Starting phenix.real_space_refine
on Thu Mar  5 00:49:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nk9_12434/03_2026/7nk9_12434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nk9_12434/03_2026/7nk9_12434.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nk9_12434/03_2026/7nk9_12434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nk9_12434/03_2026/7nk9_12434.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nk9_12434/03_2026/7nk9_12434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nk9_12434/03_2026/7nk9_12434.map"
  }
  resolution = 2.9
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    5873      2.51       5
     N    1460      2.21       5
     O    1560      1.98       5
     H    9158      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18081
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "G"
      Number of atoms: 446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 446
          Classifications: {'peptide': 30}
          Link IDs: {'PTRANS': 3, 'TRANS': 26}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 1239
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 3, 'TRANS': 75}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "M"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "N"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "O"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "P"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "Q"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "R"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "S"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "T"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "a"
      Number of atoms: 3767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3767
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 10, 'TRANS': 227}
    Chain: "b"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 957
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 3, 'TRANS': 57}
    Chain: "d"
      Number of atoms: 920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 920
          Classifications: {'peptide': 59}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 56}
  Time building chain proxies: 3.25, per 1000 atoms: 0.18
  Number of scatterers: 18081
  At special positions: 0
  Unit cell: (97.94, 79.68, 116.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     O    1560      8.00
     N    1460      7.00
     C    5873      6.00
     H    9158      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
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.67
  Conformation dependent library (CDL) restraints added in 441.8 milliseconds
  

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      82.0% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'G' and resid 53 through 60
    Processing helix  chain 'G' and resid 227 through 234
      removed outlier: 3.514A  pdb=" N   LEU G 231 " --> pdb=" O   ASP G 227 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 117
    Processing helix  chain 'L' and resid 4 through 46
    Processing helix  chain 'L' and resid 49 through 80
      removed outlier: 3.681A  pdb=" N   PHE L  54 " --> pdb=" O   GLN L  50 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   THR L  55 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      Proline residue:  L  56  - end of helix
      removed outlier: 3.954A  pdb=" N   ALA L  67 " --> pdb=" O   LEU L  63 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 4 through 46
    Processing helix  chain 'M' and resid 49 through 81
      removed outlier: 4.627A  pdb=" N   THR M  55 " --> pdb=" O   GLY M  51 " (cutoff:3.500A)
      Proline residue:  M  56  - end of helix
      removed outlier: 3.631A  pdb=" N   TYR M  68 " --> pdb=" O   VAL M  64 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 4 through 46
      removed outlier: 3.697A  pdb=" N   ILE N   8 " --> pdb=" O   ASP N   4 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 49 through 80
      removed outlier: 3.732A  pdb=" N   PHE N  54 " --> pdb=" O   GLN N  50 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR N  55 " --> pdb=" O   GLY N  51 " (cutoff:3.500A)
      Proline residue:  N  56  - end of helix
      removed outlier: 3.805A  pdb=" N   ALA N  76 " --> pdb=" O   LEU N  72 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 4 through 46
      removed outlier: 3.748A  pdb=" N   ILE O   8 " --> pdb=" O   ASP O   4 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 49 through 81
      removed outlier: 4.134A  pdb=" N   PHE O  54 " --> pdb=" O   GLN O  50 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   THR O  55 " --> pdb=" O   GLY O  51 " (cutoff:3.500A)
      Proline residue:  O  56  - end of helix
      removed outlier: 3.518A  pdb=" N   ALA O  66 " --> pdb=" O   GLY O  62 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ALA O  67 " --> pdb=" O   LEU O  63 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   TYR O  68 " --> pdb=" O   VAL O  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 4 through 46
      removed outlier: 3.568A  pdb=" N   ILE P   8 " --> pdb=" O   ASP P   4 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 49 through 80
      removed outlier: 4.259A  pdb=" N   THR P  55 " --> pdb=" O   GLY P  51 " (cutoff:3.500A)
      Proline residue:  P  56  - end of helix
      removed outlier: 3.630A  pdb=" N   ALA P  66 " --> pdb=" O   GLY P  62 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 4 through 46
      removed outlier: 3.615A  pdb=" N   ILE Q   8 " --> pdb=" O   ASP Q   4 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 49 through 80
      removed outlier: 3.976A  pdb=" N   PHE Q  54 " --> pdb=" O   GLN Q  50 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   THR Q  55 " --> pdb=" O   GLY Q  51 " (cutoff:3.500A)
      Proline residue:  Q  56  - end of helix
    Processing helix  chain 'R' and resid 4 through 46
      removed outlier: 3.701A  pdb=" N   ILE R   8 " --> pdb=" O   ASP R   4 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 80
      removed outlier: 4.846A  pdb=" N   THR R  55 " --> pdb=" O   GLY R  51 " (cutoff:3.500A)
      Proline residue:  R  56  - end of helix
      removed outlier: 4.029A  pdb=" N   ALA R  67 " --> pdb=" O   LEU R  63 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 4 through 46
      removed outlier: 3.586A  pdb=" N   ILE S   8 " --> pdb=" O   ASP S   4 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 49 through 80
      removed outlier: 4.761A  pdb=" N   THR S  55 " --> pdb=" O   GLY S  51 " (cutoff:3.500A)
      Proline residue:  S  56  - end of helix
      removed outlier: 3.832A  pdb=" N   ALA S  67 " --> pdb=" O   LEU S  63 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 46
      removed outlier: 3.635A  pdb=" N   ILE T   8 " --> pdb=" O   ASP T   4 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 49 through 81
      removed outlier: 4.197A  pdb=" N   THR T  55 " --> pdb=" O   GLY T  51 " (cutoff:3.500A)
      Proline residue:  T  56  - end of helix
      removed outlier: 3.972A  pdb=" N   ALA T  67 " --> pdb=" O   LEU T  63 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU T  77 " --> pdb=" O   ALA T  73 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 28 through 53
    Processing helix  chain 'a' and resid 60 through 81
    Processing helix  chain 'a' and resid 88 through 106
      removed outlier: 3.690A  pdb=" N   LEU a  92 " --> pdb=" O   PHE a  88 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 107 through 109
      No H-bonds generated for 'chain 'a' and resid 107 through 109'
    Processing helix  chain 'a' and resid 126 through 129
    Processing helix  chain 'a' and resid 130 through 154
      removed outlier: 3.606A  pdb=" N   VAL a 134 " --> pdb=" O   ASP a 130 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 156 through 165
      removed outlier: 3.648A  pdb=" N   ILE a 160 " --> pdb=" O   VAL a 156 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 167 through 169
      No H-bonds generated for 'chain 'a' and resid 167 through 169'
    Processing helix  chain 'a' and resid 170 through 205
      Proline residue:  a 182  - end of helix
      removed outlier: 3.737A  pdb=" N   LEU a 189 " --> pdb=" O   LEU a 185 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLY a 196 " --> pdb=" O   ASN a 192 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA a 201 " --> pdb=" O   GLY a 197 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   MET a 205 " --> pdb=" O   ALA a 201 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 207 through 245
      removed outlier: 5.712A  pdb=" N   PHE a 213 " --> pdb=" O   TYR a 209 " (cutoff:3.500A)
      Proline residue:  a 214  - end of helix
      removed outlier: 3.953A  pdb=" N   PHE a 224 " --> pdb=" O   THR a 220 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 29 through 49
      removed outlier: 3.660A  pdb=" N   ALA b  33 " --> pdb=" O   GLY b  29 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL b  49 " --> pdb=" O   ILE b  45 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 49 through 82
      removed outlier: 3.515A  pdb=" N   GLN b  82 " --> pdb=" O   VAL b  78 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 2 through 22
    Processing helix  chain 'd' and resid 22 through 59
    Processing sheet with id=AA1, first strand: chain 'G' and resid 223 through 224
      removed outlier: 6.291A  pdb=" N   SER G 223 " --> pdb=" O   VAL H  42 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   GLN H  44 " --> pdb=" O   SER G 223 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ASN H   5 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   ILE H  79 " --> pdb=" O   ASN H   5 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   GLU H   7 " --> pdb=" O   ILE H  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 31 through 34
      removed outlier: 3.862A  pdb=" N   ARG H  26 " --> pdb=" O   MET H  50 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   MET H  50 " --> pdb=" O   ARG H  26 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'a' and resid 20 through 22
    Processing sheet with id=AA4, first strand: chain 'a' and resid 112 through 114

    817 hydrogen bonds defined for protein.
    2430 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.33

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9157
        1.03 -     1.23: 5
        1.23 -     1.42: 3696
        1.42 -     1.61: 5342
        1.61 -     1.81: 59
  Bond restraints: 18259
  Sorted by residual:
  bond pdb=" CG  GLN a  76 "
       pdb=" CD  GLN a  76 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.07e+00
  bond pdb=" CG1 ILE O   9 "
       pdb=" CD1 ILE O   9 "
    ideal  model  delta    sigma   weight residual
    1.513  1.480  0.033 3.90e-02 6.57e+02 7.01e-01
  bond pdb=" CA  VAL H  23 "
       pdb=" C   VAL H  23 "
    ideal  model  delta    sigma   weight residual
    1.527  1.520  0.007 8.50e-03 1.38e+04 7.00e-01
  bond pdb=" CB  THR P  10 "
       pdb=" CG2 THR P  10 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.73e-01
  bond pdb=" CB  MET L  21 "
       pdb=" CG  MET L  21 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.40e-01
  ... (remaining 18254 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 31096
        1.04 -     2.07: 1881
        2.07 -     3.11: 79
        3.11 -     4.15: 53
        4.15 -     5.18: 13
  Bond angle restraints: 33122
  Sorted by residual:
  angle pdb=" C   CYS a 144 "
        pdb=" N   TYR a 145 "
        pdb=" CA  TYR a 145 "
      ideal   model   delta    sigma   weight residual
     121.14  116.27    4.87 1.75e+00 3.27e-01 7.74e+00
  angle pdb=" CA  PRO G 226 "
        pdb=" C   PRO G 226 "
        pdb=" N   ASP G 227 "
      ideal   model   delta    sigma   weight residual
     115.12  118.30   -3.18 1.25e+00 6.40e-01 6.49e+00
  angle pdb=" CA  TYR a 145 "
        pdb=" CB  TYR a 145 "
        pdb=" CG  TYR a 145 "
      ideal   model   delta    sigma   weight residual
     113.90  118.48   -4.58 1.80e+00 3.09e-01 6.47e+00
  angle pdb=" N   GLN a  76 "
        pdb=" CA  GLN a  76 "
        pdb=" CB  GLN a  76 "
      ideal   model   delta    sigma   weight residual
     110.12  113.73   -3.61 1.47e+00 4.63e-01 6.03e+00
  angle pdb=" N   TYR a 145 "
        pdb=" CA  TYR a 145 "
        pdb=" CB  TYR a 145 "
      ideal   model   delta    sigma   weight residual
     110.40  114.08   -3.68 1.63e+00 3.76e-01 5.10e+00
  ... (remaining 33117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 7446
       16.94 -    33.87: 658
       33.87 -    50.81: 217
       50.81 -    67.75: 206
       67.75 -    84.68: 6
  Dihedral angle restraints: 8533
    sinusoidal: 4581
      harmonic: 3952
  Sorted by residual:
  dihedral pdb=" CA  GLU G 225 "
           pdb=" C   GLU G 225 "
           pdb=" N   PRO G 226 "
           pdb=" CA  PRO G 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.81   16.19     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  PHE P  58 "
           pdb=" C   PHE P  58 "
           pdb=" N   ILE P  59 "
           pdb=" CA  ILE P  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.29   15.71     0      5.00e+00 4.00e-02 9.87e+00
  dihedral pdb=" CA  ARG M  45 "
           pdb=" CB  ARG M  45 "
           pdb=" CG  ARG M  45 "
           pdb=" CD  ARG M  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.04  -53.96     3      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 8530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 929
       0.029 -    0.059: 305
       0.059 -    0.088: 180
       0.088 -    0.118: 39
       0.118 -    0.147: 7
  Chirality restraints: 1460
  Sorted by residual:
  chirality pdb=" CA  PRO H  36 "
            pdb=" N   PRO H  36 "
            pdb=" C   PRO H  36 "
            pdb=" CB  PRO H  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.39e-01
  chirality pdb=" CA  ILE H  63 "
            pdb=" N   ILE H  63 "
            pdb=" C   ILE H  63 "
            pdb=" CB  ILE H  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  TYR a 145 "
            pdb=" N   TYR a 145 "
            pdb=" C   TYR a 145 "
            pdb=" CB  TYR a 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.13 2.00e-01 2.50e+01 3.91e-01
  ... (remaining 1457 not shown)

  Planarity restraints: 2738
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE a  99 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.11e+00
        pdb=" C   PHE a  99 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   PHE a  99 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ILE a 100 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE a  97 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.34e+00
        pdb=" C   PHE a  97 "    0.032 2.00e-02 2.50e+03
        pdb=" O   PHE a  97 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL a  98 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR a  95 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   THR a  95 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   THR a  95 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE a  96 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2735 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 1681
        2.23 -     2.82: 41110
        2.82 -     3.42: 52733
        3.42 -     4.01: 70737
        4.01 -     4.60: 109853
  Nonbonded interactions: 276114
  Sorted by model distance:
  nonbonded pdb=" O   LEU G  57 "
            pdb=" HG  SER G  61 "
     model   vdw
     1.639 2.450
  nonbonded pdb=" OD1 ASN a 132 "
            pdb=" H   ASN b  28 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" H   THR H  21 "
            pdb=" O   GLU H  54 "
     model   vdw
     1.657 2.450
  nonbonded pdb=" OE1 GLN R  46 "
            pdb="HH22 ARG R  52 "
     model   vdw
     1.660 2.450
  nonbonded pdb=" HE  ARG H  37 "
            pdb=" OE2 GLU T  48 "
     model   vdw
     1.666 2.450
  ... (remaining 276109 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 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = (chain 'O' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG  \ 
or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23))  \ 
or resid 4 through 86))
  selection = chain 'P'
  selection = (chain 'Q' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG  \ 
or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23))  \ 
or resid 4 through 86))
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     17.970
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9101  Z= 0.167
  Angle     :  0.495   5.183  12360  Z= 0.277
  Chirality :  0.039   0.147   1460
  Planarity :  0.005   0.043   1587
  Dihedral  : 13.032  84.683   3095
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.26), residues: 1189
  helix:  1.21 (0.18), residues: 950
  sheet: -1.10 (0.85), residues: 34
  loop :  1.28 (0.49), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  45 
 TYR   0.010   0.001   TYR a 145 
 PHE   0.014   0.001   PHE P  69 
 TRP   0.012   0.001   TRP a 218 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9101)
  covalent geometry    : angle       0.49514 (12360)
  hydrogen bonds       : bond        0.13880 (  817)
  hydrogen bonds       : angle       6.97867 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   47 PRO cc_start: 0.8191 (Cg_exo) cc_final: 0.7991 (Cg_endo)
REVERT: d   33 GLN cc_start: 0.8232 (tp40) cc_final: 0.7868 (tp40)
  outliers start: 0
  outliers final: 1
  residues processed: 119
  average time/residue: 1.4013
  time to fit residues: 177.1508
Evaluate side-chains
  78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.0030
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 113 optimal weight:    0.0030
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0060
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.3216

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

Flipped N/Q/H residues before XYZ refinement:
Q   6 ASN
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.078122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.065882 restraints weight = 59609.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.11
r_work: 0.2938 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9101  Z= 0.144
  Angle     :  0.517   5.439  12360  Z= 0.277
  Chirality :  0.040   0.151   1460
  Planarity :  0.005   0.076   1587
  Dihedral  :  3.879  27.959   1264
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  8.25 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.87 (0.25), residues: 1189
  helix:  2.15 (0.17), residues: 957
  sheet: -0.83 (0.94), residues: 34
  loop :  1.38 (0.51), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  45 
 TYR   0.029   0.001   TYR a 145 
 PHE   0.015   0.001   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9101)
  covalent geometry    : angle       0.51738 (12360)
  hydrogen bonds       : bond        0.05013 (  817)
  hydrogen bonds       : angle       4.33516 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: H   61 LEU cc_start: 0.8414 (mp) cc_final: 0.8109 (mt)
REVERT: S   65 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7773 (mp0)
REVERT: b   46 SER cc_start: 0.9240 (m) cc_final: 0.8980 (m)
REVERT: d   33 GLN cc_start: 0.8521 (tp40) cc_final: 0.8127 (tp40)
  outliers start: 13
  outliers final: 3
  residues processed: 98
  average time/residue: 1.1518
  time to fit residues: 121.6631
Evaluate side-chains
  83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   77 LEU
Chi-restraints excluded: chain S residue   65 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.076294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.063839 restraints weight = 60280.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 2.12
r_work: 0.2887 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9101  Z= 0.197
  Angle     :  0.523   5.637  12360  Z= 0.279
  Chirality :  0.040   0.161   1460
  Planarity :  0.004   0.046   1587
  Dihedral  :  3.925  29.090   1264
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.99 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.50 (0.24), residues: 1189
  helix:  2.73 (0.17), residues: 927
  sheet: -0.70 (0.96), residues: 34
  loop :  1.12 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  45 
 TYR   0.025   0.001   TYR a 145 
 PHE   0.015   0.001   PHE Q  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 9101)
  covalent geometry    : angle       0.52254 (12360)
  hydrogen bonds       : bond        0.04887 (  817)
  hydrogen bonds       : angle       4.06898 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  117 LEU cc_start: 0.8818 (pp) cc_final: 0.7509 (pp)
REVERT: M   75 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8494 (tmm)
REVERT: S   65 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7758 (mp0)
REVERT: b   46 SER cc_start: 0.9230 (m) cc_final: 0.9022 (m)
REVERT: d   33 GLN cc_start: 0.8535 (tp40) cc_final: 0.8141 (tp40)
  outliers start: 17
  outliers final: 7
  residues processed: 88
  average time/residue: 1.2175
  time to fit residues: 115.3070
Evaluate side-chains
  86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 ASN
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain O residue   65 GLU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue   65 GLU
Chi-restraints excluded: chain S residue   75 MET
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 115 optimal weight:    0.7980
   chunk 112 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 100 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.076057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.063793 restraints weight = 60055.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.08
r_work: 0.2899 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9101  Z= 0.176
  Angle     :  0.511   5.342  12360  Z= 0.272
  Chirality :  0.040   0.154   1460
  Planarity :  0.004   0.045   1587
  Dihedral  :  3.861  28.245   1261
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.15 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.70 (0.24), residues: 1189
  helix:  2.90 (0.16), residues: 925
  sheet: -0.78 (0.94), residues: 34
  loop :  1.11 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b  72 
 TYR   0.023   0.001   TYR a 145 
 PHE   0.015   0.001   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS a  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9101)
  covalent geometry    : angle       0.51077 (12360)
  hydrogen bonds       : bond        0.04680 (  817)
  hydrogen bonds       : angle       3.95198 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   75 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8512 (tmm)
REVERT: S   65 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7791 (mp0)
REVERT: a  247 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8038 (mp)
REVERT: d   33 GLN cc_start: 0.8598 (tp40) cc_final: 0.8217 (tp40)
  outliers start: 19
  outliers final: 8
  residues processed: 88
  average time/residue: 1.1881
  time to fit residues: 112.5631
Evaluate side-chains
  87 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   55 THR
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue   65 GLU
Chi-restraints excluded: chain S residue   75 MET
Chi-restraints excluded: chain T residue   72 LEU
Chi-restraints excluded: chain a residue   80 SER
Chi-restraints excluded: chain a residue  247 LEU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 115 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** M  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.075668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.063276 restraints weight = 60030.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 2.13
r_work: 0.2880 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9101  Z= 0.197
  Angle     :  0.519   5.402  12360  Z= 0.278
  Chirality :  0.040   0.161   1460
  Planarity :  0.004   0.047   1587
  Dihedral  :  3.886  25.938   1261
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 11.15 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.73 (0.24), residues: 1189
  helix:  2.93 (0.16), residues: 925
  sheet: -0.82 (0.95), residues: 34
  loop :  1.07 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  72 
 TYR   0.022   0.001   TYR a 145 
 PHE   0.016   0.001   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 9101)
  covalent geometry    : angle       0.51884 (12360)
  hydrogen bonds       : bond        0.04722 (  817)
  hydrogen bonds       : angle       3.94594 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   61 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8388 (t)
REVERT: M   75 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8536 (tmm)
REVERT: S   65 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7811 (mp0)
REVERT: a  247 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8099 (mp)
REVERT: d   33 GLN cc_start: 0.8648 (tp40) cc_final: 0.8280 (tp40)
  outliers start: 25
  outliers final: 10
  residues processed: 93
  average time/residue: 1.1650
  time to fit residues: 117.0611
Evaluate side-chains
  90 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   61 VAL
Chi-restraints excluded: chain M residue   55 THR
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain N residue   55 THR
Chi-restraints excluded: chain P residue    3 LEU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue   65 GLU
Chi-restraints excluded: chain S residue   75 MET
Chi-restraints excluded: chain T residue   72 LEU
Chi-restraints excluded: chain a residue   80 SER
Chi-restraints excluded: chain a residue  247 LEU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0870
   chunk 93 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** M  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.076386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.063995 restraints weight = 59671.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.12
r_work: 0.2894 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9101  Z= 0.162
  Angle     :  0.507   5.310  12360  Z= 0.269
  Chirality :  0.039   0.149   1460
  Planarity :  0.004   0.045   1587
  Dihedral  :  3.852  23.227   1261
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.89 %
    Favored  : 85.13 %
  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 are not related in a simple way.
  whole:  3.86 (0.24), residues: 1189
  helix:  3.00 (0.16), residues: 927
  sheet: -0.78 (0.94), residues: 34
  loop :  1.20 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b  72 
 TYR   0.021   0.001   TYR a 145 
 PHE   0.015   0.001   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9101)
  covalent geometry    : angle       0.50672 (12360)
  hydrogen bonds       : bond        0.04549 (  817)
  hydrogen bonds       : angle       3.87088 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   56 GLU cc_start: 0.7781 (mp0) cc_final: 0.7574 (mp0)
REVERT: M   75 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8462 (tmm)
REVERT: a  247 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8105 (mp)
REVERT: d   33 GLN cc_start: 0.8638 (tp40) cc_final: 0.8274 (tp40)
  outliers start: 17
  outliers final: 11
  residues processed: 90
  average time/residue: 1.1585
  time to fit residues: 112.7065
Evaluate side-chains
  91 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 ASN
Chi-restraints excluded: chain M residue   55 THR
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain N residue   55 THR
Chi-restraints excluded: chain P residue    3 LEU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue   75 MET
Chi-restraints excluded: chain T residue   72 LEU
Chi-restraints excluded: chain a residue   80 SER
Chi-restraints excluded: chain a residue  247 LEU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** M  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.075358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.062927 restraints weight = 60308.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.13
r_work: 0.2875 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9101  Z= 0.212
  Angle     :  0.531   5.426  12360  Z= 0.284
  Chirality :  0.040   0.166   1460
  Planarity :  0.004   0.048   1587
  Dihedral  :  3.900  22.855   1261
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.01 %
    Favored  : 84.67 %
  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 are not related in a simple way.
  whole:  3.77 (0.24), residues: 1189
  helix:  2.95 (0.16), residues: 927
  sheet: -0.84 (0.93), residues: 34
  loop :  1.07 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  72 
 TYR   0.021   0.001   TYR a 145 
 PHE   0.016   0.002   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9101)
  covalent geometry    : angle       0.53119 (12360)
  hydrogen bonds       : bond        0.04726 (  817)
  hydrogen bonds       : angle       3.91651 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   56 GLU cc_start: 0.7797 (mp0) cc_final: 0.7593 (mp0)
REVERT: L   21 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8613 (mmp)
REVERT: L   61 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8440 (t)
REVERT: M   75 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8449 (tmm)
REVERT: a  247 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8105 (mp)
REVERT: b   76 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8042 (pp20)
REVERT: d   33 GLN cc_start: 0.8642 (tp40) cc_final: 0.8276 (tp40)
  outliers start: 20
  outliers final: 11
  residues processed: 89
  average time/residue: 1.1788
  time to fit residues: 112.9859
Evaluate side-chains
  93 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 ASN
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   61 VAL
Chi-restraints excluded: chain M residue   55 THR
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain N residue   55 THR
Chi-restraints excluded: chain P residue    3 LEU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue   75 MET
Chi-restraints excluded: chain T residue   72 LEU
Chi-restraints excluded: chain a residue   80 SER
Chi-restraints excluded: chain a residue  247 LEU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain b residue   76 GLU
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.075489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.063184 restraints weight = 60401.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.12
r_work: 0.2877 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9101  Z= 0.199
  Angle     :  0.526   5.966  12360  Z= 0.280
  Chirality :  0.040   0.160   1460
  Planarity :  0.004   0.047   1587
  Dihedral  :  3.919  22.938   1261
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.36 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.78 (0.24), residues: 1189
  helix:  2.96 (0.16), residues: 926
  sheet: -0.90 (0.92), residues: 34
  loop :  1.11 (0.42), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG b  72 
 TYR   0.020   0.001   TYR a 145 
 PHE   0.016   0.001   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 9101)
  covalent geometry    : angle       0.52580 (12360)
  hydrogen bonds       : bond        0.04674 (  817)
  hydrogen bonds       : angle       3.89731 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   61 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8415 (t)
REVERT: M   75 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8432 (tmm)
REVERT: P   21 MET cc_start: 0.8858 (mmp) cc_final: 0.8507 (mmm)
REVERT: a  247 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8075 (mp)
REVERT: d   33 GLN cc_start: 0.8675 (tp40) cc_final: 0.8313 (tp40)
  outliers start: 20
  outliers final: 11
  residues processed: 91
  average time/residue: 1.1477
  time to fit residues: 112.3700
Evaluate side-chains
  91 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 ASN
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   61 VAL
Chi-restraints excluded: chain M residue   55 THR
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain N residue   55 THR
Chi-restraints excluded: chain P residue    3 LEU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue   75 MET
Chi-restraints excluded: chain T residue   72 LEU
Chi-restraints excluded: chain a residue  247 LEU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** M  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.075742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.063338 restraints weight = 60115.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 2.13
r_work: 0.2884 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9101  Z= 0.183
  Angle     :  0.535   6.685  12360  Z= 0.283
  Chirality :  0.040   0.156   1460
  Planarity :  0.004   0.051   1587
  Dihedral  :  3.896  22.559   1261
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.59 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.82 (0.24), residues: 1189
  helix:  2.98 (0.16), residues: 926
  sheet: -0.75 (0.92), residues: 34
  loop :  1.13 (0.43), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b  72 
 TYR   0.020   0.001   TYR a 145 
 PHE   0.015   0.001   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9101)
  covalent geometry    : angle       0.53532 (12360)
  hydrogen bonds       : bond        0.04604 (  817)
  hydrogen bonds       : angle       3.86541 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   61 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8419 (t)
REVERT: M   75 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8534 (tmm)
REVERT: N   65 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7091 (mp0)
REVERT: P   21 MET cc_start: 0.8879 (mmp) cc_final: 0.8511 (mmm)
REVERT: a  247 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: b   76 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8027 (pp20)
REVERT: d   33 GLN cc_start: 0.8671 (tp40) cc_final: 0.8312 (tp40)
  outliers start: 20
  outliers final: 12
  residues processed: 93
  average time/residue: 1.1671
  time to fit residues: 116.7869
Evaluate side-chains
  97 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 ASN
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   61 VAL
Chi-restraints excluded: chain M residue   55 THR
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain N residue   55 THR
Chi-restraints excluded: chain N residue   65 GLU
Chi-restraints excluded: chain P residue    3 LEU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain T residue   21 MET
Chi-restraints excluded: chain T residue   72 LEU
Chi-restraints excluded: chain a residue   80 SER
Chi-restraints excluded: chain a residue  247 LEU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain b residue   76 GLU
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** M  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.075899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.063584 restraints weight = 60067.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.13
r_work: 0.2884 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9101  Z= 0.170
  Angle     :  0.533   6.569  12360  Z= 0.280
  Chirality :  0.040   0.153   1460
  Planarity :  0.005   0.108   1587
  Dihedral  :  3.891  22.561   1261
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.05 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.88 (0.24), residues: 1189
  helix:  3.03 (0.16), residues: 927
  sheet: -0.70 (0.92), residues: 34
  loop :  1.11 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG b  72 
 TYR   0.020   0.001   TYR a 145 
 PHE   0.015   0.001   PHE M  74 
 TRP   0.012   0.001   TRP a 218 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9101)
  covalent geometry    : angle       0.53269 (12360)
  hydrogen bonds       : bond        0.04520 (  817)
  hydrogen bonds       : angle       3.82737 ( 2430)

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

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

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2378 Ramachandran restraints generated.
    1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   61 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8369 (t)
REVERT: N   65 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7145 (mp0)
REVERT: P   21 MET cc_start: 0.8861 (mmp) cc_final: 0.8487 (mmm)
REVERT: a  247 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8069 (mp)
REVERT: b   76 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8009 (pp20)
REVERT: d   33 GLN cc_start: 0.8681 (tp40) cc_final: 0.8330 (tp40)
  outliers start: 21
  outliers final: 12
  residues processed: 96
  average time/residue: 1.1693
  time to fit residues: 120.7753
Evaluate side-chains
  97 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   61 VAL
Chi-restraints excluded: chain M residue   55 THR
Chi-restraints excluded: chain M residue   75 MET
Chi-restraints excluded: chain N residue   55 THR
Chi-restraints excluded: chain N residue   65 GLU
Chi-restraints excluded: chain O residue   77 LEU
Chi-restraints excluded: chain P residue    3 LEU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain T residue   72 LEU
Chi-restraints excluded: chain a residue   80 SER
Chi-restraints excluded: chain a residue  247 LEU
Chi-restraints excluded: chain b residue   61 GLU
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain b residue   76 GLU
Chi-restraints excluded: chain d residue   46 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0970
   overall best weight:    0.7978

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

Flipped N/Q/H residues before XYZ refinement:
** M  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  71 ASN
** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.075774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.063424 restraints weight = 59918.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.13
r_work: 0.2888 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9101  Z= 0.184
  Angle     :  0.541   6.340  12360  Z= 0.284
  Chirality :  0.040   0.158   1460
  Planarity :  0.004   0.047   1587
  Dihedral  :  3.873  22.206   1261
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.05 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.85 (0.24), residues: 1189
  helix:  3.02 (0.16), residues: 927
  sheet: -0.70 (0.92), residues: 34
  loop :  1.07 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  72 
 TYR   0.020   0.001   TYR a 145 
 PHE   0.016   0.001   PHE M  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 9101)
  covalent geometry    : angle       0.54146 (12360)
  hydrogen bonds       : bond        0.04558 (  817)
  hydrogen bonds       : angle       3.83073 ( 2430)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5295.25 seconds
wall clock time: 90 minutes 14.57 seconds (5414.57 seconds total)