Starting phenix.real_space_refine
on Fri Aug 22 22:25:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jew_36201/08_2025/8jew_36201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jew_36201/08_2025/8jew_36201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2025/8jew_36201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2025/8jew_36201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2025/8jew_36201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jew_36201/08_2025/8jew_36201.cif"
  }
  resolution = 2.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      58      5.16       5
     Na      4      4.78       5
     C    5504      2.51       5
     N    1246      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8284
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 3881
          Classifications: {'peptide': 512}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 478}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 261
          Unusual residues: {' NA': 2, 'ASC': 1, 'AV0': 2, 'CLR': 2, 'LBN': 1, 'NAG': 1, 'PLM': 1}
          Classifications: {'undetermined': 10, 'water': 3}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'LBN:plan-3': 1, 'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.24, per 1000 atoms: 0.39
  Number of scatterers: 8284
  At special positions: 0
  Unit cell: (94.62, 108.564, 77.688, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      58     16.00
     P       2     15.00
     Na      4     11.00
     O    1470      8.00
     N    1246      7.00
     C    5504      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 308.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1852

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 2 sheets defined
      74.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 60
      removed outlier: 3.720A  pdb=" N   LEU A  46 " --> pdb=" O   TYR A  42 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLY A  58 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
      removed outlier: 3.775A  pdb=" N   PHE A  64 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 101
    Processing helix  chain 'A' and resid 111 through 123
      removed outlier: 3.860A  pdb=" N   LEU A 115 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      Proline residue:  A 117  - end of helix
    Processing helix  chain 'A' and resid 124 through 128
    Processing helix  chain 'A' and resid 131 through 136
      removed outlier: 3.559A  pdb=" N   ILE A 135 " --> pdb=" O   PRO A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 173
      Proline residue:  A 151  - end of helix
      removed outlier: 3.562A  pdb=" N   GLU A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 3.894A  pdb=" N   LEU A 180 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 198
      Proline residue:  A 190  - end of helix
    Processing helix  chain 'A' and resid 199 through 208
    Processing helix  chain 'A' and resid 210 through 227
    Processing helix  chain 'A' and resid 255 through 274
    Processing helix  chain 'A' and resid 285 through 289
    Processing helix  chain 'A' and resid 317 through 346
      removed outlier: 3.895A  pdb=" N   SER A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA A 327 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 374
    Processing helix  chain 'A' and resid 382 through 393
      removed outlier: 3.682A  pdb=" N   ILE A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 413
      removed outlier: 3.715A  pdb=" N   VAL A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 421
    Processing helix  chain 'A' and resid 424 through 445
      removed outlier: 3.540A  pdb=" N   THR A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 454 through 478
      Proline residue:  A 472  - end of helix
    Processing helix  chain 'A' and resid 479 through 482
      removed outlier: 4.509A  pdb=" N   ILE A 482 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 479 through 482'
    Processing helix  chain 'A' and resid 486 through 498
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 541 through 545
    Processing helix  chain 'A' and resid 549 through 554
    Processing helix  chain 'A' and resid 556 through 561
    Processing helix  chain 'B' and resid 40 through 60
      removed outlier: 3.720A  pdb=" N   LEU B  46 " --> pdb=" O   TYR B  42 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLY B  58 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.775A  pdb=" N   PHE B  64 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 101
    Processing helix  chain 'B' and resid 111 through 123
      removed outlier: 3.860A  pdb=" N   LEU B 115 " --> pdb=" O   ALA B 111 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL B 116 " --> pdb=" O   PHE B 112 " (cutoff:3.500A)
      Proline residue:  B 117  - end of helix
    Processing helix  chain 'B' and resid 124 through 128
    Processing helix  chain 'B' and resid 131 through 136
      removed outlier: 3.559A  pdb=" N   ILE B 135 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 173
      Proline residue:  B 151  - end of helix
      removed outlier: 3.562A  pdb=" N   GLU B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL B 166 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU B 167 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 180
      removed outlier: 3.894A  pdb=" N   LEU B 180 " --> pdb=" O   PRO B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 198
      Proline residue:  B 190  - end of helix
    Processing helix  chain 'B' and resid 199 through 208
    Processing helix  chain 'B' and resid 210 through 227
    Processing helix  chain 'B' and resid 255 through 274
    Processing helix  chain 'B' and resid 285 through 289
    Processing helix  chain 'B' and resid 317 through 346
      removed outlier: 3.895A  pdb=" N   SER B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ALA B 327 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 374
    Processing helix  chain 'B' and resid 382 through 393
      removed outlier: 3.682A  pdb=" N   ILE B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 413
      removed outlier: 3.715A  pdb=" N   VAL B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 421
    Processing helix  chain 'B' and resid 424 through 445
      removed outlier: 3.540A  pdb=" N   THR B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 450
    Processing helix  chain 'B' and resid 454 through 478
      Proline residue:  B 472  - end of helix
    Processing helix  chain 'B' and resid 479 through 482
      removed outlier: 4.509A  pdb=" N   ILE B 482 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 479 through 482'
    Processing helix  chain 'B' and resid 486 through 498
    Processing helix  chain 'B' and resid 499 through 515
    Processing helix  chain 'B' and resid 541 through 545
    Processing helix  chain 'B' and resid 549 through 554
    Processing helix  chain 'B' and resid 556 through 561
    Processing sheet with id=1, first strand: chain 'A' and resid 108 through 110
    Processing sheet with id=2, first strand: chain 'B' and resid 108 through 110

    506 hydrogen bonds defined for protein.
    1452 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: 1.33

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1206
        1.31 -     1.44: 2212
        1.44 -     1.58: 4978
        1.58 -     1.71: 4
        1.71 -     1.84: 88
  Bond restraints: 8488
  Sorted by residual:
  bond pdb=" C   TYR B 474 "
       pdb=" O   TYR B 474 "
    ideal  model  delta    sigma   weight residual
    1.236  1.293 -0.057 1.15e-02 7.56e+03 2.45e+01
  bond pdb=" C   TYR A 474 "
       pdb=" O   TYR A 474 "
    ideal  model  delta    sigma   weight residual
    1.236  1.293 -0.057 1.15e-02 7.56e+03 2.45e+01
  bond pdb=" C   PRO A 301 "
       pdb=" O   PRO A 301 "
    ideal  model  delta    sigma   weight residual
    1.233  1.179  0.054 1.19e-02 7.06e+03 2.06e+01
  bond pdb=" C   PRO B 301 "
       pdb=" O   PRO B 301 "
    ideal  model  delta    sigma   weight residual
    1.233  1.179  0.054 1.19e-02 7.06e+03 2.06e+01
  bond pdb=" C   GLN B 287 "
       pdb=" O   GLN B 287 "
    ideal  model  delta    sigma   weight residual
    1.236  1.176  0.060 1.35e-02 5.49e+03 1.98e+01
  ... (remaining 8483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 8676
        2.07 -     4.14: 2672
        4.14 -     6.21: 224
        6.21 -     8.29: 12
        8.29 -    10.36: 4
  Bond angle restraints: 11588
  Sorted by residual:
  angle pdb=" N   TYR A  42 "
        pdb=" CA  TYR A  42 "
        pdb=" C   TYR A  42 "
      ideal   model   delta    sigma   weight residual
     111.71  106.27    5.44 1.15e+00 7.56e-01 2.24e+01
  angle pdb=" N   TYR B  42 "
        pdb=" CA  TYR B  42 "
        pdb=" C   TYR B  42 "
      ideal   model   delta    sigma   weight residual
     111.71  106.27    5.44 1.15e+00 7.56e-01 2.24e+01
  angle pdb=" CA  ILE A 218 "
        pdb=" C   ILE A 218 "
        pdb=" O   ILE A 218 "
      ideal   model   delta    sigma   weight residual
     121.17  116.22    4.95 1.06e+00 8.90e-01 2.18e+01
  angle pdb=" CA  ILE B 218 "
        pdb=" C   ILE B 218 "
        pdb=" O   ILE B 218 "
      ideal   model   delta    sigma   weight residual
     121.17  116.22    4.95 1.06e+00 8.90e-01 2.18e+01
  angle pdb=" O   ILE A 218 "
        pdb=" C   ILE A 218 "
        pdb=" N   LEU A 219 "
      ideal   model   delta    sigma   weight residual
     121.91  126.38   -4.47 9.80e-01 1.04e+00 2.08e+01
  ... (remaining 11583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.32: 5262
       28.32 -    56.64: 200
       56.64 -    84.95: 32
       84.95 -   113.27: 0
      113.27 -   141.59: 8
  Dihedral angle restraints: 5502
    sinusoidal: 2602
      harmonic: 2900
  Sorted by residual:
  dihedral pdb=" C1  LBN B 605 "
           pdb=" O1  LBN B 605 "
           pdb=" P1  LBN B 605 "
           pdb=" O3  LBN B 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.60   56.99 -141.59     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" C1  LBN A 605 "
           pdb=" O1  LBN A 605 "
           pdb=" P1  LBN A 605 "
           pdb=" O3  LBN A 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.60   56.99 -141.59     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" O5  LBN A 605 "
           pdb=" C2  LBN A 605 "
           pdb=" C3  LBN A 605 "
           pdb=" O7  LBN A 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67  -60.77  123.44     1      3.00e+01 1.11e-03 1.65e+01
  ... (remaining 5499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 630
       0.049 -    0.098: 436
       0.098 -    0.147: 232
       0.147 -    0.196: 100
       0.196 -    0.244: 24
  Chirality restraints: 1422
  Sorted by residual:
  chirality pdb=" CA  PRO B 563 "
            pdb=" N   PRO B 563 "
            pdb=" C   PRO B 563 "
            pdb=" CB  PRO B 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  PRO A 563 "
            pdb=" N   PRO A 563 "
            pdb=" C   PRO A 563 "
            pdb=" CB  PRO A 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  TRP B 149 "
            pdb=" N   TRP B 149 "
            pdb=" C   TRP B 149 "
            pdb=" CB  TRP B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1419 not shown)

  Planarity restraints: 1352
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 609 "   -0.056 2.00e-02 2.50e+03   4.63e-02 2.67e+01
        pdb=" C7  NAG A 609 "    0.006 2.00e-02 2.50e+03
        pdb=" C8  NAG A 609 "   -0.040 2.00e-02 2.50e+03
        pdb=" N2  NAG A 609 "    0.076 2.00e-02 2.50e+03
        pdb=" O7  NAG A 609 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 609 "   -0.056 2.00e-02 2.50e+03   4.63e-02 2.67e+01
        pdb=" C7  NAG B 609 "    0.006 2.00e-02 2.50e+03
        pdb=" C8  NAG B 609 "   -0.040 2.00e-02 2.50e+03
        pdb=" N2  NAG B 609 "    0.076 2.00e-02 2.50e+03
        pdb=" O7  NAG B 609 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 311 "   -0.027 2.00e-02 2.50e+03   2.91e-02 2.11e+01
        pdb=" CG  TRP A 311 "    0.000 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 311 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 311 "    0.058 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 311 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 311 "    0.031 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 311 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 311 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 311 "   -0.039 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 311 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1349 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 32
        2.53 -     3.12: 6304
        3.12 -     3.71: 13560
        3.71 -     4.31: 19920
        4.31 -     4.90: 32382
  Nonbonded interactions: 72198
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 338 "
            pdb="NA    NA A 602 "
     model   vdw
     1.932 2.470
  nonbonded pdb=" OD2 ASP B 338 "
            pdb="NA    NA B 602 "
     model   vdw
     1.932 2.470
  nonbonded pdb=" ND2 ASN B 144 "
            pdb=" C1  NAG B 609 "
     model   vdw
     2.059 3.550
  nonbonded pdb=" ND2 ASN A 144 "
            pdb=" C1  NAG A 609 "
     model   vdw
     2.059 3.550
  nonbonded pdb=" OAI AV0 A 604 "
            pdb=" OH  TYR B 474 "
     model   vdw
     2.228 3.040
  ... (remaining 72193 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.110
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.000
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
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      :  0.015   0.069   8490  Z= 1.059
  Angle     :  1.791  10.357  11588  Z= 1.295
  Chirality :  0.085   0.244   1422
  Planarity :  0.014   0.117   1352
  Dihedral  : 15.566 141.589   3650
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 12.38 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.24), residues: 1012
  helix: -0.06 (0.18), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.56 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG B 555 
 TYR   0.043   0.009   TYR B 474 
 PHE   0.050   0.010   PHE A 459 
 TRP   0.058   0.012   TRP A 311 
 HIS   0.014   0.005   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.01479 ( 8488)
  covalent geometry    : angle       1.79076 (11588)
  hydrogen bonds       : bond        0.18082 (  506)
  hydrogen bonds       : angle       7.15593 ( 1452)
  Misc. bond           : bond        0.01839 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A   78 MET cc_start: 0.8861 (tmt) cc_final: 0.8390 (tmt)
REVERT: A   99 THR cc_start: 0.8314 (t) cc_final: 0.8100 (p)
REVERT: A  119 LYS cc_start: 0.7518 (pttp) cc_final: 0.7301 (mtmm)
REVERT: A  161 MET cc_start: 0.8740 (mtp) cc_final: 0.8324 (mtm)
REVERT: A  172 LEU cc_start: 0.8139 (tp) cc_final: 0.7673 (mt)
REVERT: A  201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7092 (mt0)
REVERT: A  251 ILE cc_start: 0.7110 (tt) cc_final: 0.6770 (pt)
REVERT: A  334 GLU cc_start: 0.8383 (tt0) cc_final: 0.8141 (tt0)
REVERT: A  381 SER cc_start: 0.8036 (m) cc_final: 0.7664 (p)
REVERT: A  476 GLU cc_start: 0.7849 (tp30) cc_final: 0.7310 (mm-30)
REVERT: A  500 GLU cc_start: 0.7758 (mp0) cc_final: 0.7470 (mp0)
REVERT: A  550 MET cc_start: 0.3350 (tpt) cc_final: 0.3060 (tpt)
REVERT: B   78 MET cc_start: 0.8858 (tmt) cc_final: 0.8387 (tmt)
REVERT: B   99 THR cc_start: 0.8316 (t) cc_final: 0.8101 (p)
REVERT: B  119 LYS cc_start: 0.7520 (pttp) cc_final: 0.7302 (mtmm)
REVERT: B  161 MET cc_start: 0.8740 (mtp) cc_final: 0.8323 (mtm)
REVERT: B  172 LEU cc_start: 0.8133 (tp) cc_final: 0.7668 (mt)
REVERT: B  201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7093 (mt0)
REVERT: B  251 ILE cc_start: 0.7110 (tt) cc_final: 0.6772 (pt)
REVERT: B  334 GLU cc_start: 0.8380 (tt0) cc_final: 0.8139 (tt0)
REVERT: B  381 SER cc_start: 0.8037 (m) cc_final: 0.7664 (p)
REVERT: B  476 GLU cc_start: 0.7850 (tp30) cc_final: 0.7312 (mm-30)
REVERT: B  500 GLU cc_start: 0.7762 (mp0) cc_final: 0.7473 (mp0)
REVERT: B  550 MET cc_start: 0.3351 (tpt) cc_final: 0.3063 (tpt)
  outliers start: 4
  outliers final: 0
  residues processed: 148
  average time/residue: 0.5366
  time to fit residues: 84.7407
Evaluate side-chains
  120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0270
   overall best weight:    2.1444

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 108 GLN
B 147 HIS
B 483 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.151846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.116923 restraints weight = 7854.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.16
r_work: 0.3098 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.109   8490  Z= 0.244
  Angle     :  1.251  38.440  11588  Z= 0.576
  Chirality :  0.067   0.518   1422
  Planarity :  0.013   0.186   1352
  Dihedral  : 13.081 127.622   1940
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.08 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 12.98 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.52 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.25), residues: 1012
  helix:  0.14 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -0.88 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.073   0.005   ARG B 456 
 TYR   0.184   0.008   TYR B 402 
 PHE   0.108   0.006   PHE B 255 
 TRP   0.078   0.004   TRP B 265 
 HIS   0.060   0.007   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 8488)
  covalent geometry    : angle       1.25068 (11588)
  hydrogen bonds       : bond        0.06724 (  506)
  hydrogen bonds       : angle       5.62812 ( 1452)
  Misc. bond           : bond        0.00015 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   46 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6869 (tm)
REVERT: A   78 MET cc_start: 0.8791 (tmt) cc_final: 0.8318 (tmt)
REVERT: A  161 MET cc_start: 0.9012 (mtp) cc_final: 0.8575 (mtm)
REVERT: A  172 LEU cc_start: 0.8615 (tp) cc_final: 0.8184 (mt)
REVERT: A  251 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7209 (pt)
REVERT: A  550 MET cc_start: 0.4888 (tpt) cc_final: 0.4387 (tpt)
REVERT: B   78 MET cc_start: 0.8710 (tmt) cc_final: 0.8193 (tmt)
REVERT: B  172 LEU cc_start: 0.8545 (tp) cc_final: 0.8115 (OUTLIER)
REVERT: B  249 ILE cc_start: 0.5807 (OUTLIER) cc_final: 0.5006 (mm)
REVERT: B  251 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7253 (pt)
REVERT: B  282 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7395 (mtpm)
REVERT: B  550 MET cc_start: 0.4964 (tpt) cc_final: 0.4482 (tpt)
  outliers start: 38
  outliers final: 9
  residues processed: 160
  average time/residue: 0.5331
  time to fit residues: 91.6322
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 21 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0870
   chunk 40 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    1.1362

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 GLN
B 108 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.151801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.114809 restraints weight = 7854.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.25
r_work: 0.3121 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8490  Z= 0.132
  Angle     :  0.630   8.306  11588  Z= 0.305
  Chirality :  0.042   0.183   1422
  Planarity :  0.005   0.045   1352
  Dihedral  : 12.503 131.458   1940
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.71 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1012
  helix:  1.24 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop :  0.14 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 456 
 TYR   0.014   0.001   TYR B 339 
 PHE   0.017   0.002   PHE A 558 
 TRP   0.014   0.001   TRP A 149 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8488)
  covalent geometry    : angle       0.63023 (11588)
  hydrogen bonds       : bond        0.04971 (  506)
  hydrogen bonds       : angle       4.92615 ( 1452)
  Misc. bond           : bond        0.00022 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   74 HIS cc_start: 0.8021 (m-70) cc_final: 0.7806 (m-70)
REVERT: A  161 MET cc_start: 0.9002 (mtp) cc_final: 0.8563 (mtm)
REVERT: A  172 LEU cc_start: 0.8477 (tp) cc_final: 0.8104 (mt)
REVERT: A  251 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7205 (pt)
REVERT: A  254 MET cc_start: 0.7328 (mtp) cc_final: 0.7103 (mtm)
REVERT: A  550 MET cc_start: 0.4961 (tpt) cc_final: 0.4395 (tpt)
REVERT: B  172 LEU cc_start: 0.8523 (tp) cc_final: 0.8021 (mt)
REVERT: B  251 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7360 (pt)
REVERT: B  282 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7493 (mtpm)
REVERT: B  476 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7536 (pt0)
REVERT: B  550 MET cc_start: 0.5054 (tpt) cc_final: 0.4520 (tpt)
  outliers start: 20
  outliers final: 4
  residues processed: 134
  average time/residue: 0.5787
  time to fit residues: 82.8474
Evaluate side-chains
  125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  476 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 35 optimal weight:   40.0000
   chunk 91 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 77 optimal weight:    0.1980
   chunk 76 optimal weight:   20.0000
   chunk 43 optimal weight:    9.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN
B  76 GLN
B 483 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.152009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.114601 restraints weight = 7979.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.28
r_work: 0.3063 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8490  Z= 0.127
  Angle     :  0.604   8.480  11588  Z= 0.291
  Chirality :  0.041   0.135   1422
  Planarity :  0.005   0.049   1352
  Dihedral  : 12.215 134.867   1940
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 14.76 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.26), residues: 1012
  helix:  1.63 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  0.87 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 456 
 TYR   0.008   0.001   TYR B 339 
 PHE   0.016   0.002   PHE B 361 
 TRP   0.014   0.001   TRP A 149 
 HIS   0.002   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8488)
  covalent geometry    : angle       0.60426 (11588)
  hydrogen bonds       : bond        0.04724 (  506)
  hydrogen bonds       : angle       4.72394 ( 1452)
  Misc. bond           : bond        0.00009 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   78 MET cc_start: 0.8791 (tmt) cc_final: 0.8535 (tmt)
REVERT: A  161 MET cc_start: 0.9027 (mtp) cc_final: 0.8608 (mtm)
REVERT: A  167 GLU cc_start: 0.8426 (tt0) cc_final: 0.8210 (tt0)
REVERT: A  172 LEU cc_start: 0.8454 (tp) cc_final: 0.8076 (mt)
REVERT: A  251 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7230 (pt)
REVERT: A  550 MET cc_start: 0.4908 (tpt) cc_final: 0.4433 (tpt)
REVERT: B  172 LEU cc_start: 0.8570 (tp) cc_final: 0.8071 (mt)
REVERT: B  251 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7292 (pt)
REVERT: B  254 MET cc_start: 0.7218 (mtp) cc_final: 0.6995 (mtm)
REVERT: B  282 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7443 (mtpm)
REVERT: B  550 MET cc_start: 0.5009 (tpt) cc_final: 0.4373 (tpt)
  outliers start: 23
  outliers final: 7
  residues processed: 125
  average time/residue: 0.6126
  time to fit residues: 81.4935
Evaluate side-chains
  117 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 95 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.148977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.111860 restraints weight = 7890.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.25
r_work: 0.3064 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8490  Z= 0.176
  Angle     :  0.668   7.963  11588  Z= 0.324
  Chirality :  0.044   0.152   1422
  Planarity :  0.006   0.051   1352
  Dihedral  : 12.560 134.584   1940
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.83 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.26), residues: 1012
  helix:  1.56 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  1.00 (0.37), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 456 
 TYR   0.012   0.002   TYR A  42 
 PHE   0.019   0.002   PHE A 200 
 TRP   0.014   0.002   TRP A 149 
 HIS   0.003   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8488)
  covalent geometry    : angle       0.66752 (11588)
  hydrogen bonds       : bond        0.05594 (  506)
  hydrogen bonds       : angle       4.94812 ( 1452)
  Misc. bond           : bond        0.00023 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9041 (mtp) cc_final: 0.8616 (mtm)
REVERT: A  167 GLU cc_start: 0.8453 (tt0) cc_final: 0.8202 (tt0)
REVERT: A  172 LEU cc_start: 0.8481 (tp) cc_final: 0.8102 (mt)
REVERT: A  251 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7189 (pt)
REVERT: A  550 MET cc_start: 0.5137 (tpt) cc_final: 0.4464 (tpt)
REVERT: B  172 LEU cc_start: 0.8643 (tp) cc_final: 0.8147 (mt)
REVERT: B  251 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7296 (pt)
REVERT: B  254 MET cc_start: 0.7390 (mtp) cc_final: 0.7144 (mtm)
REVERT: B  282 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7394 (mtpm)
REVERT: B  476 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7619 (mp0)
REVERT: B  550 MET cc_start: 0.5079 (tpt) cc_final: 0.4406 (tpt)
  outliers start: 26
  outliers final: 13
  residues processed: 125
  average time/residue: 0.5829
  time to fit residues: 77.8067
Evaluate side-chains
  130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  476 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN
B 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.149308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.112201 restraints weight = 7877.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.26
r_work: 0.3076 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8490  Z= 0.152
  Angle     :  0.643   8.899  11588  Z= 0.308
  Chirality :  0.043   0.143   1422
  Planarity :  0.005   0.049   1352
  Dihedral  : 12.392 134.606   1940
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.19 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.27), residues: 1012
  helix:  1.59 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.22 (0.38), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 456 
 TYR   0.010   0.001   TYR A  42 
 PHE   0.016   0.002   PHE A 459 
 TRP   0.015   0.001   TRP A 149 
 HIS   0.002   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8488)
  covalent geometry    : angle       0.64324 (11588)
  hydrogen bonds       : bond        0.05200 (  506)
  hydrogen bonds       : angle       4.87140 ( 1452)
  Misc. bond           : bond        0.00021 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9029 (mtp) cc_final: 0.8605 (mtm)
REVERT: A  167 GLU cc_start: 0.8442 (tt0) cc_final: 0.8192 (tt0)
REVERT: A  172 LEU cc_start: 0.8467 (tp) cc_final: 0.8074 (mt)
REVERT: A  251 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7259 (pt)
REVERT: A  526 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.6200 (mt0)
REVERT: A  550 MET cc_start: 0.5135 (tpt) cc_final: 0.4376 (tpt)
REVERT: B  172 LEU cc_start: 0.8549 (tp) cc_final: 0.8115 (mt)
REVERT: B  251 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7337 (pt)
REVERT: B  282 LYS cc_start: 0.7878 (mtmm) cc_final: 0.7461 (mtpm)
REVERT: B  550 MET cc_start: 0.5073 (tpt) cc_final: 0.4080 (tpt)
  outliers start: 21
  outliers final: 11
  residues processed: 125
  average time/residue: 0.6082
  time to fit residues: 81.0852
Evaluate side-chains
  124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.148297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.111366 restraints weight = 7962.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.25
r_work: 0.3074 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8490  Z= 0.188
  Angle     :  0.695   8.069  11588  Z= 0.336
  Chirality :  0.045   0.164   1422
  Planarity :  0.006   0.047   1352
  Dihedral  : 12.630 133.646   1940
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.67 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.26), residues: 1012
  helix:  1.46 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop :  1.15 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 456 
 TYR   0.014   0.002   TYR A  42 
 PHE   0.021   0.003   PHE A 200 
 TRP   0.015   0.002   TRP A 149 
 HIS   0.003   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 8488)
  covalent geometry    : angle       0.69537 (11588)
  hydrogen bonds       : bond        0.05776 (  506)
  hydrogen bonds       : angle       5.00190 ( 1452)
  Misc. bond           : bond        0.00030 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9030 (mtp) cc_final: 0.8643 (mtm)
REVERT: A  172 LEU cc_start: 0.8541 (tp) cc_final: 0.8134 (mt)
REVERT: A  251 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7225 (pt)
REVERT: A  526 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.6216 (mt0)
REVERT: A  550 MET cc_start: 0.5054 (tpt) cc_final: 0.4188 (tpt)
REVERT: B  172 LEU cc_start: 0.8552 (tp) cc_final: 0.8114 (mt)
REVERT: B  251 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7279 (pt)
REVERT: B  282 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7383 (mtpm)
REVERT: B  476 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7605 (mp0)
  outliers start: 23
  outliers final: 13
  residues processed: 124
  average time/residue: 0.5905
  time to fit residues: 78.1353
Evaluate side-chains
  129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  476 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   chunk 75 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0870
   chunk 17 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    3.6166

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.148747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.111924 restraints weight = 7930.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.25
r_work: 0.3073 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8490  Z= 0.180
  Angle     :  0.675   8.028  11588  Z= 0.328
  Chirality :  0.045   0.159   1422
  Planarity :  0.006   0.044   1352
  Dihedral  : 12.606 133.058   1940
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.43 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.26), residues: 1012
  helix:  1.51 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  1.07 (0.37), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 456 
 TYR   0.013   0.002   TYR A  42 
 PHE   0.021   0.002   PHE A 436 
 TRP   0.016   0.002   TRP A 149 
 HIS   0.002   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8488)
  covalent geometry    : angle       0.67482 (11588)
  hydrogen bonds       : bond        0.05589 (  506)
  hydrogen bonds       : angle       4.98997 ( 1452)
  Misc. bond           : bond        0.00027 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9036 (mtp) cc_final: 0.8603 (mtm)
REVERT: A  172 LEU cc_start: 0.8524 (tp) cc_final: 0.8124 (mt)
REVERT: A  251 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7167 (pt)
REVERT: A  526 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.6194 (mt0)
REVERT: A  550 MET cc_start: 0.5003 (tpt) cc_final: 0.4123 (tpt)
REVERT: B  172 LEU cc_start: 0.8502 (tp) cc_final: 0.8100 (mt)
REVERT: B  251 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7348 (pt)
REVERT: B  282 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7451 (mtpm)
  outliers start: 21
  outliers final: 15
  residues processed: 121
  average time/residue: 0.6095
  time to fit residues: 78.6115
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  412 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 77 optimal weight:    0.1980
   chunk 1 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 42 optimal weight:    0.4980
   chunk 13 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
B  50 GLN
B 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.154311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.119420 restraints weight = 8204.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.23
r_work: 0.3115 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8490  Z= 0.112
  Angle     :  0.578   7.219  11588  Z= 0.278
  Chirality :  0.041   0.137   1422
  Planarity :  0.005   0.046   1352
  Dihedral  : 11.859 135.710   1940
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.38 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.27), residues: 1012
  helix:  1.90 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.40 (0.39), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 522 
 TYR   0.006   0.001   TYR B  42 
 PHE   0.017   0.002   PHE B 361 
 TRP   0.016   0.001   TRP A 149 
 HIS   0.001   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8488)
  covalent geometry    : angle       0.57796 (11588)
  hydrogen bonds       : bond        0.04187 (  506)
  hydrogen bonds       : angle       4.60300 ( 1452)
  Misc. bond           : bond        0.00011 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9000 (mtp) cc_final: 0.8590 (mtm)
REVERT: A  172 LEU cc_start: 0.8365 (tp) cc_final: 0.7993 (mt)
REVERT: A  251 ILE cc_start: 0.7542 (tt) cc_final: 0.7242 (pt)
REVERT: A  520 GLU cc_start: 0.7648 (mp0) cc_final: 0.7357 (mp0)
REVERT: A  526 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.6125 (mt0)
REVERT: A  550 MET cc_start: 0.5088 (tpt) cc_final: 0.4287 (tpt)
REVERT: B  172 LEU cc_start: 0.8339 (tp) cc_final: 0.7990 (mt)
REVERT: B  282 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7483 (mtpm)
REVERT: B  452 MET cc_start: 0.8458 (mmp) cc_final: 0.8247 (mmm)
REVERT: B  520 GLU cc_start: 0.7665 (mp0) cc_final: 0.7445 (mp0)
  outliers start: 16
  outliers final: 8
  residues processed: 120
  average time/residue: 0.5932
  time to fit residues: 75.8057
Evaluate side-chains
  121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0370
   chunk 95 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   overall best weight:    1.7462

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

Flipped N/Q/H residues before XYZ refinement:
A 483 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.151158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.114613 restraints weight = 7920.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.25
r_work: 0.3104 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8490  Z= 0.133
  Angle     :  0.612   7.465  11588  Z= 0.296
  Chirality :  0.042   0.134   1422
  Planarity :  0.005   0.043   1352
  Dihedral  : 11.944 136.017   1940
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.98 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.37 (0.27), residues: 1012
  helix:  1.78 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop :  1.40 (0.39), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 456 
 TYR   0.009   0.001   TYR B  42 
 PHE   0.020   0.002   PHE B 420 
 TRP   0.013   0.001   TRP A 149 
 HIS   0.002   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8488)
  covalent geometry    : angle       0.61176 (11588)
  hydrogen bonds       : bond        0.04784 (  506)
  hydrogen bonds       : angle       4.67842 ( 1452)
  Misc. bond           : bond        0.00013 (    2)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  161 MET cc_start: 0.9044 (mtp) cc_final: 0.8632 (mtm)
REVERT: A  172 LEU cc_start: 0.8403 (tp) cc_final: 0.8033 (mt)
REVERT: A  251 ILE cc_start: 0.7549 (tt) cc_final: 0.7249 (pt)
REVERT: A  526 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.6175 (mt0)
REVERT: B  172 LEU cc_start: 0.8421 (tp) cc_final: 0.8052 (mt)
REVERT: B  282 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7474 (mtpm)
  outliers start: 12
  outliers final: 9
  residues processed: 112
  average time/residue: 0.5548
  time to fit residues: 66.1247
Evaluate side-chains
  117 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  407 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 30 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.149624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.115077 restraints weight = 8150.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.17
r_work: 0.3060 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8490  Z= 0.224
  Angle     :  0.733   8.378  11588  Z= 0.359
  Chirality :  0.047   0.175   1422
  Planarity :  0.006   0.045   1352
  Dihedral  : 12.721 133.337   1940
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.21 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.26), residues: 1012
  helix:  1.36 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  1.09 (0.37), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 456 
 TYR   0.016   0.002   TYR A  42 
 PHE   0.024   0.003   PHE A 200 
 TRP   0.014   0.002   TRP B 149 
 HIS   0.004   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 8488)
  covalent geometry    : angle       0.73322 (11588)
  hydrogen bonds       : bond        0.06106 (  506)
  hydrogen bonds       : angle       5.05917 ( 1452)
  Misc. bond           : bond        0.00030 (    2)

===============================================================================
Job complete
usr+sys time: 3434.05 seconds
wall clock time: 59 minutes 22.35 seconds (3562.35 seconds total)