Starting phenix.real_space_refine
on Mon Mar 11 06:38:52 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/03_2024/7n76_24221.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/03_2024/7n76_24221.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/03_2024/7n76_24221.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/03_2024/7n76_24221.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/03_2024/7n76_24221.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/03_2024/7n76_24221.pdb"
  }
  resolution = 2.9
  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=   0.001 sd=   0.023
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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    4748      2.51       5
     N    1280      2.21       5
     O    1327      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  832": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7399
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1039, 7399
          Classifications: {'peptide': 1036, 'water': 3}
          Incomplete info: {'truncation_to_alanine': 176}
          Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963, None: 3}
            Not linked:
              pdbres="PRO A1168 "
              pdbres="HOH A1201 "
            Not linked:
              pdbres="HOH A1201 "
              pdbres="HOH A1202 "
            Not linked:
              pdbres="HOH A1202 "
              pdbres="HOH A1203 "
          Chain breaks: 5
          Unresolved chain link angles: 18
          Unresolved non-hydrogen bonds: 650
          Unresolved non-hydrogen angles: 835
          Unresolved non-hydrogen dihedrals: 549
          Unresolved non-hydrogen chiralities: 59
          Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 6, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 347
  Time building chain proxies: 4.34, per 1000 atoms: 0.59
  Number of scatterers: 7399
  At special positions: 0
  Unit cell: (90.214, 102.802, 130.076, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1327      8.00
     N    1280      7.00
     C    4748      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  - 3.50
        Amino acid           : False - 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: 2.87
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      52.7% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 57
    Processing helix  chain 'A' and resid 59 through 68
    Processing helix  chain 'A' and resid 68 through 77
      removed outlier: 4.194A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 3.508A  pdb=" N   MET A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   VAL A 206 " --> pdb=" O   GLN A 202 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 232
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 251 through 284
      removed outlier: 3.532A  pdb=" N   SER A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 393 through 396
    Processing helix  chain 'A' and resid 397 through 408
    Processing helix  chain 'A' and resid 419 through 445
    Processing helix  chain 'A' and resid 448 through 463
      removed outlier: 3.843A  pdb=" N   VAL A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 487
    Processing helix  chain 'A' and resid 492 through 499
      removed outlier: 3.766A  pdb=" N   ASN A 497 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 4.011A  pdb=" N   ARG A 540 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 651 through 659
    Processing helix  chain 'A' and resid 660 through 664
    Processing helix  chain 'A' and resid 667 through 678
      removed outlier: 3.524A  pdb=" N   ALA A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 701
      removed outlier: 3.704A  pdb=" N   GLN A 701 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 709
    Processing helix  chain 'A' and resid 726 through 737
      removed outlier: 3.581A  pdb=" N   VAL A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 759
    Processing helix  chain 'A' and resid 821 through 832
    Processing helix  chain 'A' and resid 835 through 842
    Processing helix  chain 'A' and resid 850 through 864
      removed outlier: 3.535A  pdb=" N   THR A 855 " --> pdb=" O   PRO A 851 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 864 " --> pdb=" O   GLU A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 884
    Processing helix  chain 'A' and resid 909 through 949
    Processing helix  chain 'A' and resid 954 through 964
    Processing helix  chain 'A' and resid 964 through 974
      removed outlier: 3.681A  pdb=" N   VAL A 969 " --> pdb=" O   ILE A 965 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   SER A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1020
      removed outlier: 3.974A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.827A  pdb=" N   LEU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1072
    Processing helix  chain 'A' and resid 1073 through 1093
    Processing helix  chain 'A' and resid 1109 through 1145
      Proline residue:  A1138  - end of helix
    Processing helix  chain 'A' and resid 1152 through 1164
      removed outlier: 3.508A  pdb=" N   GLN A1164 " --> pdb=" O   GLU A1160 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37
    Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41
      removed outlier: 4.240A  pdb=" N   ARG A  78 " --> pdb=" O   CYS A  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109
      removed outlier: 5.098A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 176 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 293
    Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315
      removed outlier: 4.533A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU A 387 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ASP A 325 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.660A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490
      removed outlier: 5.975A  pdb=" N   GLY A 887 " --> pdb=" O   PHE A 901 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   SER A 903 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   SER A 889 " --> pdb=" O   SER A 903 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   LEU A 504 " --> pdb=" O   GLY A 869 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   ALA A 741 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   PHE A 846 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   MET A 743 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   THR A 844 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   LEU A 818 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   PHE A 846 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU A 820 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   LEU A 768 " --> pdb=" O   MET A 789 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER A 783 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 519 through 525
      removed outlier: 4.903A  pdb=" N   VAL A 520 " --> pdb=" O   ARG A 720 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ARG A 720 " --> pdb=" O   VAL A 520 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY A 522 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL A 718 " --> pdb=" O   GLY A 522 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   LEU A 713 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   SER A 687 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   ARG A 631 " --> pdb=" O   PHE A 625 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   PHE A 625 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER A 633 " --> pdb=" O   PHE A 623 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ALA A 637 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL A 619 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL A 579 " --> pdb=" O   GLY A 591 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559
      removed outlier: 3.503A  pdb=" N   SER A 557 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1302 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: 3.01

  Time building geometry restraints manager: 3.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2163
        1.33 -     1.45: 1028
        1.45 -     1.57: 4280
        1.57 -     1.69: 0
        1.69 -     1.81: 65
  Bond restraints: 7536
  Sorted by residual:
  bond pdb=" CB  VAL A 107 "
       pdb=" CG2 VAL A 107 "
    ideal  model  delta    sigma   weight residual
    1.521  1.349  0.172 3.30e-02 9.18e+02 2.73e+01
  bond pdb=" CB  TYR A 935 "
       pdb=" CG  TYR A 935 "
    ideal  model  delta    sigma   weight residual
    1.512  1.437  0.075 2.20e-02 2.07e+03 1.17e+01
  bond pdb=" C   TYR A 935 "
       pdb=" N   SER A 936 "
    ideal  model  delta    sigma   weight residual
    1.335  1.293  0.042 1.31e-02 5.83e+03 1.02e+01
  bond pdb=" CG  TYR A 935 "
       pdb=" CD1 TYR A 935 "
    ideal  model  delta    sigma   weight residual
    1.389  1.328  0.061 2.10e-02 2.27e+03 8.55e+00
  bond pdb=" CG  GLN A 108 "
       pdb=" CD  GLN A 108 "
    ideal  model  delta    sigma   weight residual
    1.516  1.452  0.064 2.50e-02 1.60e+03 6.54e+00
  ... (remaining 7531 not shown)

  Histogram of bond angle deviations from ideal:
       99.83 -   106.67: 278
      106.67 -   113.51: 4289
      113.51 -   120.35: 2727
      120.35 -   127.19: 2929
      127.19 -   134.03: 81
  Bond angle restraints: 10304
  Sorted by residual:
  angle pdb=" CA  TYR A 935 "
        pdb=" CB  TYR A 935 "
        pdb=" CG  TYR A 935 "
      ideal   model   delta    sigma   weight residual
     113.90  105.40    8.50 1.80e+00 3.09e-01 2.23e+01
  angle pdb=" CG1 VAL A 107 "
        pdb=" CB  VAL A 107 "
        pdb=" CG2 VAL A 107 "
      ideal   model   delta    sigma   weight residual
     110.80  102.10    8.70 2.20e+00 2.07e-01 1.57e+01
  angle pdb=" CB  LEU A 270 "
        pdb=" CG  LEU A 270 "
        pdb=" CD2 LEU A 270 "
      ideal   model   delta    sigma   weight residual
     110.70  122.12  -11.42 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CA  GLN A 108 "
        pdb=" CB  GLN A 108 "
        pdb=" CG  GLN A 108 "
      ideal   model   delta    sigma   weight residual
     114.10  106.65    7.45 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" N   VAL A 107 "
        pdb=" CA  VAL A 107 "
        pdb=" C   VAL A 107 "
      ideal   model   delta    sigma   weight residual
     107.75  112.37   -4.62 1.46e+00 4.69e-01 1.00e+01
  ... (remaining 10299 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 4191
       17.56 -    35.11: 269
       35.11 -    52.67: 39
       52.67 -    70.23: 6
       70.23 -    87.79: 4
  Dihedral angle restraints: 4509
    sinusoidal: 1516
      harmonic: 2993
  Sorted by residual:
  dihedral pdb=" CA  VAL A 964 "
           pdb=" C   VAL A 964 "
           pdb=" N   ILE A 965 "
           pdb=" CA  ILE A 965 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.37  -18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  LEU A 934 "
           pdb=" C   LEU A 934 "
           pdb=" N   TYR A 935 "
           pdb=" CA  TYR A 935 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  SER A 889 "
           pdb=" C   SER A 889 "
           pdb=" N   LEU A 890 "
           pdb=" CA  LEU A 890 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4506 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.370: 1268
       0.370 -    0.741: 0
       0.741 -    1.111: 0
       1.111 -    1.482: 0
       1.482 -    1.852: 1
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CG  LEU A 270 "
            pdb=" CB  LEU A 270 "
            pdb=" CD1 LEU A 270 "
            pdb=" CD2 LEU A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.74   -1.85 2.00e-01 2.50e+01 8.58e+01
  chirality pdb=" CA  TYR A 935 "
            pdb=" N   TYR A 935 "
            pdb=" C   TYR A 935 "
            pdb=" CB  TYR A 935 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CG  LEU A 158 "
            pdb=" CB  LEU A 158 "
            pdb=" CD1 LEU A 158 "
            pdb=" CD2 LEU A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1266 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 934 "   -0.020 2.00e-02 2.50e+03   4.02e-02 1.62e+01
        pdb=" C   LEU A 934 "    0.070 2.00e-02 2.50e+03
        pdb=" O   LEU A 934 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   TYR A 935 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 935 "   -0.028 2.00e-02 2.50e+03   2.77e-02 1.54e+01
        pdb=" CG  TYR A 935 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 935 "    0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 935 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 935 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 935 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 935 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 935 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 107 "    0.013 2.00e-02 2.50e+03   2.57e-02 6.61e+00
        pdb=" C   VAL A 107 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL A 107 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 108 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 72
        2.64 -     3.20: 7035
        3.20 -     3.77: 11463
        3.77 -     4.33: 15443
        4.33 -     4.90: 26475
  Nonbonded interactions: 60488
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 359 "
            pdb=" OG1 THR A 368 "
     model   vdw
     2.074 2.440
  nonbonded pdb=" OE2 GLU A 172 "
            pdb=" NE2 GLN A 175 "
     model   vdw
     2.159 2.520
  nonbonded pdb=" NH1 ARG A 816 "
            pdb=" O   PRO A1167 "
     model   vdw
     2.239 2.520
  nonbonded pdb=" O   ASP A 325 "
            pdb=" OG1 THR A 391 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" O   PHE A 958 "
            pdb=" ND2 ASN A 962 "
     model   vdw
     2.311 2.520
  ... (remaining 60483 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.400
  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:          5.930
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     24.580
  Find NCS groups from input model:        0.200
  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:12.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
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      :  0.005   0.172   7536  Z= 0.339
  Angle     :  0.643  11.421  10304  Z= 0.341
  Chirality :  0.068   1.852   1269
  Planarity :  0.004   0.063   1316
  Dihedral  : 12.160  87.785   2575
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  0.22 (0.26), residues: 1024
  helix:  0.65 (0.23), residues: 501
  sheet:  0.25 (0.41), residues: 151
  loop : -0.42 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 100 
 HIS   0.014   0.001   HIS A 364 
 PHE   0.024   0.002   PHE A 958 
 TYR   0.052   0.002   TYR A 935 
 ARG   0.012   0.001   ARG A 281 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A  761 MET cc_start: 0.8769 (mtt) cc_final: 0.8546 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 1.1438
  time to fit residues: 62.5321
Evaluate side-chains
  36 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.4980
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:   50.0000
   chunk 41 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 939 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7536  Z= 0.190
  Angle     :  0.561   9.004  10304  Z= 0.278
  Chirality :  0.042   0.151   1269
  Planarity :  0.005   0.055   1316
  Dihedral  :  4.179  17.205   1099
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  4.64 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.09 (0.26), residues: 1024
  helix:  1.45 (0.23), residues: 503
  sheet:  0.33 (0.42), residues: 151
  loop :  0.02 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1166 
 HIS   0.002   0.000   HIS A 408 
 PHE   0.023   0.002   PHE A 958 
 TYR   0.026   0.001   TYR A 935 
 ARG   0.010   0.000   ARG A 984 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A  761 MET cc_start: 0.8860 (mtt) cc_final: 0.8545 (mtt)
  outliers start: 6
  outliers final: 4
  residues processed: 44
  average time/residue: 0.9202
  time to fit residues: 44.3434
Evaluate side-chains
  40 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:   40.0000
   chunk 29 optimal weight:    0.0370
   chunk 77 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 93 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6862

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7536  Z= 0.177
  Angle     :  0.522   8.912  10304  Z= 0.256
  Chirality :  0.041   0.148   1269
  Planarity :  0.004   0.050   1316
  Dihedral  :  3.915  16.358   1099
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  6.19 %
    Favored  : 92.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.45 (0.26), residues: 1024
  helix:  1.77 (0.23), residues: 505
  sheet:  0.39 (0.42), residues: 151
  loop :  0.20 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 408 
 PHE   0.017   0.001   PHE A 958 
 TYR   0.015   0.001   TYR A 935 
 ARG   0.005   0.000   ARG A 984 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.872 
Fit side-chains
  outliers start: 12
  outliers final: 3
  residues processed: 45
  average time/residue: 0.8480
  time to fit residues: 42.2319
Evaluate side-chains
  40 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:   40.0000
   chunk 62 optimal weight:    0.9980
   chunk 94 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:   20.0000
   chunk 89 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7536  Z= 0.214
  Angle     :  0.511   7.770  10304  Z= 0.251
  Chirality :  0.041   0.135   1269
  Planarity :  0.004   0.050   1316
  Dihedral  :  3.794  15.991   1099
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.59 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.75 (0.27), residues: 1024
  helix:  2.01 (0.23), residues: 503
  sheet:  0.35 (0.41), residues: 157
  loop :  0.45 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.017   0.001   PHE A 958 
 TYR   0.013   0.001   TYR A 935 
 ARG   0.004   0.000   ARG A 984 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A 1004 MET cc_start: 0.8285 (mmm) cc_final: 0.8081 (mmm)
  outliers start: 9
  outliers final: 2
  residues processed: 43
  average time/residue: 0.8704
  time to fit residues: 41.4882
Evaluate side-chains
  40 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 74 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:   50.0000
   chunk 89 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   7536  Z= 0.407
  Angle     :  0.585  11.019  10304  Z= 0.288
  Chirality :  0.044   0.166   1269
  Planarity :  0.004   0.050   1316
  Dihedral  :  3.980  16.207   1099
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.70 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.74 (0.27), residues: 1024
  helix:  1.97 (0.23), residues: 503
  sheet:  0.35 (0.41), residues: 157
  loop :  0.49 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 301 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.016   0.002   PHE A 940 
 TYR   0.016   0.002   TYR A  40 
 ARG   0.003   0.000   ARG A 757 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.870 
Fit side-chains
  outliers start: 12
  outliers final: 5
  residues processed: 44
  average time/residue: 0.8570
  time to fit residues: 41.7771
Evaluate side-chains
  43 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 58 optimal weight:   50.0000
   chunk 24 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 46 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   7536  Z= 0.433
  Angle     :  0.605  11.454  10304  Z= 0.296
  Chirality :  0.044   0.171   1269
  Planarity :  0.004   0.049   1316
  Dihedral  :  4.093  16.978   1099
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 10.55 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.70 (0.27), residues: 1024
  helix:  1.93 (0.23), residues: 506
  sheet:  0.45 (0.41), residues: 156
  loop :  0.42 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1166 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.017   0.002   PHE A1154 
 TYR   0.015   0.002   TYR A  40 
 ARG   0.003   0.000   ARG A 207 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A 1153 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7654 (tpt170)
  outliers start: 16
  outliers final: 7
  residues processed: 50
  average time/residue: 0.8184
  time to fit residues: 45.2398
Evaluate side-chains
  46 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  414 PHE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue 1031 VAL
Chi-restraints excluded: chain A residue 1153 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0570
   chunk 55 optimal weight:   10.0000
   chunk 99 optimal weight:    0.8980
   chunk 62 optimal weight:    0.4980
   chunk 60 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7536  Z= 0.163
  Angle     :  0.509  11.914  10304  Z= 0.247
  Chirality :  0.041   0.152   1269
  Planarity :  0.004   0.048   1316
  Dihedral  :  3.753  18.642   1099
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.95 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.07 (0.27), residues: 1024
  helix:  2.28 (0.23), residues: 503
  sheet:  0.39 (0.41), residues: 152
  loop :  0.66 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1166 
 HIS   0.002   0.000   HIS A 408 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.014   0.001   TYR A 935 
 ARG   0.001   0.000   ARG A 984 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.852 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.8150
  time to fit residues: 41.5300
Evaluate side-chains
  41 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:   40.0000
   chunk 29 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0670
   chunk 95 optimal weight:    1.9990
   overall best weight:    1.4126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7536  Z= 0.267
  Angle     :  0.557  11.922  10304  Z= 0.267
  Chirality :  0.042   0.168   1269
  Planarity :  0.004   0.048   1316
  Dihedral  :  3.777  17.670   1099
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.38 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.12 (0.27), residues: 1024
  helix:  2.33 (0.23), residues: 503
  sheet:  0.43 (0.41), residues: 157
  loop :  0.66 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 301 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.014   0.001   PHE A 940 
 TYR   0.011   0.001   TYR A  40 
 ARG   0.002   0.000   ARG A 984 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.818 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 45
  average time/residue: 0.8685
  time to fit residues: 43.1655
Evaluate side-chains
  41 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7536  Z= 0.219
  Angle     :  0.537  11.014  10304  Z= 0.257
  Chirality :  0.042   0.211   1269
  Planarity :  0.004   0.047   1316
  Dihedral  :  3.700  17.298   1099
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.95 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.16 (0.27), residues: 1024
  helix:  2.39 (0.23), residues: 504
  sheet:  0.46 (0.41), residues: 157
  loop :  0.64 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1166 
 HIS   0.002   0.000   HIS A 408 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 207 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.918 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 45
  average time/residue: 0.8871
  time to fit residues: 44.2151
Evaluate side-chains
  44 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  414 PHE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:   50.0000
   chunk 46 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:   50.0000
   chunk 64 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7536  Z= 0.190
  Angle     :  0.543  11.515  10304  Z= 0.257
  Chirality :  0.041   0.206   1269
  Planarity :  0.004   0.047   1316
  Dihedral  :  3.629  16.322   1099
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 12.80 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.23 (0.27), residues: 1024
  helix:  2.46 (0.23), residues: 505
  sheet:  0.50 (0.41), residues: 156
  loop :  0.63 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 408 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 984 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  472 MET cc_start: 0.8204 (mmm) cc_final: 0.7877 (mmt)
  outliers start: 6
  outliers final: 6
  residues processed: 43
  average time/residue: 0.8688
  time to fit residues: 41.3212
Evaluate side-chains
  43 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  414 PHE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0870
   chunk 81 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0870
   overall best weight:    0.5536

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.095546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.068160 restraints weight = 19380.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.79
r_work: 0.3095 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7536  Z= 0.156
  Angle     :  0.520  11.549  10304  Z= 0.248
  Chirality :  0.041   0.203   1269
  Planarity :  0.004   0.046   1316
  Dihedral  :  3.554  15.908   1099
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 13.08 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 (0.27), residues: 1024
  helix:  2.55 (0.24), residues: 505
  sheet:  0.56 (0.41), residues: 156
  loop :  0.66 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 408 
 PHE   0.012   0.001   PHE A 940 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 984 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1976.62 seconds
wall clock time: 36 minutes 8.20 seconds (2168.20 seconds total)