Starting phenix.real_space_refine
on Sun Aug 24 17:52:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dq1_27646/08_2025/8dq1_27646_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dq1_27646/08_2025/8dq1_27646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dq1_27646/08_2025/8dq1_27646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dq1_27646/08_2025/8dq1_27646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dq1_27646/08_2025/8dq1_27646_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dq1_27646/08_2025/8dq1_27646_trim.cif"
  }
  resolution = 4.1
  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=   0.000 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4735 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Br      2      7.06       5
     P      34      5.49       5
     S      52      5.16       5
     C    5840      2.51       5
     N    1704      2.21       5
     O    1779      1.98       5
     H    8343      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17754
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 3772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 3772
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 10, 'TRANS': 230}
    Chain: "D"
      Number of atoms: 3728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3728
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 10, 'TRANS': 227}
    Chain: "A"
      Number of atoms: 4749
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 298, 4741
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
      Conformer: "B"
        Number of residues, atoms: 298, 4741
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
          bond proxies already assigned to first conformer: 4787
    Chain: "B"
      Number of atoms: 4733
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 298, 4725
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
      Conformer: "B"
        Number of residues, atoms: 298, 4725
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
          bond proxies already assigned to first conformer: 4771
    Chain: "I"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 363
          Classifications: {'DNA': 18}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 17}
    Chain: "J"
      Number of atoms: 369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 369
          Classifications: {'DNA': 18}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 17}
    Chain: "C"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'K5G': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'K5G': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.57, per 1000 atoms: 0.26
  Number of scatterers: 17754
  At special positions: 0
  Unit cell: (77.4, 108.36, 140.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Br      2     34.99
     S      52     16.00
     P      34     15.00
     O    1779      8.00
     N    1704      7.00
     C    5840      6.00
     H    8343      1.00
    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
      
  Atom "HETATM17750  O05 K5G D 301 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 716.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 7 sheets defined
      52.0% alpha, 11.9% beta
      6 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 3.22
  Creating SS restraints...
    Processing helix  chain 'C' and resid 5 through 19
    Processing helix  chain 'C' and resid 23 through 35
    Processing helix  chain 'C' and resid 65 through 76
    Processing helix  chain 'C' and resid 76 through 81
      removed outlier: 4.571A  pdb=" N   VAL C  80 " --> pdb=" O   ASN C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 90
      removed outlier: 3.776A  pdb=" N   LEU C  85 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLY C  87 " --> pdb=" O   ALA C  83 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   LEU C  88 " --> pdb=" O   ILE C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 114
      removed outlier: 4.205A  pdb=" N   TRP C 108 " --> pdb=" O   SER C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 169
      removed outlier: 4.601A  pdb=" N   GLU C 149 " --> pdb=" O   SER C 145 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   GLU C 150 " --> pdb=" O   PHE C 146 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE C 151 " --> pdb=" O   GLU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 194
    Processing helix  chain 'C' and resid 197 through 206
    Processing helix  chain 'C' and resid 208 through 224
    Processing helix  chain 'C' and resid 227 through 238
      removed outlier: 3.682A  pdb=" N   ALA C 231 " --> pdb=" O   ASN C 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 19
      removed outlier: 3.994A  pdb=" N   GLY D  13 " --> pdb=" O   LEU D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 39
    Processing helix  chain 'D' and resid 65 through 76
    Processing helix  chain 'D' and resid 81 through 90
      removed outlier: 4.263A  pdb=" N   GLY D  87 " --> pdb=" O   ALA D  83 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU D  88 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG D  89 " --> pdb=" O   LEU D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 4.457A  pdb=" N   GLN D 103 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 114
      removed outlier: 3.885A  pdb=" N   TRP D 108 " --> pdb=" O   SER D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 169
      removed outlier: 4.323A  pdb=" N   GLU D 149 " --> pdb=" O   SER D 145 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLU D 150 " --> pdb=" O   PHE D 146 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE D 159 " --> pdb=" O   LEU D 155 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLU D 160 " --> pdb=" O   ARG D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 194
      removed outlier: 3.680A  pdb=" N   ASP D 194 " --> pdb=" O   GLN D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 206
    Processing helix  chain 'D' and resid 208 through 224
      removed outlier: 3.556A  pdb=" N   VAL D 212 " --> pdb=" O   SER D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 239
      removed outlier: 3.588A  pdb=" N   ALA D 231 " --> pdb=" O   ASN D 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 56
      removed outlier: 3.588A  pdb=" N   ALA A  50 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 60
      No H-bonds generated for 'chain 'A' and resid 58 through 60'
    Processing helix  chain 'A' and resid 71 through 76
      removed outlier: 3.827A  pdb=" N   GLY A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.525A  pdb=" N   LEU A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 102
      removed outlier: 3.738A  pdb=" N   GLN A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 116
      removed outlier: 4.101A  pdb=" N   VAL A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A 107 " --> pdb=" O   GLU A 103 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL A 108 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 132
    Processing helix  chain 'A' and resid 198 through 211
      removed outlier: 3.532A  pdb=" N   GLU A 203 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 232
    Processing helix  chain 'A' and resid 232 through 255
    Processing helix  chain 'A' and resid 257 through 270
      removed outlier: 4.049A  pdb=" N   LEU A 261 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 296
      removed outlier: 3.579A  pdb=" N   GLY A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 43
      No H-bonds generated for 'chain 'B' and resid 41 through 43'
    Processing helix  chain 'B' and resid 44 through 56
      removed outlier: 3.539A  pdb=" N   ALA B  50 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ARG B  54 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TRP B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 60
      No H-bonds generated for 'chain 'B' and resid 58 through 60'
    Processing helix  chain 'B' and resid 71 through 75
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 106 through 116
    Processing helix  chain 'B' and resid 197 through 210
      removed outlier: 3.760A  pdb=" N   GLU B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
      removed outlier: 3.740A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 227 through 232'
    Processing helix  chain 'B' and resid 232 through 255
    Processing helix  chain 'B' and resid 257 through 274
      removed outlier: 3.778A  pdb=" N   LEU B 261 " --> pdb=" O   SER B 257 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   GLY B 271 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   GLN B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   SER B 273 " --> pdb=" O   TRP B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 297
    Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 62
    Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 62
      removed outlier: 3.699A  pdb=" N   VAL D  94 " --> pdb=" O   THR D 121 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 11
      removed outlier: 6.693A  pdb=" N   LEU A  14 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   TRP A  34 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
      removed outlier: 8.644A  pdb=" N   LEU A  66 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LEU A  36 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   VAL A  90 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL A 137 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ALA A  92 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146
      removed outlier: 6.491A  pdb=" N   HIS A 149 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 9.738A  pdb=" N   VAL A 164 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   GLY A 177 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LEU A 174 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4
      removed outlier: 3.507A  pdb=" N   LEU B 224 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   LEU B 174 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE B 166 " --> pdb=" O   PHE B 175 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 11
      removed outlier: 5.983A  pdb=" N   GLN B   9 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   LEU B  16 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TRP B  34 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   TYR B  64 " --> pdb=" O   TRP B  34 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 184

    429 hydrogen bonds defined for protein.
    1223 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      16 hydrogen bonds
      32 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 4.15

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        0.82 -     1.04: 8318
        1.04 -     1.27: 1502
        1.27 -     1.49: 4395
        1.49 -     1.72: 3748
        1.72 -     1.94: 83
  Bond restraints: 18046
  Sorted by residual:
  bond pdb=" C12 K5G D 301 "
       pdb=" C13 K5G D 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.874 -0.354 2.00e-02 2.50e+03 3.13e+02
  bond pdb=" C12 K5G C 301 "
       pdb=" C13 K5G C 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.871 -0.351 2.00e-02 2.50e+03 3.08e+02
  bond pdb=" CA  MET C 173 "
       pdb=" C   MET C 173 "
    ideal  model  delta    sigma   weight residual
    1.524  1.412  0.111 1.27e-02 6.20e+03 7.70e+01
  bond pdb=" C   LEU C 130 "
       pdb=" O   LEU C 130 "
    ideal  model  delta    sigma   weight residual
    1.234  1.141  0.093 1.20e-02 6.94e+03 6.00e+01
  bond pdb=" CA  ARG C  37 "
       pdb=" C   ARG C  37 "
    ideal  model  delta    sigma   weight residual
    1.522  1.423  0.100 1.38e-02 5.25e+03 5.22e+01
  ... (remaining 18041 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 31722
        3.26 -     6.52: 468
        6.52 -     9.77: 33
        9.77 -    13.03: 8
       13.03 -    16.29: 1
  Bond angle restraints: 32232
  Sorted by residual:
  angle pdb=" N   ARG C  36 "
        pdb=" CA  ARG C  36 "
        pdb=" C   ARG C  36 "
      ideal   model   delta    sigma   weight residual
     113.12  102.45   10.67 1.25e+00 6.40e-01 7.28e+01
  angle pdb=" N   LEU C 174 "
        pdb=" CA  LEU C 174 "
        pdb=" C   LEU C 174 "
      ideal   model   delta    sigma   weight residual
     113.38  122.22   -8.84 1.23e+00 6.61e-01 5.17e+01
  angle pdb=" C   PHE A 276 "
        pdb=" CA  PHE A 276 "
        pdb=" CB  PHE A 276 "
      ideal   model   delta    sigma   weight residual
     109.27  120.18  -10.91 1.64e+00 3.72e-01 4.43e+01
  angle pdb=" N   LEU B 117 "
        pdb=" CA  LEU B 117 "
        pdb=" C   LEU B 117 "
      ideal   model   delta    sigma   weight residual
     108.23  119.56  -11.33 1.72e+00 3.38e-01 4.34e+01
  angle pdb=" N   ARG B 114 "
        pdb=" CA  ARG B 114 "
        pdb=" C   ARG B 114 "
      ideal   model   delta    sigma   weight residual
     111.28  104.25    7.03 1.09e+00 8.42e-01 4.15e+01
  ... (remaining 32227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.73: 7687
       26.73 -    53.47: 600
       53.47 -    80.20: 151
       80.20 -   106.94: 12
      106.94 -   133.67: 1
  Dihedral angle restraints: 8451
    sinusoidal: 4790
      harmonic: 3661
  Sorted by residual:
  dihedral pdb=" C   PHE A 276 "
           pdb=" N   PHE A 276 "
           pdb=" CA  PHE A 276 "
           pdb=" CB  PHE A 276 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.46   16.86     0      2.50e+00 1.60e-01 4.55e+01
  dihedral pdb=" CA  GLU C 147 "
           pdb=" C   GLU C 147 "
           pdb=" N   ARG C 148 "
           pdb=" CA  ARG C 148 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.68  -28.32     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" N   PHE A 276 "
           pdb=" C   PHE A 276 "
           pdb=" CA  PHE A 276 "
           pdb=" CB  PHE A 276 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.83  -13.03     0      2.50e+00 1.60e-01 2.72e+01
  ... (remaining 8448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.123: 1374
       0.123 -    0.245: 55
       0.245 -    0.368: 9
       0.368 -    0.490: 3
       0.490 -    0.613: 2
  Chirality restraints: 1443
  Sorted by residual:
  chirality pdb=" CA  PHE A 276 "
            pdb=" N   PHE A 276 "
            pdb=" C   PHE A 276 "
            pdb=" CB  PHE A 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.39e+00
  chirality pdb=" CA  LEU B 117 "
            pdb=" N   LEU B 117 "
            pdb=" C   LEU B 117 "
            pdb=" CB  LEU B 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.46e+00
  chirality pdb=" CA  ARG D 156 "
            pdb=" N   ARG D 156 "
            pdb=" C   ARG D 156 "
            pdb=" CB  ARG D 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.36e+00
  ... (remaining 1440 not shown)

  Planarity restraints: 2605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 129 "   -0.285 2.00e-02 2.50e+03   3.09e-01 1.43e+03
        pdb=" CG  ASN C 129 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 129 "    0.274 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 129 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN C 129 "    0.449 2.00e-02 2.50e+03
        pdb="HD22 ASN C 129 "   -0.462 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 115 "   -0.204 2.00e-02 2.50e+03   2.41e-01 8.73e+02
        pdb=" CD  GLN B 115 "    0.015 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 115 "    0.195 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 115 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN B 115 "    0.364 2.00e-02 2.50e+03
        pdb="HE22 GLN B 115 "   -0.370 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 121 "    0.205 2.00e-02 2.50e+03   2.29e-01 7.89e+02
        pdb=" CD  GLN B 121 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 121 "   -0.185 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 121 "    0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN B 121 "   -0.337 2.00e-02 2.50e+03
        pdb="HE22 GLN B 121 "    0.353 2.00e-02 2.50e+03
  ... (remaining 2602 not shown)

  Histogram of nonbonded interaction distances:
        0.86 -     1.63: 6
        1.63 -     2.40: 7039
        2.40 -     3.17: 55063
        3.17 -     3.93: 74460
        3.93 -     4.70: 122223
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 258791
  Sorted by model distance:
  nonbonded pdb="HH11 ARG C  37 "
            pdb="HD23 LEU A 211 "
     model   vdw
     0.863 2.270
  nonbonded pdb=" HB3 ARG B  43 "
            pdb="HD23 LEU B 117 "
     model   vdw
     1.095 2.440
  nonbonded pdb="HG12 VAL D  60 "
            pdb="BR1  K5G D 301 "
     model   vdw
     1.389 3.070
  nonbonded pdb="HH11 ARG C  37 "
            pdb=" CD2 LEU A 211 "
     model   vdw
     1.513 2.750
  nonbonded pdb=" OE1 GLN B 115 "
            pdb=" HG3 PRO B 278 "
     model   vdw
     1.539 2.620
  ... (remaining 258786 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 1 through 59 or resid 61 through 117 or (resid 118 and (na \ 
me N or name CA or name C or name O or name CB or name CG or name CD or name NE  \ 
or name CZ or name NH1 or name NH2)) or (resid 119 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 120 through 244 or resid 246 through 254 or \ 
 (resid 255 and (name N or name CA or name C or name O )) or resid 256 through 2 \ 
98))
  selection = (chain 'B' and (resid 1 through 59 or resid 61 through 230 or (resid 231 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 232 through 244 or re \ 
sid 246 through 298))
}
ncs_group {
  reference = (chain 'C' and (resid 4 through 49 or (resid 50 and (name N or name CA or name C \ 
 or name O or name CB or name OG1 or name CG2)) or resid 51 through 68 or (resid \ 
 69 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ 
 or name CD2)) or resid 70 through 129 or (resid 130 and (name N or name CA or n \ 
ame C or name O or name CB or name CG or name CD1 or name CD2)) or resid 131 thr \ 
ough 155 or (resid 156 and (name N or name CA or name C or name O or name CB or  \ 
name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 157  \ 
through 161 or (resid 162 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD1 or name CD2)) or resid 163 through 211 or (resid 212 and  \ 
(name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or r \ 
esid 213 through 301))
  selection = (chain 'D' and (resid 4 through 9 or (resid 10 and (name N or name CA or name C  \ 
or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2  \ 
or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 11 through 35 or (res \ 
id 36 and (name N or name CA or name C or name O or name CB or name CG or name C \ 
D or name NE or name CZ or name NH1 or name NH2)) or resid 37 or (resid 38 and ( \ 
name N or name CA or name C or name O or name CB or name CG or name CD1 or name  \ 
CD2)) or resid 39 through 173 or (resid 174 and (name N or name CA or name C or  \ 
name O or name CB or name CG or name CD1 or name CD2)) or resid 175 through 301) \ 
)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.680
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
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      :  0.011   0.354   9703  Z= 0.578
  Angle     :  1.104  11.602  13309  Z= 0.600
  Chirality :  0.065   0.613   1443
  Planarity :  0.007   0.086   1599
  Dihedral  : 19.210 133.673   3695
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  1.52 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.30 %
  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 aren not related in a simple way.
  whole: -1.40 (0.25), residues: 1069
  helix:  0.07 (0.23), residues: 482
  sheet: -1.96 (0.40), residues: 144
  loop : -1.60 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.033   0.001   ARG D  89 
 TYR   0.041   0.004   TYR B 201 
 PHE   0.037   0.003   PHE A  25 
 TRP   0.053   0.003   TRP A 100 
 HIS   0.020   0.003   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.01065 ( 9703)
  covalent geometry    : angle       1.10372 (13309)
  hydrogen bonds       : bond        0.17804 (  445)
  hydrogen bonds       : angle       6.81786 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 302
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   41 ASP cc_start: 0.7948 (m-30) cc_final: 0.7589 (m-30)
REVERT: C   55 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7295 (ttm110)
REVERT: C   75 GLN cc_start: 0.7361 (mt0) cc_final: 0.6917 (mt0)
REVERT: C   76 ASN cc_start: 0.8454 (t0) cc_final: 0.8175 (t0)
REVERT: C   85 LEU cc_start: 0.8336 (mt) cc_final: 0.8096 (mt)
REVERT: C  109 ASN cc_start: 0.7980 (m110) cc_final: 0.7629 (m-40)
REVERT: C  142 ASN cc_start: 0.7395 (m110) cc_final: 0.7099 (t0)
REVERT: C  218 ASN cc_start: 0.7852 (m110) cc_final: 0.7600 (m110)
REVERT: D   32 GLU cc_start: 0.6369 (tt0) cc_final: 0.6168 (tt0)
REVERT: D   55 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7708 (tmm160)
REVERT: D   74 MET cc_start: 0.7536 (mmt) cc_final: 0.7255 (mmm)
REVERT: D   76 ASN cc_start: 0.8728 (t0) cc_final: 0.8407 (t0)
REVERT: D   77 TYR cc_start: 0.7363 (m-80) cc_final: 0.5796 (m-80)
REVERT: D  106 MET cc_start: 0.4932 (tmm) cc_final: 0.4706 (tpp)
REVERT: D  107 LEU cc_start: 0.7668 (mm) cc_final: 0.7430 (tp)
REVERT: D  109 ASN cc_start: 0.7576 (m-40) cc_final: 0.7259 (m110)
REVERT: D  147 GLU cc_start: 0.8012 (tt0) cc_final: 0.7592 (tt0)
REVERT: D  156 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6876 (ttm-80)
REVERT: D  214 PHE cc_start: 0.7954 (t80) cc_final: 0.7540 (t80)
REVERT: A   13 ASP cc_start: 0.8533 (p0) cc_final: 0.8094 (p0)
REVERT: A  118 ARG cc_start: 0.7923 (mpt-90) cc_final: 0.7523 (mmm160)
REVERT: A  122 ARG cc_start: 0.7441 (mpp80) cc_final: 0.7229 (mtt90)
REVERT: A  144 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: A  161 ASP cc_start: 0.8461 (m-30) cc_final: 0.8101 (m-30)
REVERT: A  256 GLU cc_start: 0.5493 (tt0) cc_final: 0.4896 (mt-10)
REVERT: A  276 PHE cc_start: 0.8958 (p90) cc_final: 0.8739 (p90)
REVERT: A  289 MET cc_start: 0.8645 (ttt) cc_final: 0.8432 (ttp)
REVERT: B  167 TYR cc_start: 0.7656 (t80) cc_final: 0.7337 (t80)
REVERT: B  264 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6934 (tt0)
  outliers start: 8
  outliers final: 4
  residues processed: 305
  average time/residue: 0.2404
  time to fit residues: 99.0258
Evaluate side-chains
  262 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 257
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
C 129 ASN
C 142 ASN
C 164 GLN
C 215 HIS
D  86 ASN
D 220 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.167682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.127069 restraints weight = 38083.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.132651 restraints weight = 16274.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.136167 restraints weight = 8694.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.138411 restraints weight = 5714.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.139755 restraints weight = 4370.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9703  Z= 0.141
  Angle     :  0.575   5.916  13309  Z= 0.306
  Chirality :  0.038   0.137   1443
  Planarity :  0.005   0.061   1599
  Dihedral  : 17.958  89.953   1610
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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 aren not related in a simple way.
  whole: -0.67 (0.26), residues: 1069
  helix:  0.83 (0.24), residues: 486
  sheet: -1.82 (0.41), residues: 149
  loop : -1.34 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 122 
 TYR   0.031   0.002   TYR C  72 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.021   0.001   TRP A 100 
 HIS   0.008   0.001   HIS B 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9703)
  covalent geometry    : angle       0.57497 (13309)
  hydrogen bonds       : bond        0.04533 (  445)
  hydrogen bonds       : angle       5.39344 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   55 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7361 (ttm110)
REVERT: C   75 GLN cc_start: 0.7313 (mt0) cc_final: 0.6910 (mt0)
REVERT: C  105 ARG cc_start: 0.6350 (mtt-85) cc_final: 0.5780 (mtt-85)
REVERT: C  109 ASN cc_start: 0.8071 (m110) cc_final: 0.7823 (m-40)
REVERT: D   32 GLU cc_start: 0.6764 (tt0) cc_final: 0.6426 (tt0)
REVERT: D   37 ARG cc_start: 0.6367 (tmt170) cc_final: 0.6071 (ttt-90)
REVERT: D   74 MET cc_start: 0.7136 (mmt) cc_final: 0.6890 (mmm)
REVERT: D   89 ARG cc_start: 0.7659 (mmm160) cc_final: 0.7148 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7647 (tt0) cc_final: 0.7433 (tt0)
REVERT: D  157 CYS cc_start: 0.8989 (m) cc_final: 0.8608 (m)
REVERT: D  214 PHE cc_start: 0.7990 (t80) cc_final: 0.7363 (t80)
REVERT: A   13 ASP cc_start: 0.8173 (p0) cc_final: 0.7626 (p0)
REVERT: A   28 ARG cc_start: 0.8601 (ttt90) cc_final: 0.8374 (ttt-90)
REVERT: A   87 ASN cc_start: 0.8809 (p0) cc_final: 0.8554 (p0)
REVERT: A  161 ASP cc_start: 0.7598 (m-30) cc_final: 0.7391 (m-30)
REVERT: A  187 GLU cc_start: 0.8402 (tp30) cc_final: 0.8101 (tp30)
REVERT: A  196 ASP cc_start: 0.6942 (m-30) cc_final: 0.6681 (m-30)
REVERT: A  244 LEU cc_start: 0.9022 (tp) cc_final: 0.8772 (tp)
REVERT: A  289 MET cc_start: 0.8663 (ttt) cc_final: 0.8289 (ttp)
REVERT: B   13 ASP cc_start: 0.7754 (p0) cc_final: 0.7352 (p0)
REVERT: B  155 GLU cc_start: 0.7510 (tt0) cc_final: 0.7156 (tt0)
REVERT: B  185 GLU cc_start: 0.8170 (pm20) cc_final: 0.7812 (pm20)
REVERT: B  232 ASP cc_start: 0.8773 (p0) cc_final: 0.8085 (p0)
REVERT: B  264 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7150 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.2318
  time to fit residues: 88.1499
Evaluate side-chains
  249 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  61 HIS
B 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.165353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.124342 restraints weight = 40786.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.129940 restraints weight = 17027.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.133490 restraints weight = 8966.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.135776 restraints weight = 5796.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.137165 restraints weight = 4376.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9703  Z= 0.153
  Angle     :  0.551   5.938  13309  Z= 0.292
  Chirality :  0.037   0.135   1443
  Planarity :  0.005   0.055   1599
  Dihedral  : 17.442  88.534   1610
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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 aren not related in a simple way.
  whole: -0.45 (0.26), residues: 1069
  helix:  1.03 (0.23), residues: 498
  sheet: -1.79 (0.42), residues: 140
  loop : -1.32 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 122 
 TYR   0.031   0.002   TYR C  72 
 PHE   0.017   0.001   PHE A  25 
 TRP   0.048   0.002   TRP A 100 
 HIS   0.004   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9703)
  covalent geometry    : angle       0.55073 (13309)
  hydrogen bonds       : bond        0.04133 (  445)
  hydrogen bonds       : angle       5.11833 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4433 (ttp) cc_final: 0.2750 (tmm)
REVERT: C   55 ARG cc_start: 0.7653 (mtm180) cc_final: 0.7314 (ttm110)
REVERT: C   75 GLN cc_start: 0.7176 (mt0) cc_final: 0.6836 (mt0)
REVERT: D   32 GLU cc_start: 0.6703 (tt0) cc_final: 0.6463 (tt0)
REVERT: D   89 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7329 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7691 (tt0) cc_final: 0.7376 (tt0)
REVERT: D  151 ILE cc_start: 0.7488 (mt) cc_final: 0.7282 (mt)
REVERT: D  157 CYS cc_start: 0.8887 (m) cc_final: 0.8493 (m)
REVERT: D  214 PHE cc_start: 0.8024 (t80) cc_final: 0.7499 (t80)
REVERT: A   13 ASP cc_start: 0.8197 (p0) cc_final: 0.7644 (p0)
REVERT: A   28 ARG cc_start: 0.8630 (ttt90) cc_final: 0.8383 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9173 (tp) cc_final: 0.8950 (tp)
REVERT: A  187 GLU cc_start: 0.8563 (tp30) cc_final: 0.8350 (tp30)
REVERT: A  196 ASP cc_start: 0.6902 (m-30) cc_final: 0.6586 (m-30)
REVERT: A  244 LEU cc_start: 0.9053 (tp) cc_final: 0.8844 (tp)
REVERT: A  289 MET cc_start: 0.8790 (ttt) cc_final: 0.8407 (ttp)
REVERT: B   13 ASP cc_start: 0.8107 (p0) cc_final: 0.7211 (p0)
REVERT: B  155 GLU cc_start: 0.7641 (tt0) cc_final: 0.7354 (tt0)
REVERT: B  162 ASP cc_start: 0.8098 (p0) cc_final: 0.7759 (p0)
REVERT: B  171 ARG cc_start: 0.8587 (ptp-110) cc_final: 0.8102 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8919 (p0) cc_final: 0.8463 (p0)
REVERT: B  264 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7377 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.2380
  time to fit residues: 87.9934
Evaluate side-chains
  242 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3634 r_free = 0.3634 target = 0.162421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.121268 restraints weight = 40238.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.126661 restraints weight = 16955.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.130232 restraints weight = 9054.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.132493 restraints weight = 5841.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.133788 restraints weight = 4410.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3300
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3300
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9703  Z= 0.180
  Angle     :  0.555   4.839  13309  Z= 0.296
  Chirality :  0.038   0.138   1443
  Planarity :  0.005   0.080   1599
  Dihedral  : 17.244  87.426   1610
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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 aren not related in a simple way.
  whole: -0.43 (0.26), residues: 1069
  helix:  1.06 (0.23), residues: 498
  sheet: -1.79 (0.42), residues: 142
  loop : -1.32 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 156 
 TYR   0.030   0.002   TYR C  72 
 PHE   0.017   0.001   PHE A  25 
 TRP   0.027   0.001   TRP A 100 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9703)
  covalent geometry    : angle       0.55541 (13309)
  hydrogen bonds       : bond        0.03990 (  445)
  hydrogen bonds       : angle       5.11471 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4493 (ttp) cc_final: 0.2944 (tmm)
REVERT: C   55 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7324 (ttm110)
REVERT: C   75 GLN cc_start: 0.7210 (mt0) cc_final: 0.6917 (mt0)
REVERT: C  218 ASN cc_start: 0.7625 (m110) cc_final: 0.7410 (m110)
REVERT: D   89 ARG cc_start: 0.7539 (mmm160) cc_final: 0.7042 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7690 (tt0) cc_final: 0.7402 (tt0)
REVERT: D  157 CYS cc_start: 0.8905 (m) cc_final: 0.8414 (m)
REVERT: D  214 PHE cc_start: 0.8035 (t80) cc_final: 0.7412 (t80)
REVERT: A   13 ASP cc_start: 0.8196 (p0) cc_final: 0.7652 (p0)
REVERT: A   28 ARG cc_start: 0.8638 (ttt90) cc_final: 0.8430 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9153 (tp) cc_final: 0.8911 (tp)
REVERT: A  291 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7336 (tp30)
REVERT: B  162 ASP cc_start: 0.8090 (p0) cc_final: 0.7706 (p0)
REVERT: B  197 ASP cc_start: 0.8315 (t0) cc_final: 0.8048 (t0)
REVERT: B  264 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7390 (tt0)
REVERT: B  286 MET cc_start: 0.8641 (mpp) cc_final: 0.8324 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2433
  time to fit residues: 86.3776
Evaluate side-chains
  243 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.162791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.121540 restraints weight = 40593.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.127006 restraints weight = 16931.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.130557 restraints weight = 9068.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.132886 restraints weight = 5866.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.134280 restraints weight = 4434.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9703  Z= 0.157
  Angle     :  0.539   4.249  13309  Z= 0.288
  Chirality :  0.038   0.159   1443
  Planarity :  0.005   0.077   1599
  Dihedral  : 17.142  84.187   1610
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  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 aren not related in a simple way.
  whole: -0.33 (0.26), residues: 1069
  helix:  1.18 (0.23), residues: 503
  sheet: -1.72 (0.43), residues: 140
  loop : -1.37 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 191 
 TYR   0.032   0.002   TYR C  72 
 PHE   0.016   0.001   PHE A  25 
 TRP   0.020   0.001   TRP A 100 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9703)
  covalent geometry    : angle       0.53911 (13309)
  hydrogen bonds       : bond        0.03824 (  445)
  hydrogen bonds       : angle       5.06254 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4616 (ttp) cc_final: 0.3127 (tmm)
REVERT: C   55 ARG cc_start: 0.7564 (mtm180) cc_final: 0.7215 (ttm110)
REVERT: C   75 GLN cc_start: 0.7236 (mt0) cc_final: 0.6936 (mt0)
REVERT: C  192 THR cc_start: 0.8279 (m) cc_final: 0.7953 (m)
REVERT: D   32 GLU cc_start: 0.6685 (tt0) cc_final: 0.6461 (tt0)
REVERT: D   89 ARG cc_start: 0.7544 (mmm160) cc_final: 0.7046 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7689 (tt0) cc_final: 0.7436 (tt0)
REVERT: D  157 CYS cc_start: 0.8891 (m) cc_final: 0.8427 (m)
REVERT: D  214 PHE cc_start: 0.8066 (t80) cc_final: 0.7480 (t80)
REVERT: A   13 ASP cc_start: 0.8151 (p0) cc_final: 0.7626 (p0)
REVERT: A   28 ARG cc_start: 0.8618 (ttt90) cc_final: 0.8416 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9152 (tp) cc_final: 0.8910 (tp)
REVERT: A  196 ASP cc_start: 0.6849 (m-30) cc_final: 0.6553 (m-30)
REVERT: A  235 GLU cc_start: 0.8165 (tt0) cc_final: 0.7846 (tt0)
REVERT: B  162 ASP cc_start: 0.8046 (p0) cc_final: 0.7714 (p0)
REVERT: B  171 ARG cc_start: 0.8794 (ptp-110) cc_final: 0.8227 (ptp-110)
REVERT: B  182 GLU cc_start: 0.8135 (tt0) cc_final: 0.7899 (tt0)
REVERT: B  191 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7729 (tpp80)
REVERT: B  197 ASP cc_start: 0.8120 (t0) cc_final: 0.7856 (t0)
REVERT: B  264 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7322 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.2311
  time to fit residues: 83.9820
Evaluate side-chains
  242 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 79 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.164910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.121845 restraints weight = 41778.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.127661 restraints weight = 17326.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.131415 restraints weight = 9243.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.133629 restraints weight = 6004.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.135268 restraints weight = 4554.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9703  Z= 0.130
  Angle     :  0.508   4.254  13309  Z= 0.270
  Chirality :  0.037   0.139   1443
  Planarity :  0.005   0.061   1599
  Dihedral  : 17.023  80.500   1610
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.41 %
    Favored  : 98.48 %
  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 aren not related in a simple way.
  whole: -0.14 (0.26), residues: 1069
  helix:  1.39 (0.23), residues: 503
  sheet: -1.66 (0.43), residues: 142
  loop : -1.32 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 122 
 TYR   0.017   0.002   TYR D  72 
 PHE   0.016   0.001   PHE A  25 
 TRP   0.016   0.001   TRP A 100 
 HIS   0.005   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9703)
  covalent geometry    : angle       0.50770 (13309)
  hydrogen bonds       : bond        0.03555 (  445)
  hydrogen bonds       : angle       4.92762 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4471 (ttp) cc_final: 0.2970 (tmm)
REVERT: C   55 ARG cc_start: 0.7560 (mtm180) cc_final: 0.7213 (ttm110)
REVERT: C   63 THR cc_start: 0.8465 (p) cc_final: 0.8163 (p)
REVERT: C  214 PHE cc_start: 0.7041 (t80) cc_final: 0.6684 (t80)
REVERT: D   32 GLU cc_start: 0.6664 (tt0) cc_final: 0.6442 (tt0)
REVERT: D   89 ARG cc_start: 0.7407 (mmm160) cc_final: 0.7150 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7675 (tt0) cc_final: 0.7398 (tt0)
REVERT: D  157 CYS cc_start: 0.8902 (m) cc_final: 0.8465 (m)
REVERT: D  214 PHE cc_start: 0.8050 (t80) cc_final: 0.7557 (t80)
REVERT: A   13 ASP cc_start: 0.8108 (p0) cc_final: 0.7561 (p0)
REVERT: A   28 ARG cc_start: 0.8612 (ttt90) cc_final: 0.8205 (ttt-90)
REVERT: A   38 GLU cc_start: 0.8493 (tp30) cc_final: 0.8261 (tp30)
REVERT: A   77 LEU cc_start: 0.9134 (tp) cc_final: 0.8918 (tp)
REVERT: A  196 ASP cc_start: 0.6814 (m-30) cc_final: 0.6473 (m-30)
REVERT: A  291 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7356 (tp30)
REVERT: B  162 ASP cc_start: 0.7986 (p0) cc_final: 0.7679 (p0)
REVERT: B  191 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7896 (tpp80)
REVERT: B  197 ASP cc_start: 0.8077 (t0) cc_final: 0.7820 (t0)
REVERT: B  258 LEU cc_start: 0.7926 (pt) cc_final: 0.7448 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2057
  time to fit residues: 74.6753
Evaluate side-chains
  241 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 52 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.0562

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
B  89 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.162608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.119443 restraints weight = 41080.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.125062 restraints weight = 17443.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.128726 restraints weight = 9508.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.131086 restraints weight = 6234.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.132501 restraints weight = 4749.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9703  Z= 0.178
  Angle     :  0.545   4.792  13309  Z= 0.291
  Chirality :  0.038   0.147   1443
  Planarity :  0.005   0.059   1599
  Dihedral  : 16.943  81.288   1610
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.20 %
    Favored  : 98.69 %
  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 aren not related in a simple way.
  whole: -0.26 (0.26), residues: 1069
  helix:  1.25 (0.23), residues: 508
  sheet: -1.59 (0.44), residues: 140
  loop : -1.41 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 122 
 TYR   0.021   0.002   TYR B 167 
 PHE   0.016   0.001   PHE A  25 
 TRP   0.014   0.001   TRP D  96 
 HIS   0.005   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9703)
  covalent geometry    : angle       0.54544 (13309)
  hydrogen bonds       : bond        0.03707 (  445)
  hydrogen bonds       : angle       5.00766 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4593 (ttp) cc_final: 0.2999 (tmm)
REVERT: C   55 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7236 (ttm110)
REVERT: C   63 THR cc_start: 0.8429 (p) cc_final: 0.8180 (p)
REVERT: C   75 GLN cc_start: 0.7111 (mt0) cc_final: 0.6792 (mt0)
REVERT: C  214 PHE cc_start: 0.7143 (t80) cc_final: 0.6842 (t80)
REVERT: D   89 ARG cc_start: 0.7440 (mmm160) cc_final: 0.7199 (mmm-85)
REVERT: D  141 GLN cc_start: 0.7579 (mp10) cc_final: 0.7344 (mp10)
REVERT: D  147 GLU cc_start: 0.7628 (tt0) cc_final: 0.7382 (tt0)
REVERT: D  157 CYS cc_start: 0.9069 (m) cc_final: 0.8711 (m)
REVERT: D  214 PHE cc_start: 0.8073 (t80) cc_final: 0.7517 (t80)
REVERT: A   13 ASP cc_start: 0.8143 (p0) cc_final: 0.7612 (p0)
REVERT: A   28 ARG cc_start: 0.8642 (ttt90) cc_final: 0.8397 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9158 (tp) cc_final: 0.8928 (tp)
REVERT: A  196 ASP cc_start: 0.6888 (m-30) cc_final: 0.6593 (m-30)
REVERT: A  235 GLU cc_start: 0.8257 (tt0) cc_final: 0.7945 (tt0)
REVERT: A  272 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8122 (pp30)
REVERT: B  162 ASP cc_start: 0.8059 (p0) cc_final: 0.7682 (p0)
REVERT: B  197 ASP cc_start: 0.8093 (t0) cc_final: 0.7858 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 264
  average time/residue: 0.2371
  time to fit residues: 85.3580
Evaluate side-chains
  245 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 244
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D 164 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.163567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.121908 restraints weight = 36334.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.127313 restraints weight = 15729.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.130858 restraints weight = 8666.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.133083 restraints weight = 5734.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.134422 restraints weight = 4401.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9703  Z= 0.148
  Angle     :  0.536   5.693  13309  Z= 0.286
  Chirality :  0.037   0.139   1443
  Planarity :  0.005   0.057   1599
  Dihedral  : 16.790  83.519   1610
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  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 aren not related in a simple way.
  whole: -0.21 (0.26), residues: 1069
  helix:  1.34 (0.23), residues: 507
  sheet: -1.75 (0.43), residues: 145
  loop : -1.36 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 122 
 TYR   0.023   0.002   TYR D  77 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.018   0.001   TRP C  68 
 HIS   0.007   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9703)
  covalent geometry    : angle       0.53629 (13309)
  hydrogen bonds       : bond        0.03628 (  445)
  hydrogen bonds       : angle       4.94486 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4589 (ttp) cc_final: 0.2939 (tmm)
REVERT: C   55 ARG cc_start: 0.7524 (mtm180) cc_final: 0.7192 (ttm110)
REVERT: C   63 THR cc_start: 0.8388 (p) cc_final: 0.8126 (p)
REVERT: C   77 TYR cc_start: 0.7474 (m-80) cc_final: 0.7038 (m-80)
REVERT: C  217 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7429 (mtpt)
REVERT: D   32 GLU cc_start: 0.6536 (tt0) cc_final: 0.6319 (tt0)
REVERT: D   89 ARG cc_start: 0.7446 (mmm160) cc_final: 0.7207 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7693 (tt0) cc_final: 0.7393 (tt0)
REVERT: D  214 PHE cc_start: 0.8095 (t80) cc_final: 0.7556 (t80)
REVERT: A   13 ASP cc_start: 0.8103 (p0) cc_final: 0.7575 (p0)
REVERT: A   28 ARG cc_start: 0.8617 (ttt90) cc_final: 0.8333 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9148 (tp) cc_final: 0.8948 (tp)
REVERT: A  196 ASP cc_start: 0.6838 (m-30) cc_final: 0.6537 (m-30)
REVERT: A  235 GLU cc_start: 0.8260 (tt0) cc_final: 0.7952 (tt0)
REVERT: A  291 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7355 (tp30)
REVERT: B  162 ASP cc_start: 0.7993 (p0) cc_final: 0.7630 (p0)
REVERT: B  197 ASP cc_start: 0.8057 (t0) cc_final: 0.7825 (t0)
REVERT: B  286 MET cc_start: 0.8739 (mpp) cc_final: 0.8379 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.2317
  time to fit residues: 83.8404
Evaluate side-chains
  249 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0010
   chunk 85 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.164658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.121636 restraints weight = 36949.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.127595 restraints weight = 15007.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.131483 restraints weight = 7923.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.133894 restraints weight = 5120.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.135405 restraints weight = 3860.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9703  Z= 0.131
  Angle     :  0.527   4.948  13309  Z= 0.281
  Chirality :  0.037   0.142   1443
  Planarity :  0.005   0.056   1599
  Dihedral  : 16.722  82.397   1610
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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 aren not related in a simple way.
  whole: -0.13 (0.26), residues: 1069
  helix:  1.36 (0.23), residues: 509
  sheet: -1.68 (0.43), residues: 145
  loop : -1.28 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 122 
 TYR   0.020   0.002   TYR D  77 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.021   0.001   TRP C  68 
 HIS   0.015   0.001   HIS B 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9703)
  covalent geometry    : angle       0.52652 (13309)
  hydrogen bonds       : bond        0.03512 (  445)
  hydrogen bonds       : angle       4.87883 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4723 (ttp) cc_final: 0.3181 (tmm)
REVERT: C   55 ARG cc_start: 0.7530 (mtm180) cc_final: 0.7185 (ttm110)
REVERT: C   63 THR cc_start: 0.8334 (p) cc_final: 0.8089 (p)
REVERT: C   77 TYR cc_start: 0.7430 (m-80) cc_final: 0.6938 (m-80)
REVERT: C  217 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7288 (mtpt)
REVERT: D   32 GLU cc_start: 0.6496 (tt0) cc_final: 0.6292 (tt0)
REVERT: D   89 ARG cc_start: 0.7501 (mmm160) cc_final: 0.7242 (mmm-85)
REVERT: D  141 GLN cc_start: 0.7483 (mp10) cc_final: 0.7198 (mp10)
REVERT: D  147 GLU cc_start: 0.7688 (tt0) cc_final: 0.7459 (tt0)
REVERT: D  214 PHE cc_start: 0.8096 (t80) cc_final: 0.7556 (t80)
REVERT: A   13 ASP cc_start: 0.8148 (p0) cc_final: 0.7577 (p0)
REVERT: A   28 ARG cc_start: 0.8496 (ttt90) cc_final: 0.8159 (ttt-90)
REVERT: A   38 GLU cc_start: 0.8545 (tp30) cc_final: 0.8258 (tp30)
REVERT: A  196 ASP cc_start: 0.6863 (m-30) cc_final: 0.6523 (m-30)
REVERT: A  235 GLU cc_start: 0.8318 (tt0) cc_final: 0.8016 (tt0)
REVERT: A  291 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7394 (tp30)
REVERT: B  162 ASP cc_start: 0.7937 (p0) cc_final: 0.7555 (p0)
REVERT: B  197 ASP cc_start: 0.8045 (t0) cc_final: 0.7826 (t0)
REVERT: B  258 LEU cc_start: 0.7847 (pt) cc_final: 0.7383 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2548
  time to fit residues: 91.6131
Evaluate side-chains
  248 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 91 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.163209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.121590 restraints weight = 36425.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.126962 restraints weight = 15725.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.130459 restraints weight = 8644.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.132665 restraints weight = 5682.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.134009 restraints weight = 4356.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9703  Z= 0.148
  Angle     :  0.533   4.579  13309  Z= 0.284
  Chirality :  0.037   0.140   1443
  Planarity :  0.005   0.056   1599
  Dihedral  : 16.695  83.832   1610
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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 aren not related in a simple way.
  whole: -0.15 (0.26), residues: 1069
  helix:  1.34 (0.23), residues: 509
  sheet: -1.69 (0.44), residues: 145
  loop : -1.28 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 122 
 TYR   0.020   0.002   TYR B 167 
 PHE   0.014   0.001   PHE A  25 
 TRP   0.030   0.001   TRP C  68 
 HIS   0.008   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9703)
  covalent geometry    : angle       0.53293 (13309)
  hydrogen bonds       : bond        0.03547 (  445)
  hydrogen bonds       : angle       4.89056 ( 1255)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4641 (ttp) cc_final: 0.2991 (tmm)
REVERT: C   55 ARG cc_start: 0.7536 (mtm180) cc_final: 0.7200 (ttm110)
REVERT: C   63 THR cc_start: 0.8410 (p) cc_final: 0.8104 (p)
REVERT: C  217 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7349 (mtpt)
REVERT: C  218 ASN cc_start: 0.7632 (m110) cc_final: 0.7412 (m110)
REVERT: D   89 ARG cc_start: 0.7459 (mmm160) cc_final: 0.7229 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7713 (tt0) cc_final: 0.7392 (tt0)
REVERT: D  214 PHE cc_start: 0.8082 (t80) cc_final: 0.7554 (t80)
REVERT: A   13 ASP cc_start: 0.8096 (p0) cc_final: 0.7568 (p0)
REVERT: A   28 ARG cc_start: 0.8591 (ttt90) cc_final: 0.8286 (ttt-90)
REVERT: A   38 GLU cc_start: 0.8530 (tp30) cc_final: 0.8296 (tp30)
REVERT: A  196 ASP cc_start: 0.6817 (m-30) cc_final: 0.6495 (m-30)
REVERT: A  235 GLU cc_start: 0.8251 (tt0) cc_final: 0.7976 (tt0)
REVERT: A  283 LEU cc_start: 0.8610 (tp) cc_final: 0.8377 (tt)
REVERT: A  291 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7396 (tp30)
REVERT: B  162 ASP cc_start: 0.7954 (p0) cc_final: 0.7596 (p0)
REVERT: B  197 ASP cc_start: 0.8044 (t0) cc_final: 0.7806 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2209
  time to fit residues: 81.4339
Evaluate side-chains
  253 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0770
   chunk 89 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
C 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.164460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.121577 restraints weight = 42942.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.127368 restraints weight = 17771.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.131119 restraints weight = 9469.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.133480 restraints weight = 6093.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.135036 restraints weight = 4562.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9703  Z= 0.136
  Angle     :  0.528   5.883  13309  Z= 0.281
  Chirality :  0.037   0.138   1443
  Planarity :  0.005   0.057   1599
  Dihedral  : 16.655  85.438   1610
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.26), residues: 1069
  helix:  1.41 (0.23), residues: 509
  sheet: -1.65 (0.44), residues: 145
  loop : -1.24 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 122 
 TYR   0.017   0.002   TYR D  77 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.026   0.001   TRP C  68 
 HIS   0.008   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9703)
  covalent geometry    : angle       0.52754 (13309)
  hydrogen bonds       : bond        0.03500 (  445)
  hydrogen bonds       : angle       4.84533 ( 1255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3524.83 seconds
wall clock time: 60 minutes 44.41 seconds (3644.41 seconds total)