: 0.6866 (mtm) REVERT: D 81 LYS cc_start: 0.8424 (ttpp) cc_final: 0.7799 (tptt) REVERT: D 113 GLN cc_start: 0.8370 (tp40) cc_final: 0.8131 (mm-40) REVERT: E 52 MET cc_start: 0.7346 (mtp) cc_final: 0.6708 (mtp) REVERT: E 81 LYS cc_start: 0.8456 (ttpp) cc_final: 0.7716 (tptt) outliers start: 7 outliers final: 7 residues processed: 91 average time/residue: 0.1862 time to fit residues: 24.9621 Evaluate side-chains 96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 10 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113954 restraints weight = 28588.635| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.19 r_work: 0.3005 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9265 Z= 0.177 Angle : 0.442 5.808 12505 Z= 0.229 Chirality : 0.034 0.112 1450 Planarity : 0.003 0.031 1605 Dihedral : 8.650 59.080 1495 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.00 % Allowed : 15.44 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.24), residues: 1175 helix: 3.04 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.07 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 75 HIS 0.002 0.000 HIS E 242 PHE 0.005 0.001 PHE A 169 TYR 0.020 0.002 TYR A 159 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.919 Fit side-chains REVERT: A 52 MET cc_start: 0.7367 (mtp) cc_final: 0.6586 (mtm) REVERT: A 81 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7856 (tptt) REVERT: A 96 GLN cc_start: 0.8683 (tt0) cc_final: 0.8476 (mt0) REVERT: B 52 MET cc_start: 0.7476 (mtp) cc_final: 0.6765 (mtm) REVERT: B 81 LYS cc_start: 0.8356 (ttpp) cc_final: 0.7616 (tptt) REVERT: B 159 TYR cc_start: 0.7837 (t80) cc_final: 0.7573 (t80) REVERT: C 52 MET cc_start: 0.7289 (mtp) cc_final: 0.6567 (mtm) REVERT: C 81 LYS cc_start: 0.8465 (ttpp) cc_final: 0.7742 (tptt) REVERT: C 113 GLN cc_start: 0.8262 (tp40) cc_final: 0.8042 (tp40) REVERT: C 252 GLN cc_start: 0.8327 (tt0) cc_final: 0.7789 (tt0) REVERT: D 52 MET cc_start: 0.7452 (mtp) cc_final: 0.6793 (mtm) REVERT: D 81 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7785 (tptt) REVERT: D 113 GLN cc_start: 0.8359 (tp40) cc_final: 0.8132 (mm-40) REVERT: E 52 MET cc_start: 0.7368 (mtp) cc_final: 0.6687 (mtp) REVERT: E 81 LYS cc_start: 0.8415 (ttpp) cc_final: 0.7673 (tptt) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.2021 time to fit residues: 27.3251 Evaluate side-chains 96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114518 restraints weight = 25952.133| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.03 r_work: 0.3027 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9265 Z= 0.181 Angle : 0.440 5.809 12505 Z= 0.229 Chirality : 0.034 0.112 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.636 59.919 1495 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.11 % Allowed : 15.44 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.24), residues: 1175 helix: 3.08 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.03 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 75 HIS 0.002 0.000 HIS B 242 PHE 0.006 0.001 PHE A 169 TYR 0.034 0.002 TYR E 159 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 3.053 Fit side-chains REVERT: A 52 MET cc_start: 0.7390 (mtp) cc_final: 0.6602 (mtm) REVERT: A 81 LYS cc_start: 0.8499 (ttpp) cc_final: 0.7809 (tptt) REVERT: A 96 GLN cc_start: 0.8694 (tt0) cc_final: 0.8491 (mt0) REVERT: B 52 MET cc_start: 0.7551 (mtp) cc_final: 0.6836 (mtm) REVERT: B 81 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7627 (tptt) REVERT: B 159 TYR cc_start: 0.7856 (t80) cc_final: 0.7597 (t80) REVERT: C 52 MET cc_start: 0.7326 (mtp) cc_final: 0.6600 (mtm) REVERT: C 81 LYS cc_start: 0.8482 (ttpp) cc_final: 0.7768 (tptt) REVERT: C 113 GLN cc_start: 0.8221 (tp40) cc_final: 0.8016 (tp40) REVERT: C 252 GLN cc_start: 0.8327 (tt0) cc_final: 0.7790 (tt0) REVERT: D 52 MET cc_start: 0.7486 (mtp) cc_final: 0.6830 (mtm) REVERT: D 81 LYS cc_start: 0.8412 (ttpp) cc_final: 0.7805 (tptt) REVERT: D 113 GLN cc_start: 0.8333 (tp40) cc_final: 0.8098 (mm-40) REVERT: E 52 MET cc_start: 0.7385 (mtp) cc_final: 0.6703 (mtp) REVERT: E 81 LYS cc_start: 0.8433 (ttpp) cc_final: 0.7715 (tptt) outliers start: 10 outliers final: 10 residues processed: 90 average time/residue: 0.2854 time to fit residues: 38.2116 Evaluate side-chains 100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 1 optimal weight: 0.0000 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115516 restraints weight = 25310.758| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.98 r_work: 0.3046 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9265 Z= 0.163 Angle : 0.430 5.765 12505 Z= 0.224 Chirality : 0.034 0.111 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.514 58.699 1495 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.22 % Allowed : 15.33 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.24), residues: 1175 helix: 3.17 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -2.97 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 75 HIS 0.002 0.000 HIS D 242 PHE 0.005 0.001 PHE A 169 TYR 0.037 0.002 TYR E 159 ARG 0.001 0.000 ARG D 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.961 Fit side-chains REVERT: A 52 MET cc_start: 0.7349 (mtp) cc_final: 0.6578 (mtm) REVERT: A 81 LYS cc_start: 0.8469 (ttpp) cc_final: 0.7826 (tptt) REVERT: B 52 MET cc_start: 0.7482 (mtp) cc_final: 0.6789 (mtm) REVERT: B 81 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7606 (tptt) REVERT: B 159 TYR cc_start: 0.7797 (t80) cc_final: 0.7542 (t80) REVERT: B 204 LEU cc_start: 0.7634 (tt) cc_final: 0.7297 (tt) REVERT: C 52 MET cc_start: 0.7274 (mtp) cc_final: 0.6560 (mtm) REVERT: C 81 LYS cc_start: 0.8445 (ttpp) cc_final: 0.7733 (tptt) REVERT: C 113 GLN cc_start: 0.8204 (tp40) cc_final: 0.7994 (tp40) REVERT: C 252 GLN cc_start: 0.8298 (tt0) cc_final: 0.7760 (tt0) REVERT: D 52 MET cc_start: 0.7423 (mtp) cc_final: 0.6796 (mtm) REVERT: D 81 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7770 (tptt) REVERT: D 113 GLN cc_start: 0.8320 (tp40) cc_final: 0.8100 (mm-40) REVERT: D 126 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7313 (t0) REVERT: D 252 GLN cc_start: 0.8289 (tt0) cc_final: 0.7810 (tt0) REVERT: E 52 MET cc_start: 0.7329 (mtp) cc_final: 0.6665 (mtp) REVERT: E 81 LYS cc_start: 0.8390 (ttpp) cc_final: 0.7750 (tptt) outliers start: 11 outliers final: 10 residues processed: 99 average time/residue: 0.1822 time to fit residues: 26.6543 Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 92 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114164 restraints weight = 31297.784| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.31 r_work: 0.3022 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9265 Z= 0.167 Angle : 0.441 8.742 12505 Z= 0.227 Chirality : 0.034 0.111 1450 Planarity : 0.003 0.030 1605 Dihedral : 8.488 57.879 1495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.22 % Allowed : 15.78 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.24), residues: 1175 helix: 3.21 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -3.00 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 75 HIS 0.002 0.000 HIS C 198 PHE 0.005 0.001 PHE A 169 TYR 0.037 0.002 TYR E 159 ARG 0.001 0.000 ARG D 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.69 seconds wall clock time: 74 minutes 53.81 seconds (4493.81 seconds total)