Starting phenix.real_space_refine
on Tue Feb 11 15:20:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gec_29965/02_2025/8gec_29965.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gec_29965/02_2025/8gec_29965.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gec_29965/02_2025/8gec_29965.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gec_29965/02_2025/8gec_29965.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gec_29965/02_2025/8gec_29965.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gec_29965/02_2025/8gec_29965.cif"
  }
  resolution = 3.5
  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=   0.029
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      26      5.16       5
     C    3961      2.51       5
     N    1081      2.21       5
     O    1057      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6125
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1622
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 314
          Unresolved non-hydrogen angles: 380
          Unresolved non-hydrogen dihedrals: 250
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 194
    Chain: "B"
      Number of atoms: 2236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2236
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 100}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 292
          Unresolved non-hydrogen angles: 365
          Unresolved non-hydrogen dihedrals: 219
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 10, 'ASN:plan1': 7, 'ASP:plan': 24}
          Unresolved non-hydrogen planarities: 195
    Chain: "G"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 305
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 42
    Chain: "R"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1947
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 320
          Unresolved non-hydrogen angles: 402
          Unresolved non-hydrogen dihedrals: 259
          Unresolved non-hydrogen chiralities: 38
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 141
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.27, per 1000 atoms: 0.70
  Number of scatterers: 6125
  At special positions: 0
  Unit cell: (67.84, 97.52, 127.2, 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      26     16.00
     O    1057      8.00
     N    1081      7.00
     C    3961      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 987.6 milliseconds
  

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      49.3% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.461A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.555A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.907A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.122A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.622A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.536A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.933A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.384A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 238
    Processing helix  chain 'R' and resid 270 through 298
      removed outlier: 4.127A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.206A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 322
      removed outlier: 3.955A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 322 through 327
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 9.709A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50
      removed outlier: 5.828A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61
      removed outlier: 7.005A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.665A  pdb=" N   LEU B 139 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.591A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.576A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.897A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.917A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)

    380 hydrogen bonds defined for protein.
    1107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2008
        1.34 -     1.46: 1459
        1.46 -     1.58: 2758
        1.58 -     1.69: 0
        1.69 -     1.81: 34
  Bond restraints: 6259
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.62e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.047 2.00e-02 2.50e+03 5.54e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.40e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 2.00e-02 2.50e+03 4.58e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.481 -0.030 2.00e-02 2.50e+03 2.28e+00
  ... (remaining 6254 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 8531
        1.99 -     3.98: 51
        3.98 -     5.96: 6
        5.96 -     7.95: 3
        7.95 -     9.94: 1
  Bond angle restraints: 8592
  Sorted by residual:
  angle pdb=" C   THR B 223 "
        pdb=" CA  THR B 223 "
        pdb=" CB  THR B 223 "
      ideal   model   delta    sigma   weight residual
     116.63  110.50    6.13 1.16e+00 7.43e-01 2.79e+01
  angle pdb=" CA  THR B 223 "
        pdb=" C   THR B 223 "
        pdb=" N   GLY B 224 "
      ideal   model   delta    sigma   weight residual
     119.63  117.22    2.41 8.10e-01 1.52e+00 8.89e+00
  angle pdb=" CA  LEU A 282 "
        pdb=" CB  LEU A 282 "
        pdb=" CG  LEU A 282 "
      ideal   model   delta    sigma   weight residual
     116.30  126.24   -9.94 3.50e+00 8.16e-02 8.06e+00
  angle pdb=" N   PHE B 235 "
        pdb=" CA  PHE B 235 "
        pdb=" C   PHE B 235 "
      ideal   model   delta    sigma   weight residual
     109.64  106.67    2.97 1.27e+00 6.20e-01 5.45e+00
  angle pdb=" C   THR B 243 "
        pdb=" N   GLY B 244 "
        pdb=" CA  GLY B 244 "
      ideal   model   delta    sigma   weight residual
     122.36  120.26    2.10 9.70e-01 1.06e+00 4.71e+00
  ... (remaining 8587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.57: 3093
       12.57 -    25.13: 312
       25.13 -    37.70: 108
       37.70 -    50.26: 47
       50.26 -    62.83: 13
  Dihedral angle restraints: 3573
    sinusoidal: 972
      harmonic: 2601
  Sorted by residual:
  dihedral pdb=" CA  ARG B  68 "
           pdb=" C   ARG B  68 "
           pdb=" N   LEU B  69 "
           pdb=" CA  LEU B  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" N   LYS B  78 "
           pdb=" CA  LYS B  78 "
           pdb=" CB  LYS B  78 "
           pdb=" CG  LYS B  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.08  -59.92     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS A 293 "
           pdb=" CD  LYS A 293 "
           pdb=" CE  LYS A 293 "
           pdb=" NZ  LYS A 293 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    4.05   55.95     3      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 3570 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 699
       0.033 -    0.067: 242
       0.067 -    0.100: 76
       0.100 -    0.133: 21
       0.133 -    0.167: 2
  Chirality restraints: 1040
  Sorted by residual:
  chirality pdb=" CA  ARG B  52 "
            pdb=" N   ARG B  52 "
            pdb=" C   ARG B  52 "
            pdb=" CB  ARG B  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.54   -0.14 2.00e-01 2.50e+01 5.04e-01
  chirality pdb=" CA  ILE A 288 "
            pdb=" N   ILE A 288 "
            pdb=" C   ILE A 288 "
            pdb=" CB  ILE A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 1037 not shown)

  Planarity restraints: 1094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO B 236 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO G  49 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.019 5.00e-02 4.00e+02   2.88e-02 1.32e+00
        pdb=" N   PRO B 194 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1091 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1341
        2.78 -     3.31: 5831
        3.31 -     3.84: 10167
        3.84 -     4.37: 10628
        4.37 -     4.90: 19785
  Nonbonded interactions: 47752
  Sorted by model distance:
  nonbonded pdb=" NE  ARG B 251 "
            pdb=" OE2 GLU B 260 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE1 GLU R 107 "
            pdb=" OH  TYR R 174 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   TYR B 145 "
            pdb=" N   GLY B 162 "
     model   vdw
     2.376 3.120
  ... (remaining 47747 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 group one per residue
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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     18.300
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
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      :  0.003   0.051   6259  Z= 0.204
  Angle     :  0.474   9.938   8592  Z= 0.264
  Chirality :  0.039   0.167   1040
  Planarity :  0.003   0.040   1094
  Dihedral  : 13.971  62.827   1878
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 21.38 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.29), residues: 871
  helix:  2.62 (0.26), residues: 399
  sheet: -0.36 (0.39), residues: 173
  loop : -0.71 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.009   0.001   PHE B 235 
 TYR   0.014   0.001   TYR A 311 
 ARG   0.002   0.000   ARG B  49 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.627 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.1319
  time to fit residues: 13.9210
Evaluate side-chains
  68 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  266 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    0.4980
   chunk 68 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0770
   chunk 51 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.133459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.115321 restraints weight = 10402.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.118302 restraints weight = 5948.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.120424 restraints weight = 4080.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.0640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6259  Z= 0.169
  Angle     :  0.439   8.101   8592  Z= 0.242
  Chirality :  0.039   0.139   1040
  Planarity :  0.003   0.035   1094
  Dihedral  :  4.581  40.474    957
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 18.79 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.29), residues: 871
  helix:  2.76 (0.26), residues: 402
  sheet:  0.02 (0.40), residues: 165
  loop : -0.84 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 222 
 TYR   0.012   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B  49 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.691 
Fit side-chains
REVERT: B   54 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7914 (m-70)
  outliers start: 20
  outliers final: 10
  residues processed: 80
  average time/residue: 0.1128
  time to fit residues: 14.0636
Evaluate side-chains
  76 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 51 optimal weight:    0.4980
   chunk 14 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 84 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.131445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.113184 restraints weight = 10370.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.116221 restraints weight = 5911.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.118320 restraints weight = 4044.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6259  Z= 0.194
  Angle     :  0.437   6.545   8592  Z= 0.239
  Chirality :  0.039   0.135   1040
  Planarity :  0.003   0.033   1094
  Dihedral  :  4.128  24.772    955
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 17.93 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.29), residues: 871
  helix:  2.70 (0.25), residues: 402
  sheet:  0.04 (0.40), residues: 165
  loop : -0.84 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.011   0.001   PHE B 222 
 TYR   0.012   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B  49 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 69
  time to evaluate  : 0.673 
Fit side-chains
REVERT: B   54 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8172 (m-70)
REVERT: B   82 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.7629 (m-10)
REVERT: B  209 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8433 (mtpp)
REVERT: B  234 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8351 (t80)
REVERT: R   82 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6396 (ttm)
REVERT: R  113 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7617 (t0)
REVERT: R  300 ASP cc_start: 0.7251 (t70) cc_final: 0.6775 (t70)
  outliers start: 26
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1240
  time to fit residues: 16.0327
Evaluate side-chains
  82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.1980
   chunk 50 optimal weight:    0.3980
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 8 optimal weight:    0.1980
   chunk 58 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.133784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.115608 restraints weight = 10356.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.118744 restraints weight = 5868.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.120913 restraints weight = 3978.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6259  Z= 0.136
  Angle     :  0.408   6.036   8592  Z= 0.225
  Chirality :  0.038   0.133   1040
  Planarity :  0.003   0.031   1094
  Dihedral  :  3.886  24.352    955
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 19.01 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.29), residues: 871
  helix:  2.75 (0.25), residues: 403
  sheet:  0.01 (0.40), residues: 165
  loop : -0.80 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.009   0.001   PHE B 222 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.003   0.000   ARG B 251 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  237 CYS cc_start: 0.7869 (m) cc_final: 0.7657 (m)
REVERT: B   54 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7961 (m-70)
REVERT: B   82 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.7588 (m-10)
REVERT: B  234 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8314 (t80)
REVERT: R   82 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6313 (ttm)
REVERT: R  113 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7635 (t0)
REVERT: R  300 ASP cc_start: 0.7269 (t70) cc_final: 0.6799 (t70)
  outliers start: 23
  outliers final: 13
  residues processed: 85
  average time/residue: 0.1182
  time to fit residues: 15.1434
Evaluate side-chains
  81 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0770
   chunk 20 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.132145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.114136 restraints weight = 10340.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.117183 restraints weight = 5895.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.119309 restraints weight = 4024.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6259  Z= 0.179
  Angle     :  0.419   6.240   8592  Z= 0.230
  Chirality :  0.039   0.134   1040
  Planarity :  0.003   0.030   1094
  Dihedral  :  3.875  25.655    955
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 19.22 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.50 (0.29), residues: 871
  helix:  2.70 (0.25), residues: 404
  sheet: -0.07 (0.39), residues: 169
  loop : -0.77 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.009   0.001   PHE B 235 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 251 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.627 
Fit side-chains
REVERT: B   45 MET cc_start: 0.8139 (mmt) cc_final: 0.7558 (mtp)
REVERT: B   54 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.8054 (m-70)
REVERT: B   82 TRP cc_start: 0.7881 (OUTLIER) cc_final: 0.7502 (m-10)
REVERT: B  234 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8308 (t80)
REVERT: R   82 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6360 (ttm)
REVERT: R  113 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7697 (t0)
REVERT: R  300 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6777 (t70)
  outliers start: 27
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1164
  time to fit residues: 15.0846
Evaluate side-chains
  83 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  300 ASP
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0020
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.132728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114677 restraints weight = 10248.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.117726 restraints weight = 5864.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.119845 restraints weight = 4020.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6259  Z= 0.170
  Angle     :  0.414   6.499   8592  Z= 0.227
  Chirality :  0.039   0.133   1040
  Planarity :  0.003   0.030   1094
  Dihedral  :  3.842  26.066    955
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 18.57 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.29), residues: 871
  helix:  2.68 (0.25), residues: 405
  sheet:  0.07 (0.40), residues: 164
  loop : -0.82 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.008   0.001   PHE B 222 
 TYR   0.013   0.001   TYR R 185 
 ARG   0.002   0.000   ARG B 251 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.647 
Fit side-chains
REVERT: B   45 MET cc_start: 0.8143 (mmt) cc_final: 0.7611 (mtp)
REVERT: B   54 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (m-70)
REVERT: B   82 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.7445 (m-10)
REVERT: B  234 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8265 (t80)
REVERT: B  286 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8132 (mt)
REVERT: R   82 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6368 (ttm)
REVERT: R  113 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7633 (t0)
REVERT: R  300 ASP cc_start: 0.7291 (t70) cc_final: 0.6800 (t70)
  outliers start: 29
  outliers final: 17
  residues processed: 89
  average time/residue: 0.1169
  time to fit residues: 15.9512
Evaluate side-chains
  87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0870
   chunk 3 optimal weight:    0.8980
   chunk 74 optimal weight:    0.2980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.132525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.114417 restraints weight = 10332.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.117486 restraints weight = 5895.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.119614 restraints weight = 4037.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6259  Z= 0.176
  Angle     :  0.423   6.709   8592  Z= 0.231
  Chirality :  0.039   0.133   1040
  Planarity :  0.003   0.029   1094
  Dihedral  :  3.832  25.803    955
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 19.22 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.29), residues: 871
  helix:  2.68 (0.25), residues: 405
  sheet:  0.12 (0.40), residues: 162
  loop : -0.85 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.009   0.001   PHE B 235 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 251 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.9150 (mm) cc_final: 0.8798 (mt)
REVERT: B   45 MET cc_start: 0.8166 (mmt) cc_final: 0.7658 (mtp)
REVERT: B   54 HIS cc_start: 0.8329 (OUTLIER) cc_final: 0.8122 (m-70)
REVERT: B   82 TRP cc_start: 0.7794 (OUTLIER) cc_final: 0.7436 (m-10)
REVERT: B  234 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8288 (t80)
REVERT: B  286 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8113 (mt)
REVERT: R   82 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6382 (ttm)
REVERT: R  113 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7635 (t0)
REVERT: R  300 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6920 (t70)
  outliers start: 28
  outliers final: 17
  residues processed: 87
  average time/residue: 0.1278
  time to fit residues: 17.0140
Evaluate side-chains
  87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.0980
   chunk 43 optimal weight:    0.0170
   chunk 81 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 74 optimal weight:    0.2980
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.133408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.115386 restraints weight = 10285.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.118466 restraints weight = 5862.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.120613 restraints weight = 4006.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6259  Z= 0.151
  Angle     :  0.410   6.377   8592  Z= 0.224
  Chirality :  0.038   0.132   1040
  Planarity :  0.003   0.028   1094
  Dihedral  :  3.773  25.405    955
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 20.09 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.29), residues: 871
  helix:  2.71 (0.25), residues: 405
  sheet:  0.11 (0.39), residues: 162
  loop : -0.81 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.007   0.001   PHE B 222 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 251 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.9144 (mm) cc_final: 0.8791 (mt)
REVERT: B   45 MET cc_start: 0.8133 (mmt) cc_final: 0.7638 (mtp)
REVERT: B   82 TRP cc_start: 0.7744 (OUTLIER) cc_final: 0.7409 (m-10)
REVERT: B  234 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8291 (t80)
REVERT: B  286 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8124 (mt)
REVERT: R   82 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6370 (ttm)
REVERT: R  113 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7613 (t0)
  outliers start: 25
  outliers final: 17
  residues processed: 86
  average time/residue: 0.1156
  time to fit residues: 15.1282
Evaluate side-chains
  87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 14 optimal weight:   10.0000
   chunk 35 optimal weight:    0.4980
   chunk 78 optimal weight:    0.0570
   chunk 75 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0980
   chunk 61 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.4098

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.134015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.116012 restraints weight = 10353.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.119159 restraints weight = 5868.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.121299 restraints weight = 3979.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6259  Z= 0.146
  Angle     :  0.413   6.238   8592  Z= 0.225
  Chirality :  0.038   0.131   1040
  Planarity :  0.003   0.028   1094
  Dihedral  :  3.733  24.963    955
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 21.38 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.29), residues: 871
  helix:  2.74 (0.25), residues: 405
  sheet:  0.11 (0.39), residues: 162
  loop : -0.82 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.007   0.001   PHE B 222 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 251 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.9153 (mm) cc_final: 0.8779 (mt)
REVERT: B   45 MET cc_start: 0.8111 (mmt) cc_final: 0.7860 (mtt)
REVERT: B   82 TRP cc_start: 0.7707 (OUTLIER) cc_final: 0.7434 (m-10)
REVERT: B  234 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8258 (t80)
REVERT: B  286 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8108 (mt)
REVERT: R   82 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6324 (ttm)
REVERT: R  113 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7587 (t0)
REVERT: R  300 ASP cc_start: 0.7310 (t70) cc_final: 0.6898 (t70)
  outliers start: 22
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1169
  time to fit residues: 14.9279
Evaluate side-chains
  87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0970
   chunk 49 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.132459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114242 restraints weight = 10243.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.117353 restraints weight = 5785.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.119541 restraints weight = 3940.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6259  Z= 0.171
  Angle     :  0.420   6.310   8592  Z= 0.230
  Chirality :  0.039   0.133   1040
  Planarity :  0.003   0.030   1094
  Dihedral  :  3.765  25.067    955
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 21.38 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.29), residues: 871
  helix:  2.72 (0.25), residues: 405
  sheet:  0.03 (0.39), residues: 162
  loop : -0.86 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.007   0.001   PHE B 222 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 251 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.9156 (mm) cc_final: 0.8796 (mt)
REVERT: B   45 MET cc_start: 0.8114 (mmt) cc_final: 0.7881 (mtt)
REVERT: B   82 TRP cc_start: 0.7774 (OUTLIER) cc_final: 0.7494 (m-10)
REVERT: B  234 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8319 (t80)
REVERT: B  286 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8102 (mt)
REVERT: R   82 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6396 (ttm)
REVERT: R  113 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7622 (t0)
REVERT: R  300 ASP cc_start: 0.7275 (t70) cc_final: 0.6864 (t70)
  outliers start: 23
  outliers final: 16
  residues processed: 84
  average time/residue: 0.1170
  time to fit residues: 14.9372
Evaluate side-chains
  89 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0570
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.132105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.113898 restraints weight = 10496.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.116977 restraints weight = 5988.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.119088 restraints weight = 4088.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6259  Z= 0.198
  Angle     :  0.436   6.976   8592  Z= 0.238
  Chirality :  0.039   0.134   1040
  Planarity :  0.003   0.030   1094
  Dihedral  :  3.839  25.470    955
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 21.81 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.29), residues: 871
  helix:  2.66 (0.25), residues: 405
  sheet: -0.02 (0.39), residues: 162
  loop : -0.88 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.008   0.001   PHE B 235 
 TYR   0.012   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 251 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1945.11 seconds
wall clock time: 35 minutes 29.09 seconds (2129.09 seconds total)