Starting phenix.real_space_refine
on Wed Mar  4 00:13:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tyi_20583/03_2026/6tyi_20583.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tyi_20583/03_2026/6tyi_20583.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2026/6tyi_20583.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2026/6tyi_20583.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2026/6tyi_20583.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2026/6tyi_20583.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.148
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      36      5.16       5
     C    5894      2.51       5
     N    1567      2.21       5
     O    1683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9184
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 1702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1702
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 221}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1704
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 4, 'TRANS': 220}
    Chain: "C"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1712
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 4, 'TRANS': 221}
    Chain: "D"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1712
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 4, 'TRANS': 221}
    Chain: "E"
      Number of atoms: 1696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1696
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 4, 'TRANS': 219}
    Chain: "Y"
      Number of atoms: 236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 236
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 2, 'TRANS': 28}
    Chain: "Z"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 224
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 2, 'TRANS': 26}
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'PEV': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'PEV': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'PEV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.00, per 1000 atoms: 0.22
  Number of scatterers: 9184
  At special positions: 0
  Unit cell: (84.8, 84.8, 121.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P       4     15.00
     O    1683      8.00
     N    1567      7.00
     C    5894      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: 0.87
  Conformation dependent library (CDL) restraints added in 364.4 milliseconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2178

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 0 sheets defined
      86.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 21 through 63
      removed outlier: 4.514A  pdb=" N   VAL A  46 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   GLU A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 75
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 103 through 128
    Processing helix  chain 'A' and resid 129 through 159
      removed outlier: 3.913A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 176 through 233
      Proline residue:  A 190  - end of helix
    Processing helix  chain 'B' and resid 11 through 18
      removed outlier: 3.597A  pdb=" N   HIS B  18 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 63
    Processing helix  chain 'B' and resid 67 through 75
    Processing helix  chain 'B' and resid 76 through 78
      No H-bonds generated for 'chain 'B' and resid 76 through 78'
    Processing helix  chain 'B' and resid 82 through 98
      removed outlier: 4.075A  pdb=" N   LEU B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 127
      removed outlier: 3.694A  pdb=" N   ILE B 107 " --> pdb=" O   ASP B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 162
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 170 through 233
      removed outlier: 3.754A  pdb=" N   THR B 181 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
      Proline residue:  B 190  - end of helix
    Processing helix  chain 'C' and resid 20 through 63
    Processing helix  chain 'C' and resid 67 through 75
    Processing helix  chain 'C' and resid 76 through 78
      No H-bonds generated for 'chain 'C' and resid 76 through 78'
    Processing helix  chain 'C' and resid 82 through 98
    Processing helix  chain 'C' and resid 103 through 127
    Processing helix  chain 'C' and resid 129 through 163
      Proline residue:  C 141  - end of helix
    Processing helix  chain 'C' and resid 170 through 232
      removed outlier: 3.567A  pdb=" N   ILE C 174 " --> pdb=" O   VAL C 170 " (cutoff:3.500A)
      Proline residue:  C 190  - end of helix
    Processing helix  chain 'D' and resid 11 through 16
    Processing helix  chain 'D' and resid 21 through 63
    Processing helix  chain 'D' and resid 67 through 75
    Processing helix  chain 'D' and resid 82 through 98
    Processing helix  chain 'D' and resid 103 through 128
    Processing helix  chain 'D' and resid 129 through 161
      removed outlier: 4.063A  pdb=" N   LEU D 133 " --> pdb=" O   GLY D 129 " (cutoff:3.500A)
      Proline residue:  D 141  - end of helix
    Processing helix  chain 'D' and resid 170 through 233
      removed outlier: 3.666A  pdb=" N   ALA D 180 " --> pdb=" O   GLU D 176 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR D 181 " --> pdb=" O   ALA D 177 " (cutoff:3.500A)
      Proline residue:  D 190  - end of helix
    Processing helix  chain 'E' and resid 12 through 16
      removed outlier: 3.662A  pdb=" N   MET E  15 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR E  16 " --> pdb=" O   TRP E  13 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 12 through 16'
    Processing helix  chain 'E' and resid 23 through 63
      removed outlier: 4.278A  pdb=" N   GLY E  29 " --> pdb=" O   CYS E  25 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 67 through 75
    Processing helix  chain 'E' and resid 76 through 78
      No H-bonds generated for 'chain 'E' and resid 76 through 78'
    Processing helix  chain 'E' and resid 82 through 98
    Processing helix  chain 'E' and resid 103 through 127
    Processing helix  chain 'E' and resid 129 through 162
      Proline residue:  E 141  - end of helix
      removed outlier: 3.813A  pdb=" N   ALA E 160 " --> pdb=" O   PHE E 156 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN E 161 " --> pdb=" O   ILE E 157 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   THR E 162 " --> pdb=" O   GLY E 158 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 233
      removed outlier: 3.658A  pdb=" N   ILE E 174 " --> pdb=" O   VAL E 170 " (cutoff:3.500A)
      Proline residue:  E 190  - end of helix
    Processing helix  chain 'Y' and resid 20 through 37
      removed outlier: 3.962A  pdb=" N   VAL Y  26 " --> pdb=" O   PRO Y  22 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   MET Y  27 " --> pdb=" O   PHE Y  23 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL Y  29 " --> pdb=" O   ASP Y  25 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU Y  31 " --> pdb=" O   MET Y  27 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE Y  34 " --> pdb=" O   LEU Y  30 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 38 through 42
    Processing helix  chain 'Z' and resid 23 through 36
      removed outlier: 3.735A  pdb=" N   MET Z  27 " --> pdb=" O   PHE Z  23 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE Z  32 " --> pdb=" O   LEU Z  28 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL Z  36 " --> pdb=" O   ILE Z  32 " (cutoff:3.500A)

    816 hydrogen bonds defined for protein.
    2442 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: 1.20

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1524
        1.30 -     1.43: 2284
        1.43 -     1.55: 5412
        1.55 -     1.68: 30
        1.68 -     1.80: 67
  Bond restraints: 9317
  Sorted by residual:
  bond pdb=" C11 PGT A 301 "
       pdb=" O3  PGT A 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.431 -0.104 2.00e-02 2.50e+03 2.69e+01
  bond pdb=" C31 PGT A 301 "
       pdb=" O2  PGT A 301 "
    ideal  model  delta    sigma   weight residual
    1.331  1.404 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C31 PEV C 301 "
       pdb=" O2  PEV C 301 "
    ideal  model  delta    sigma   weight residual
    1.330  1.403 -0.073 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C31 PEV E 301 "
       pdb=" O2  PEV E 301 "
    ideal  model  delta    sigma   weight residual
    1.330  1.402 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C11 PEV C 301 "
       pdb=" O3  PEV C 301 "
    ideal  model  delta    sigma   weight residual
    1.335  1.398 -0.063 2.00e-02 2.50e+03 9.83e+00
  ... (remaining 9312 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.73: 12415
        3.73 -     7.47: 140
        7.47 -    11.20: 9
       11.20 -    14.93: 0
       14.93 -    18.66: 6
  Bond angle restraints: 12570
  Sorted by residual:
  angle pdb=" O3P PGT A 301 "
        pdb=" P   PGT A 301 "
        pdb=" O4P PGT A 301 "
      ideal   model   delta    sigma   weight residual
      92.82  111.48  -18.66 3.00e+00 1.11e-01 3.87e+01
  angle pdb=" O1P PEV C 301 "
        pdb=" P   PEV C 301 "
        pdb=" O2P PEV C 301 "
      ideal   model   delta    sigma   weight residual
     119.37  100.88   18.49 3.00e+00 1.11e-01 3.80e+01
  angle pdb=" O3P PEV C 301 "
        pdb=" P   PEV C 301 "
        pdb=" O4P PEV C 301 "
      ideal   model   delta    sigma   weight residual
      93.57  111.90  -18.33 3.00e+00 1.11e-01 3.73e+01
  angle pdb=" O1P PGT A 301 "
        pdb=" P   PGT A 301 "
        pdb=" O2P PGT A 301 "
      ideal   model   delta    sigma   weight residual
     119.10  100.80   18.30 3.00e+00 1.11e-01 3.72e+01
  angle pdb=" O3P PEV E 301 "
        pdb=" P   PEV E 301 "
        pdb=" O4P PEV E 301 "
      ideal   model   delta    sigma   weight residual
      93.57  111.77  -18.20 3.00e+00 1.11e-01 3.68e+01
  ... (remaining 12565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.60: 5232
       25.60 -    51.19: 322
       51.19 -    76.79: 49
       76.79 -   102.39: 6
      102.39 -   127.98: 2
  Dihedral angle restraints: 5611
    sinusoidal: 2239
      harmonic: 3372
  Sorted by residual:
  dihedral pdb=" CA  ALA A  19 "
           pdb=" C   ALA A  19 "
           pdb=" N   ASP A  20 "
           pdb=" CA  ASP A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.81  -22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" C3  PEV C 301 "
           pdb=" C1  PEV C 301 "
           pdb=" C2  PEV C 301 "
           pdb=" O3P PEV C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     292.80  164.82  127.98     1      3.00e+01 1.11e-03 1.72e+01
  dihedral pdb=" C3  PEV B 301 "
           pdb=" C1  PEV B 301 "
           pdb=" C2  PEV B 301 "
           pdb=" O3P PEV B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     292.80  172.73  120.07     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 5608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 968
       0.046 -    0.092: 424
       0.092 -    0.138: 60
       0.138 -    0.184: 10
       0.184 -    0.230: 3
  Chirality restraints: 1465
  Sorted by residual:
  chirality pdb=" C5  PGT A 301 "
            pdb=" C4  PGT A 301 "
            pdb=" C6  PGT A 301 "
            pdb=" O5  PGT A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.53    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" C2  PGT A 301 "
            pdb=" C1  PGT A 301 "
            pdb=" C3  PGT A 301 "
            pdb=" O2  PGT A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.55   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  VAL B 197 "
            pdb=" CA  VAL B 197 "
            pdb=" CG1 VAL B 197 "
            pdb=" CG2 VAL B 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.18 2.00e-01 2.50e+01 8.50e-01
  ... (remaining 1462 not shown)

  Planarity restraints: 1598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 113 "    0.017 2.00e-02 2.50e+03   1.73e-02 5.26e+00
        pdb=" CG  PHE A 113 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 113 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 113 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 113 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 113 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 113 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 140 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO B 141 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 141 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 141 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 171 "   -0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO E 172 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO E 172 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E 172 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1595 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 21
        2.42 -     3.04: 6027
        3.04 -     3.66: 13193
        3.66 -     4.28: 19345
        4.28 -     4.90: 32973
  Nonbonded interactions: 71559
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  98 "
            pdb=" NH1 ARG D 110 "
     model   vdw
     1.796 3.120
  nonbonded pdb=" OG  SER A  98 "
            pdb=" NH1 ARG A 110 "
     model   vdw
     2.179 3.120
  nonbonded pdb=" OE2 GLU A  58 "
            pdb=" OG  SER A  82 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG1 THR A 148 "
            pdb=" O   ALA A 177 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OE2 GLU B  58 "
            pdb=" OG  SER B  82 "
     model   vdw
     2.241 3.040
  ... (remaining 71554 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 11 through 233)
  selection = (chain 'B' and resid 11 through 233)
  selection = (chain 'C' and resid 11 through 233)
  selection = (chain 'D' and resid 11 through 233)
  selection = (chain 'E' and resid 11 through 233)
}
ncs_group {
  reference = (chain 'Y' and resid 12 through 40)
  selection = chain 'Z'
}

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:             0.430
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.690
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
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   0.798   9319  Z= 1.083
  Angle     :  1.033  18.665  12570  Z= 0.504
  Chirality :  0.049   0.230   1465
  Planarity :  0.004   0.039   1598
  Dihedral  : 16.668 127.984   3433
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.78 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 10.99 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.22), residues: 1172
  helix:  0.18 (0.15), residues: 996
  sheet:  None (None), residues: 0
  loop : -4.46 (0.30), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 118 
 TYR   0.016   0.002   TYR D 132 
 PHE   0.040   0.003   PHE A 113 
 TRP   0.012   0.002   TRP E  38 
 HIS   0.009   0.001   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.01150 ( 9317)
  covalent geometry    : angle       1.03303 (12570)
  hydrogen bonds       : bond        0.09594 (  816)
  hydrogen bonds       : angle       4.30293 ( 2442)
  Misc. bond           : bond        0.66393 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 148
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   94 GLU cc_start: 0.8723 (tp30) cc_final: 0.8202 (tp30)
REVERT: B  126 MET cc_start: 0.8050 (mmm) cc_final: 0.7532 (mmt)
REVERT: C   64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: C   94 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5210 (mm-30)
REVERT: D  128 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7521 (ttp-110)
REVERT: E  226 LEU cc_start: 0.8851 (mt) cc_final: 0.8548 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 152
  average time/residue: 0.1263
  time to fit residues: 24.7545
Evaluate side-chains
  126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain E residue  186 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
B  70 GLN
B  93 ASN
C 215 GLN
D  93 ASN
D 125 GLN
D 196 ASN
E  69 ASN
E  93 ASN
E 196 ASN
Z  16 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.169398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.134115 restraints weight = 10094.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.93
r_work: 0.3430 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9319  Z= 0.136
  Angle     :  0.518   6.757  12570  Z= 0.265
  Chirality :  0.035   0.123   1465
  Planarity :  0.003   0.029   1598
  Dihedral  : 12.021 127.447   1440
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.06 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.24), residues: 1172
  helix:  2.08 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -4.15 (0.35), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  53 
 TYR   0.010   0.001   TYR A 132 
 PHE   0.018   0.001   PHE A 113 
 TRP   0.012   0.001   TRP E  38 
 HIS   0.003   0.000   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9317)
  covalent geometry    : angle       0.51848 (12570)
  hydrogen bonds       : bond        0.05293 (  816)
  hydrogen bonds       : angle       3.43435 ( 2442)
  Misc. bond           : bond        0.00076 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: B   94 GLU cc_start: 0.8901 (tp30) cc_final: 0.8698 (tp30)
REVERT: B   96 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: B  126 MET cc_start: 0.7652 (mmm) cc_final: 0.7388 (mmt)
REVERT: B  153 MET cc_start: 0.8557 (ttp) cc_final: 0.8228 (ttt)
REVERT: C   93 ASN cc_start: 0.8407 (t0) cc_final: 0.7923 (t0)
REVERT: C  118 ARG cc_start: 0.7222 (tpm170) cc_final: 0.6856 (mmm-85)
REVERT: D  200 ARG cc_start: 0.8075 (mmm160) cc_final: 0.6838 (mtp180)
REVERT: E   58 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7918 (mt-10)
REVERT: E  226 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8147 (mp)
REVERT: Z   15 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7861 (mtt)
  outliers start: 17
  outliers final: 7
  residues processed: 126
  average time/residue: 0.1210
  time to fit residues: 19.7485
Evaluate side-chains
  121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain E residue   96 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Z residue   15 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 88 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.170730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.135329 restraints weight = 10258.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.95
r_work: 0.3394 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9319  Z= 0.137
  Angle     :  0.499   6.778  12570  Z= 0.252
  Chirality :  0.035   0.130   1465
  Planarity :  0.003   0.055   1598
  Dihedral  : 11.671 127.514   1439
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.03 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.96 (0.25), residues: 1172
  helix:  2.74 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -3.83 (0.37), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  53 
 TYR   0.007   0.001   TYR D 132 
 PHE   0.014   0.001   PHE A 113 
 TRP   0.011   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9317)
  covalent geometry    : angle       0.49875 (12570)
  hydrogen bonds       : bond        0.05105 (  816)
  hydrogen bonds       : angle       3.29552 ( 2442)
  Misc. bond           : bond        0.00228 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8222 (pt0)
REVERT: A  223 ASP cc_start: 0.7879 (m-30) cc_final: 0.7665 (m-30)
REVERT: B   17 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8487 (tp-100)
REVERT: B   94 GLU cc_start: 0.8919 (tp30) cc_final: 0.8574 (tp30)
REVERT: B   96 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7941 (mt-10)
REVERT: B  126 MET cc_start: 0.7635 (mmm) cc_final: 0.7211 (mmt)
REVERT: B  153 MET cc_start: 0.8575 (ttp) cc_final: 0.8186 (ttt)
REVERT: C  118 ARG cc_start: 0.7420 (tpm170) cc_final: 0.6958 (mmm-85)
REVERT: D   15 MET cc_start: 0.7609 (mtp) cc_final: 0.7283 (ttm)
REVERT: D   90 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7366 (mt-10)
REVERT: D  200 ARG cc_start: 0.8077 (mmm160) cc_final: 0.6907 (mtp180)
REVERT: E   99 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7833 (pt0)
REVERT: E  226 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8079 (mp)
REVERT: Z   15 MET cc_start: 0.8197 (mtm) cc_final: 0.7873 (mtt)
  outliers start: 22
  outliers final: 13
  residues processed: 125
  average time/residue: 0.1221
  time to fit residues: 19.9003
Evaluate side-chains
  125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 112 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
E  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.169535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.133687 restraints weight = 10294.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.96
r_work: 0.3447 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9319  Z= 0.132
  Angle     :  0.488   6.808  12570  Z= 0.245
  Chirality :  0.035   0.167   1465
  Planarity :  0.003   0.039   1598
  Dihedral  : 11.320 123.233   1439
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.53 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.37 (0.25), residues: 1172
  helix:  3.02 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -3.70 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  54 
 TYR   0.014   0.001   TYR B  16 
 PHE   0.012   0.001   PHE A 113 
 TRP   0.010   0.001   TRP E  38 
 HIS   0.001   0.000   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9317)
  covalent geometry    : angle       0.48785 (12570)
  hydrogen bonds       : bond        0.04920 (  816)
  hydrogen bonds       : angle       3.20838 ( 2442)
  Misc. bond           : bond        0.00306 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   64 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8103 (pt0)
REVERT: A  223 ASP cc_start: 0.7772 (m-30) cc_final: 0.7404 (m-30)
REVERT: B   94 GLU cc_start: 0.8787 (tp30) cc_final: 0.8562 (tp30)
REVERT: B   96 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: B  153 MET cc_start: 0.8482 (ttp) cc_final: 0.8097 (ttt)
REVERT: C  114 ARG cc_start: 0.6307 (tpm170) cc_final: 0.6006 (tpm170)
REVERT: C  118 ARG cc_start: 0.7257 (tpm170) cc_final: 0.6940 (mmm-85)
REVERT: D  200 ARG cc_start: 0.7932 (mmm160) cc_final: 0.6896 (mtp180)
REVERT: E  215 GLN cc_start: 0.8129 (tp40) cc_final: 0.7534 (tt0)
REVERT: E  226 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8140 (mp)
REVERT: Z   15 MET cc_start: 0.8005 (mtm) cc_final: 0.7698 (mtt)
  outliers start: 23
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1058
  time to fit residues: 18.6108
Evaluate side-chains
  117 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   59 GLN
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 111 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.187705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152782 restraints weight = 9979.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 1.87
r_work: 0.3640 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9319  Z= 0.133
  Angle     :  0.479   6.814  12570  Z= 0.241
  Chirality :  0.035   0.131   1465
  Planarity :  0.003   0.057   1598
  Dihedral  : 10.941 122.836   1438
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.21 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.60 (0.25), residues: 1172
  helix:  3.16 (0.15), residues: 1014
  sheet:  None (None), residues: 0
  loop : -3.51 (0.40), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 200 
 TYR   0.007   0.001   TYR D 132 
 PHE   0.011   0.001   PHE Z  23 
 TRP   0.010   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9317)
  covalent geometry    : angle       0.47874 (12570)
  hydrogen bonds       : bond        0.04878 (  816)
  hydrogen bonds       : angle       3.17787 ( 2442)
  Misc. bond           : bond        0.00193 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8094 (pt0)
REVERT: A  223 ASP cc_start: 0.7773 (m-30) cc_final: 0.7377 (m-30)
REVERT: B   96 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7809 (mt-10)
REVERT: B  153 MET cc_start: 0.8469 (ttp) cc_final: 0.8073 (ttt)
REVERT: C  114 ARG cc_start: 0.6343 (tpm170) cc_final: 0.6030 (tpm170)
REVERT: C  118 ARG cc_start: 0.7255 (tpm170) cc_final: 0.6929 (mmm-85)
REVERT: D  128 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7305 (ttp-170)
REVERT: D  153 MET cc_start: 0.6918 (ttp) cc_final: 0.6659 (ttt)
REVERT: D  200 ARG cc_start: 0.7850 (mmm160) cc_final: 0.7007 (mtm-85)
REVERT: E   99 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7642 (pt0)
REVERT: E  215 GLN cc_start: 0.8168 (tp40) cc_final: 0.7603 (tt0)
REVERT: E  226 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8231 (mp)
REVERT: Z   15 MET cc_start: 0.7876 (mtm) cc_final: 0.7613 (mtt)
  outliers start: 26
  outliers final: 17
  residues processed: 125
  average time/residue: 0.1117
  time to fit residues: 18.6915
Evaluate side-chains
  123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   59 GLN
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 111 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.188312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.153437 restraints weight = 10024.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 1.88
r_work: 0.3651 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9319  Z= 0.126
  Angle     :  0.471   7.501  12570  Z= 0.237
  Chirality :  0.034   0.118   1465
  Planarity :  0.003   0.046   1598
  Dihedral  : 10.536 120.203   1438
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.86 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.76 (0.25), residues: 1172
  helix:  3.23 (0.15), residues: 1017
  sheet:  None (None), residues: 0
  loop : -3.33 (0.42), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 118 
 TYR   0.006   0.001   TYR D 132 
 PHE   0.010   0.001   PHE Z  23 
 TRP   0.010   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9317)
  covalent geometry    : angle       0.47086 (12570)
  hydrogen bonds       : bond        0.04708 (  816)
  hydrogen bonds       : angle       3.12624 ( 2442)
  Misc. bond           : bond        0.00174 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8066 (pt0)
REVERT: A  181 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7448 (m)
REVERT: A  223 ASP cc_start: 0.7752 (m-30) cc_final: 0.7331 (m-30)
REVERT: B   96 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: B  153 MET cc_start: 0.8458 (ttp) cc_final: 0.8055 (ttt)
REVERT: C   64 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: C  118 ARG cc_start: 0.7146 (tpm170) cc_final: 0.6908 (mmm-85)
REVERT: D   47 GLU cc_start: 0.7783 (tp30) cc_final: 0.7580 (mm-30)
REVERT: D  128 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7272 (ttp-170)
REVERT: D  153 MET cc_start: 0.6941 (ttp) cc_final: 0.6671 (ttt)
REVERT: D  200 ARG cc_start: 0.7857 (mmm160) cc_final: 0.6953 (mtp180)
REVERT: E  226 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8167 (mp)
REVERT: Z   15 MET cc_start: 0.7867 (mtm) cc_final: 0.7625 (mtt)
  outliers start: 27
  outliers final: 19
  residues processed: 131
  average time/residue: 0.1038
  time to fit residues: 18.3419
Evaluate side-chains
  125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 89 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 92 optimal weight:    0.6980
   chunk 44 optimal weight:   20.0000
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
D 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.197071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.160336 restraints weight = 10142.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 1.94
r_work: 0.3647 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9319  Z= 0.123
  Angle     :  0.470   7.779  12570  Z= 0.236
  Chirality :  0.034   0.118   1465
  Planarity :  0.003   0.064   1598
  Dihedral  : 10.280 116.130   1438
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.83 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.90 (0.25), residues: 1172
  helix:  3.33 (0.15), residues: 1016
  sheet:  None (None), residues: 0
  loop : -3.25 (0.43), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  54 
 TYR   0.006   0.001   TYR C 132 
 PHE   0.010   0.001   PHE A 113 
 TRP   0.009   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9317)
  covalent geometry    : angle       0.47033 (12570)
  hydrogen bonds       : bond        0.04614 (  816)
  hydrogen bonds       : angle       3.09112 ( 2442)
  Misc. bond           : bond        0.00161 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8056 (pt0)
REVERT: A  181 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7534 (m)
REVERT: A  223 ASP cc_start: 0.7750 (m-30) cc_final: 0.7278 (m-30)
REVERT: B  153 MET cc_start: 0.8459 (ttp) cc_final: 0.8054 (ttt)
REVERT: C   64 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8031 (tm-30)
REVERT: D  128 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7241 (ttp-170)
REVERT: D  153 MET cc_start: 0.6956 (ttp) cc_final: 0.6682 (ttt)
REVERT: D  200 ARG cc_start: 0.7829 (mmm160) cc_final: 0.6927 (mtp180)
REVERT: E  226 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8145 (mp)
REVERT: Z   15 MET cc_start: 0.7845 (mtm) cc_final: 0.7635 (mtt)
  outliers start: 24
  outliers final: 19
  residues processed: 126
  average time/residue: 0.1108
  time to fit residues: 18.7096
Evaluate side-chains
  124 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.187894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.152882 restraints weight = 9974.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 1.87
r_work: 0.3646 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9319  Z= 0.134
  Angle     :  0.489   8.317  12570  Z= 0.245
  Chirality :  0.035   0.118   1465
  Planarity :  0.003   0.059   1598
  Dihedral  : 10.051 116.628   1437
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.37 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.90 (0.25), residues: 1172
  helix:  3.32 (0.15), residues: 1016
  sheet:  None (None), residues: 0
  loop : -3.18 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 118 
 TYR   0.012   0.001   TYR C  16 
 PHE   0.010   0.001   PHE Z  23 
 TRP   0.009   0.001   TRP E  38 
 HIS   0.001   0.000   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9317)
  covalent geometry    : angle       0.48856 (12570)
  hydrogen bonds       : bond        0.04774 (  816)
  hydrogen bonds       : angle       3.10002 ( 2442)
  Misc. bond           : bond        0.00196 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8040 (pt0)
REVERT: A  223 ASP cc_start: 0.7758 (m-30) cc_final: 0.7292 (m-30)
REVERT: B  153 MET cc_start: 0.8460 (ttp) cc_final: 0.8053 (ttt)
REVERT: C   64 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: C  114 ARG cc_start: 0.6305 (tpm170) cc_final: 0.5988 (tpm170)
REVERT: D  128 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7307 (ttp-170)
REVERT: D  153 MET cc_start: 0.6963 (ttp) cc_final: 0.6684 (ttt)
REVERT: D  200 ARG cc_start: 0.7825 (mmm160) cc_final: 0.6958 (mtp180)
REVERT: E  226 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8171 (mp)
REVERT: Z   15 MET cc_start: 0.7857 (mtm) cc_final: 0.7617 (mtt)
  outliers start: 22
  outliers final: 19
  residues processed: 125
  average time/residue: 0.1179
  time to fit residues: 19.2814
Evaluate side-chains
  122 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 108 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.197539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.160764 restraints weight = 10110.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 1.95
r_work: 0.3647 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9319  Z= 0.122
  Angle     :  0.474   8.212  12570  Z= 0.239
  Chirality :  0.034   0.117   1465
  Planarity :  0.003   0.055   1598
  Dihedral  :  9.842 115.423   1437
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.26 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.02 (0.25), residues: 1172
  helix:  3.40 (0.15), residues: 1016
  sheet:  None (None), residues: 0
  loop : -3.13 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  54 
 TYR   0.012   0.001   TYR C  16 
 PHE   0.011   0.001   PHE Z  23 
 TRP   0.009   0.001   TRP E  38 
 HIS   0.001   0.000   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9317)
  covalent geometry    : angle       0.47394 (12570)
  hydrogen bonds       : bond        0.04572 (  816)
  hydrogen bonds       : angle       3.06616 ( 2442)
  Misc. bond           : bond        0.00179 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8033 (pt0)
REVERT: A  223 ASP cc_start: 0.7765 (m-30) cc_final: 0.7289 (m-30)
REVERT: B  153 MET cc_start: 0.8454 (ttp) cc_final: 0.8052 (ttt)
REVERT: C   64 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: D  128 ARG cc_start: 0.7858 (ttm170) cc_final: 0.7247 (ttp-170)
REVERT: D  153 MET cc_start: 0.7006 (ttp) cc_final: 0.6737 (ttt)
REVERT: D  200 ARG cc_start: 0.7860 (mmm160) cc_final: 0.6953 (mtp180)
REVERT: E  226 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8166 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1089
  time to fit residues: 18.2182
Evaluate side-chains
  119 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0980
   chunk 85 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.198342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.161666 restraints weight = 9953.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.92
r_work: 0.3664 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9319  Z= 0.120
  Angle     :  0.473   8.416  12570  Z= 0.238
  Chirality :  0.034   0.117   1465
  Planarity :  0.003   0.075   1598
  Dihedral  :  9.665 114.059   1437
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.69 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.11 (0.25), residues: 1172
  helix:  3.46 (0.15), residues: 1017
  sheet:  None (None), residues: 0
  loop : -3.16 (0.46), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  54 
 TYR   0.015   0.001   TYR C  16 
 PHE   0.011   0.001   PHE Z  23 
 TRP   0.008   0.001   TRP E  38 
 HIS   0.003   0.000   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9317)
  covalent geometry    : angle       0.47266 (12570)
  hydrogen bonds       : bond        0.04476 (  816)
  hydrogen bonds       : angle       3.06575 ( 2442)
  Misc. bond           : bond        0.00169 (    2)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8054 (pt0)
REVERT: A  223 ASP cc_start: 0.7741 (m-30) cc_final: 0.7260 (m-30)
REVERT: B  153 MET cc_start: 0.8434 (ttp) cc_final: 0.8027 (ttt)
REVERT: C   64 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8109 (tm-30)
REVERT: D  153 MET cc_start: 0.6949 (ttp) cc_final: 0.6684 (ttt)
REVERT: D  200 ARG cc_start: 0.7620 (mmm160) cc_final: 0.6781 (mtm110)
REVERT: E  208 MET cc_start: 0.8105 (ttp) cc_final: 0.7892 (ttm)
REVERT: E  226 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8143 (mp)
  outliers start: 19
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1011
  time to fit residues: 15.9454
Evaluate side-chains
  116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4237 r_free = 0.4237 target = 0.195438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.158521 restraints weight = 10109.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 1.94
r_work: 0.3623 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9319  Z= 0.149
  Angle     :  0.502   8.120  12570  Z= 0.251
  Chirality :  0.035   0.118   1465
  Planarity :  0.003   0.071   1598
  Dihedral  :  9.727 112.266   1437
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.58 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.94 (0.25), residues: 1172
  helix:  3.34 (0.15), residues: 1016
  sheet:  None (None), residues: 0
  loop : -3.06 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  54 
 TYR   0.015   0.001   TYR C  16 
 PHE   0.011   0.001   PHE Z  23 
 TRP   0.009   0.001   TRP E  38 
 HIS   0.004   0.000   HIS Z  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9317)
  covalent geometry    : angle       0.50237 (12570)
  hydrogen bonds       : bond        0.04954 (  816)
  hydrogen bonds       : angle       3.14792 ( 2442)
  Misc. bond           : bond        0.00191 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1740.82 seconds
wall clock time: 30 minutes 30.30 seconds (1830.30 seconds total)