Starting phenix.real_space_refine
on Sun Aug 24 02:32:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7njv_12424/08_2025/7njv_12424_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7njv_12424/08_2025/7njv_12424.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/7njv_12424/08_2025/7njv_12424_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7njv_12424/08_2025/7njv_12424_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7njv_12424/08_2025/7njv_12424.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7njv_12424/08_2025/7njv_12424.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: 6
    Type Number    sf(0)   Gaussians
     Br      1      7.06       5
     S      28      5.16       5
     C    5378      2.51       5
     N    1318      2.21       5
     O    1401      1.98       5
     H    8337      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  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: 16463
  Number of models: 1
  Model: ""
    Number of chains: 13
    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: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    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: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    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: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 979
          Classifications: {'peptide': 63}
          Link IDs: {'PTRANS': 3, 'TRANS': 59}
    Chain: "d"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 952
          Classifications: {'peptide': 61}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 58}
    Chain: "N"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'BQ1': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C06 BQ1 N 101 " occ=0.75
      ... (35 atoms not shown)
      pdb="BR   BQ1 N 101 " occ=0.75
  Time building chain proxies: 3.34, per 1000 atoms: 0.20
  Number of scatterers: 16463
  At special positions: 0
  Unit cell: (94.62, 77.19, 116.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Br      1     34.99
     S      28     16.00
     O    1401      8.00
     N    1318      7.00
     C    5378      6.00
     H    8337      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: 1.29
  Conformation dependent library (CDL) restraints added in 514.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1904

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      88.0% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'L' and resid 4 through 46
      removed outlier: 3.645A  pdb=" N   ILE L   8 " --> pdb=" O   ASP L   4 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 49 through 81
      removed outlier: 4.398A  pdb=" N   THR L  55 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      Proline residue:  L  56  - end of helix
      removed outlier: 4.049A  pdb=" N   ALA L  67 " --> pdb=" O   LEU L  63 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR L  68 " --> pdb=" O   VAL L  64 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 4 through 46
      removed outlier: 3.671A  pdb=" N   ILE M   8 " --> pdb=" O   ASP M   4 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 47 through 51
      removed outlier: 4.393A  pdb=" N   GLY M  51 " --> pdb=" O   GLU M  48 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 53 through 80
      removed outlier: 3.632A  pdb=" N   LEU M  63 " --> pdb=" O   ILE M  59 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   TYR M  68 " --> pdb=" O   VAL M  64 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 4 through 46
    Processing helix  chain 'N' and resid 49 through 80
      removed outlier: 4.047A  pdb=" N   THR N  55 " --> pdb=" O   GLY N  51 " (cutoff:3.500A)
      Proline residue:  N  56  - end of helix
      removed outlier: 3.576A  pdb=" N   ALA N  67 " --> pdb=" O   LEU N  63 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 4 through 46
      removed outlier: 3.679A  pdb=" N   ILE O   8 " --> pdb=" O   ASP O   4 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 48 through 80
      removed outlier: 4.525A  pdb=" N   ARG O  52 " --> pdb=" O   GLU O  48 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   THR O  55 " --> pdb=" O   GLY O  51 " (cutoff:3.500A)
      Proline residue:  O  56  - end of helix
      removed outlier: 3.572A  pdb=" N   ALA O  67 " --> pdb=" O   LEU O  63 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 4 through 46
      removed outlier: 3.731A  pdb=" N   ILE P   8 " --> pdb=" O   ASP P   4 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 47 through 50
      removed outlier: 3.631A  pdb=" N   GLN P  50 " --> pdb=" O   PRO P  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 47 through 50'
    Processing helix  chain 'P' and resid 53 through 80
    Processing helix  chain 'Q' and resid 4 through 46
      removed outlier: 3.743A  pdb=" N   ILE Q   8 " --> pdb=" O   ASP Q   4 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 49 through 80
      removed outlier: 4.497A  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
    Processing helix  chain 'R' and resid 49 through 81
      removed outlier: 4.780A  pdb=" N   THR R  55 " --> pdb=" O   GLY R  51 " (cutoff:3.500A)
      Proline residue:  R  56  - end of helix
    Processing helix  chain 'S' and resid 4 through 46
    Processing helix  chain 'S' and resid 49 through 81
      removed outlier: 4.543A  pdb=" N   THR S  55 " --> pdb=" O   GLY S  51 " (cutoff:3.500A)
      Proline residue:  S  56  - end of helix
      removed outlier: 3.971A  pdb=" N   ALA S  67 " --> pdb=" O   LEU S  63 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 46
      removed outlier: 3.744A  pdb=" N   ILE T   8 " --> pdb=" O   ASP T   4 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 49 through 80
      removed outlier: 3.604A  pdb=" N   THR T  55 " --> pdb=" O   GLY T  51 " (cutoff:3.500A)
      Proline residue:  T  56  - end of helix
      removed outlier: 3.859A  pdb=" N   ALA T  67 " --> pdb=" O   LEU T  63 " (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
    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: 3.541A  pdb=" N   VAL a 134 " --> pdb=" O   ASP a 130 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 156 through 165
      removed outlier: 3.558A  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 204
      Proline residue:  a 182  - end of helix
      removed outlier: 3.858A  pdb=" N   LEU a 189 " --> pdb=" O   LEU a 185 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY a 196 " --> pdb=" O   ASN a 192 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 207 through 245
      removed outlier: 3.966A  pdb=" N   TRP a 212 " --> pdb=" O   TRP a 208 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   PHE a 213 " --> pdb=" O   TYR a 209 " (cutoff:3.500A)
      Proline residue:  a 214  - end of helix
      removed outlier: 3.906A  pdb=" N   PHE a 224 " --> pdb=" O   THR a 220 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 29 through 49
      removed outlier: 3.510A  pdb=" N   ALA b  33 " --> pdb=" O   GLY b  29 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 49 through 84
    Processing helix  chain 'd' and resid 2 through 22
    Processing helix  chain 'd' and resid 22 through 61
    Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114

    800 hydrogen bonds defined for protein.
    2388 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: 3.67

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        0.84 -     1.06: 8336
        1.06 -     1.28: 1310
        1.28 -     1.50: 3497
        1.50 -     1.72: 3436
        1.72 -     1.94: 56
  Bond restraints: 16635
  Sorted by residual:
  bond pdb=" C17 BQ1 N 101 "
       pdb=" O03 BQ1 N 101 "
    ideal  model  delta    sigma   weight residual
    1.330  1.399 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" C17 BQ1 N 101 "
       pdb=" N05 BQ1 N 101 "
    ideal  model  delta    sigma   weight residual
    1.297  1.354 -0.057 2.00e-02 2.50e+03 8.23e+00
  bond pdb=" C35 BQ1 N 101 "
       pdb="BR   BQ1 N 101 "
    ideal  model  delta    sigma   weight residual
    1.888  1.941 -0.053 2.00e-02 2.50e+03 7.01e+00
  bond pdb=" C13 BQ1 N 101 "
       pdb=" C16 BQ1 N 101 "
    ideal  model  delta    sigma   weight residual
    1.426  1.375  0.051 2.00e-02 2.50e+03 6.49e+00
  bond pdb=" C10 BQ1 N 101 "
       pdb=" C17 BQ1 N 101 "
    ideal  model  delta    sigma   weight residual
    1.437  1.392  0.045 2.00e-02 2.50e+03 5.09e+00
  ... (remaining 16630 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.61: 30160
        4.61 -     9.23: 9
        9.23 -    13.84: 4
       13.84 -    18.45: 1
       18.45 -    23.06: 1
  Bond angle restraints: 30175
  Sorted by residual:
  angle pdb=" C10 BQ1 N 101 "
        pdb=" C17 BQ1 N 101 "
        pdb=" O03 BQ1 N 101 "
      ideal   model   delta    sigma   weight residual
     115.66  138.72  -23.06 3.00e+00 1.11e-01 5.91e+01
  angle pdb=" N05 BQ1 N 101 "
        pdb=" C17 BQ1 N 101 "
        pdb=" O03 BQ1 N 101 "
      ideal   model   delta    sigma   weight residual
     119.50  101.21   18.29 3.00e+00 1.11e-01 3.72e+01
  angle pdb=" C06 BQ1 N 101 "
        pdb=" C09 BQ1 N 101 "
        pdb=" C14 BQ1 N 101 "
      ideal   model   delta    sigma   weight residual
     118.36  106.61   11.75 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" C07 BQ1 N 101 "
        pdb=" C10 BQ1 N 101 "
        pdb=" C17 BQ1 N 101 "
      ideal   model   delta    sigma   weight residual
     118.88  108.06   10.82 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" C06 BQ1 N 101 "
        pdb=" C09 BQ1 N 101 "
        pdb=" C13 BQ1 N 101 "
      ideal   model   delta    sigma   weight residual
     123.57  134.30  -10.73 3.00e+00 1.11e-01 1.28e+01
  ... (remaining 30170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 6704
       16.78 -    33.56: 668
       33.56 -    50.34: 175
       50.34 -    67.12: 232
       67.12 -    83.90: 7
  Dihedral angle restraints: 7786
    sinusoidal: 4177
      harmonic: 3609
  Sorted by residual:
  dihedral pdb=" CA  GLN L  46 "
           pdb=" C   GLN L  46 "
           pdb=" N   PRO L  47 "
           pdb=" CA  PRO L  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.08  -15.92     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  PHE P  78 "
           pdb=" C   PHE P  78 "
           pdb=" N   VAL P  79 "
           pdb=" CA  VAL P  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.42  -15.58     0      5.00e+00 4.00e-02 9.71e+00
  dihedral pdb=" CB  MET d   1 "
           pdb=" CG  MET d   1 "
           pdb=" SD  MET d   1 "
           pdb=" CE  MET d   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.65  -58.35     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 7783 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1178
       0.068 -    0.136: 145
       0.136 -    0.204: 0
       0.204 -    0.273: 0
       0.273 -    0.341: 1
  Chirality restraints: 1324
  Sorted by residual:
  chirality pdb=" C07 BQ1 N 101 "
            pdb=" C06 BQ1 N 101 "
            pdb=" C10 BQ1 N 101 "
            pdb=" C12 BQ1 N 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.74    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CA  ILE b  26 "
            pdb=" N   ILE b  26 "
            pdb=" C   ILE b  26 "
            pdb=" CB  ILE b  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  PRO L  47 "
            pdb=" N   PRO L  47 "
            pdb=" C   PRO L  47 "
            pdb=" CB  PRO L  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.14e-01
  ... (remaining 1321 not shown)

  Planarity restraints: 2498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA a  86 "    0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO a  87 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO a  87 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO a  87 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA d  42 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   ALA d  42 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ALA d  42 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLU d  43 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL P  64 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   VAL P  64 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   VAL P  64 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLU P  65 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2495 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.24: 1508
        2.24 -     2.85: 39759
        2.85 -     3.47: 50139
        3.47 -     4.08: 70642
        4.08 -     4.70: 112069
  Nonbonded interactions: 274117
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN a 132 "
            pdb=" H   ASN b  28 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" O   ASN S   6 "
            pdb=" HG1 THR S  10 "
     model   vdw
     1.681 2.450
  nonbonded pdb="HE22 GLN b  77 "
            pdb=" OD1 ASP d  55 "
     model   vdw
     1.686 2.450
  nonbonded pdb=" HG  SER a  55 "
            pdb=" OE1 GLU b  59 "
     model   vdw
     1.688 2.450
  nonbonded pdb=" O   ASN R   6 "
            pdb=" HG1 THR R  10 "
     model   vdw
     1.702 2.450
  ... (remaining 274112 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' and resid 3 through 86)
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  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=0.75 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:             9.260
  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:             0.100
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     15.580
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:8.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   33.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
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   0.069   8298  Z= 0.155
  Angle     :  0.604  23.064  11277  Z= 0.288
  Chirality :  0.039   0.341   1324
  Planarity :  0.005   0.044   1443
  Dihedral  : 13.575  83.904   2816
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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:  2.26 (0.27), residues: 1094
  helix:  1.55 (0.18), residues: 943
  sheet:  None (None), residues: 0
  loop :  1.67 (0.60), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  52 
 TYR   0.023   0.001   TYR a 145 
 PHE   0.012   0.001   PHE S  74 
 TRP   0.009   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8298)
  covalent geometry    : angle       0.60358 (11277)
  hydrogen bonds       : bond        0.13837 (  800)
  hydrogen bonds       : angle       6.81025 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: a   73 MET cc_start: 0.8879 (mmt) cc_final: 0.8643 (mmt)
REVERT: a  192 ASN cc_start: 0.8283 (t0) cc_final: 0.8082 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 1.2101
  time to fit residues: 141.4674
Evaluate side-chains
  72 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** O  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  71 ASN
a 192 ASN
d  33 GLN
d  58 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.084567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.071243 restraints weight = 39500.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 1.57
r_work: 0.2795 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8819
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8298  Z= 0.176
  Angle     :  0.504   5.352  11277  Z= 0.277
  Chirality :  0.039   0.131   1324
  Planarity :  0.004   0.037   1443
  Dihedral  :  5.527  60.439   1176
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  6.99 %
    Favored  : 91.06 %
  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:  3.61 (0.25), residues: 1094
  helix:  2.54 (0.16), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.43 (0.57), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG T  52 
 TYR   0.022   0.001   TYR a 145 
 PHE   0.015   0.002   PHE S  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8298)
  covalent geometry    : angle       0.50366 (11277)
  hydrogen bonds       : bond        0.05186 (  800)
  hydrogen bonds       : angle       4.25446 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   46 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7234 (pt0)
REVERT: Q   65 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7257 (mp0)
REVERT: a   73 MET cc_start: 0.9137 (mmt) cc_final: 0.8774 (mmt)
  outliers start: 15
  outliers final: 6
  residues processed: 85
  average time/residue: 1.1911
  time to fit residues: 108.0902
Evaluate side-chains
  80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain O residue   46 GLN
Chi-restraints excluded: chain P residue   71 ASN
Chi-restraints excluded: chain Q residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  239 LEU
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0670
   chunk 92 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
d  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.083372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.069978 restraints weight = 40031.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 1.57
r_work: 0.2773 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8298  Z= 0.181
  Angle     :  0.491   5.276  11277  Z= 0.268
  Chirality :  0.039   0.127   1324
  Planarity :  0.004   0.035   1443
  Dihedral  :  5.084  35.541   1176
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  7.64 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.94 (0.25), residues: 1094
  helix:  2.80 (0.16), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.31 (0.56), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG T  52 
 TYR   0.020   0.001   TYR a 145 
 PHE   0.013   0.002   PHE S  74 
 TRP   0.011   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8298)
  covalent geometry    : angle       0.49083 (11277)
  hydrogen bonds       : bond        0.04932 (  800)
  hydrogen bonds       : angle       4.01809 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   65 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7235 (mp0)
REVERT: a   73 MET cc_start: 0.9217 (mmt) cc_final: 0.8774 (mmt)
  outliers start: 17
  outliers final: 4
  residues processed: 85
  average time/residue: 1.1731
  time to fit residues: 106.3621
Evaluate side-chains
  76 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  239 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0770
   chunk 103 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
a 192 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.083861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.070450 restraints weight = 39254.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.57
r_work: 0.2780 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8298  Z= 0.167
  Angle     :  0.481   5.260  11277  Z= 0.261
  Chirality :  0.038   0.128   1324
  Planarity :  0.004   0.036   1443
  Dihedral  :  4.933  43.531   1176
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  8.03 %
    Favored  : 89.77 %
  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:  4.07 (0.25), residues: 1094
  helix:  2.90 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.25 (0.56), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.013   0.001   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8298)
  covalent geometry    : angle       0.48122 (11277)
  hydrogen bonds       : bond        0.04762 (  800)
  hydrogen bonds       : angle       3.92524 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: Q   65 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7249 (mp0)
REVERT: a   73 MET cc_start: 0.9250 (mmt) cc_final: 0.8804 (mmt)
REVERT: a  205 MET cc_start: 0.9079 (mtt) cc_final: 0.8874 (mtt)
  outliers start: 17
  outliers final: 4
  residues processed: 86
  average time/residue: 1.1233
  time to fit residues: 102.6823
Evaluate side-chains
  74 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  239 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 103 optimal weight:    0.3980
   chunk 4 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** 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 = 0.3102 r_free = 0.3102 target = 0.083799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.070239 restraints weight = 39769.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.61
r_work: 0.2762 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8298  Z= 0.187
  Angle     :  0.494   5.295  11277  Z= 0.269
  Chirality :  0.039   0.128   1324
  Planarity :  0.004   0.036   1443
  Dihedral  :  4.972  48.134   1176
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  8.55 %
    Favored  : 89.25 %
  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:  4.01 (0.26), residues: 1094
  helix:  2.87 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.16 (0.56), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.015   0.002   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8298)
  covalent geometry    : angle       0.49424 (11277)
  hydrogen bonds       : bond        0.04842 (  800)
  hydrogen bonds       : angle       3.92397 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
REVERT: Q   65 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7272 (mp0)
REVERT: a   73 MET cc_start: 0.9278 (mmt) cc_final: 0.8795 (mmt)
  outliers start: 17
  outliers final: 6
  residues processed: 81
  average time/residue: 1.1472
  time to fit residues: 99.0877
Evaluate side-chains
  75 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  179 LEU
Chi-restraints excluded: chain a residue  239 LEU
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0770
   chunk 23 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** 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 = 0.3100 r_free = 0.3100 target = 0.083526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.070045 restraints weight = 39425.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 1.56
r_work: 0.2774 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8298  Z= 0.169
  Angle     :  0.485   5.245  11277  Z= 0.263
  Chirality :  0.038   0.128   1324
  Planarity :  0.004   0.036   1443
  Dihedral  :  4.947  49.426   1176
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  8.94 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.09 (0.26), residues: 1094
  helix:  2.92 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.16 (0.57), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.015   0.001   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8298)
  covalent geometry    : angle       0.48547 (11277)
  hydrogen bonds       : bond        0.04731 (  800)
  hydrogen bonds       : angle       3.88186 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   65 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7294 (mp0)
REVERT: T   65 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7448 (mp0)
REVERT: a   73 MET cc_start: 0.9282 (mmt) cc_final: 0.8746 (mmt)
  outliers start: 19
  outliers final: 6
  residues processed: 81
  average time/residue: 1.1192
  time to fit residues: 96.3780
Evaluate side-chains
  77 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   65 GLU
Chi-restraints excluded: chain Q residue   71 ASN
Chi-restraints excluded: chain T residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  239 LEU
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
a 192 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.083532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.070049 restraints weight = 39620.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.59
r_work: 0.2758 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8298  Z= 0.190
  Angle     :  0.496   5.285  11277  Z= 0.270
  Chirality :  0.039   0.128   1324
  Planarity :  0.004   0.037   1443
  Dihedral  :  5.010  50.594   1176
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  9.46 %
    Favored  : 88.21 %
  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:  4.03 (0.26), residues: 1094
  helix:  2.89 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.07 (0.57), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.015   0.002   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 8298)
  covalent geometry    : angle       0.49643 (11277)
  hydrogen bonds       : bond        0.04830 (  800)
  hydrogen bonds       : angle       3.90157 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   65 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7265 (mp0)
REVERT: T   65 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7302 (mp0)
REVERT: a   73 MET cc_start: 0.9286 (mmt) cc_final: 0.8733 (mmt)
  outliers start: 18
  outliers final: 8
  residues processed: 81
  average time/residue: 1.2858
  time to fit residues: 110.8115
Evaluate side-chains
  78 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   65 GLU
Chi-restraints excluded: chain Q residue   71 ASN
Chi-restraints excluded: chain R residue   21 MET
Chi-restraints excluded: chain S residue   48 GLU
Chi-restraints excluded: chain T residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  239 LEU
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 98 optimal weight:    0.3980
   chunk 90 optimal weight:    0.9990
   chunk 68 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 79 optimal weight:    0.1980
   chunk 61 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** 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 = 0.3116 r_free = 0.3116 target = 0.084471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.071111 restraints weight = 39333.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 1.56
r_work: 0.2793 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8298  Z= 0.135
  Angle     :  0.470   5.568  11277  Z= 0.254
  Chirality :  0.038   0.130   1324
  Planarity :  0.004   0.035   1443
  Dihedral  :  4.885  51.363   1176
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.23 %
    Favored  : 87.82 %
  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:  4.26 (0.26), residues: 1094
  helix:  3.04 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.17 (0.58), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.015   0.001   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8298)
  covalent geometry    : angle       0.47037 (11277)
  hydrogen bonds       : bond        0.04513 (  800)
  hydrogen bonds       : angle       3.80847 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: T   65 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7434 (mp0)
REVERT: a   73 MET cc_start: 0.9276 (mmt) cc_final: 0.8772 (mmt)
REVERT: d   27 ARG cc_start: 0.6878 (mmt-90) cc_final: 0.6643 (ptp-170)
  outliers start: 15
  outliers final: 7
  residues processed: 85
  average time/residue: 1.4328
  time to fit residues: 129.2725
Evaluate side-chains
  77 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   71 ASN
Chi-restraints excluded: chain S residue   48 GLU
Chi-restraints excluded: chain T residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  239 LEU
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 96 optimal weight:    0.4980
   chunk 2 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:
** a 229 GLN ** 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 = 0.3095 r_free = 0.3095 target = 0.083378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.069877 restraints weight = 39855.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 1.59
r_work: 0.2761 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8298  Z= 0.201
  Angle     :  0.507   5.980  11277  Z= 0.275
  Chirality :  0.039   0.127   1324
  Planarity :  0.004   0.037   1443
  Dihedral  :  5.005  50.790   1176
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 10.36 %
    Favored  : 87.82 %
  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:  4.09 (0.26), residues: 1094
  helix:  2.94 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.08 (0.58), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.015   0.002   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8298)
  covalent geometry    : angle       0.50722 (11277)
  hydrogen bonds       : bond        0.04837 (  800)
  hydrogen bonds       : angle       3.88923 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 ARG cc_start: 0.6148 (tmt170) cc_final: 0.5651 (tpt170)
REVERT: T   65 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7352 (mp0)
REVERT: a   73 MET cc_start: 0.9290 (mmt) cc_final: 0.8741 (mmt)
REVERT: d   27 ARG cc_start: 0.6886 (mmt-90) cc_final: 0.6643 (ptp-170)
  outliers start: 14
  outliers final: 8
  residues processed: 82
  average time/residue: 1.3663
  time to fit residues: 118.9314
Evaluate side-chains
  76 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   71 ASN
Chi-restraints excluded: chain R residue   21 MET
Chi-restraints excluded: chain S residue   48 GLU
Chi-restraints excluded: chain T residue   65 GLU
Chi-restraints excluded: chain a residue   67 GLU
Chi-restraints excluded: chain a residue  239 LEU
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    0.0770
   chunk 63 optimal weight:    0.9990
   chunk 37 optimal weight:    0.1980
   chunk 13 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.1980
   chunk 98 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.2538

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.085400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.072104 restraints weight = 39150.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.57
r_work: 0.2813 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8298  Z= 0.126
  Angle     :  0.469   6.168  11277  Z= 0.252
  Chirality :  0.038   0.124   1324
  Planarity :  0.004   0.035   1443
  Dihedral  :  4.814  52.385   1176
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.01 %
    Favored  : 87.56 %
  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:  4.39 (0.26), residues: 1094
  helix:  3.13 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.27 (0.59), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.014   0.001   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.004   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8298)
  covalent geometry    : angle       0.46869 (11277)
  hydrogen bonds       : bond        0.04356 (  800)
  hydrogen bonds       : angle       3.75523 ( 2388)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: L   45 ARG cc_start: 0.6082 (tmt170) cc_final: 0.5480 (tpt170)
REVERT: T   65 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7492 (mp0)
REVERT: a   73 MET cc_start: 0.9269 (mmt) cc_final: 0.8786 (mmt)
REVERT: a  205 MET cc_start: 0.8933 (mtt) cc_final: 0.8329 (mtt)
REVERT: d   27 ARG cc_start: 0.6871 (mmt-90) cc_final: 0.6661 (ptp-170)
  outliers start: 11
  outliers final: 5
  residues processed: 77
  average time/residue: 1.4934
  time to fit residues: 121.6608
Evaluate side-chains
  75 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue    6 ASN
Chi-restraints excluded: chain Q residue   71 ASN
Chi-restraints excluded: chain S residue   48 GLU
Chi-restraints excluded: chain T residue   65 GLU
Chi-restraints excluded: chain a residue  239 LEU
Chi-restraints excluded: chain d residue   57 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0670
   chunk 76 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** a 229 GLN ** 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 = 0.3119 r_free = 0.3119 target = 0.084684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.071371 restraints weight = 39051.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 1.55
r_work: 0.2799 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2698 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8298  Z= 0.150
  Angle     :  0.483   5.821  11277  Z= 0.259
  Chirality :  0.038   0.125   1324
  Planarity :  0.004   0.036   1443
  Dihedral  :  4.817  52.577   1176
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.79 %
    Favored  : 87.44 %
  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:  4.41 (0.26), residues: 1094
  helix:  3.14 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop :  1.26 (0.59), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 188 
 TYR   0.019   0.001   TYR a 145 
 PHE   0.014   0.001   PHE N  74 
 TRP   0.010   0.001   TRP a 218 
 HIS   0.003   0.001   HIS a 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8298)
  covalent geometry    : angle       0.48295 (11277)
  hydrogen bonds       : bond        0.04481 (  800)
  hydrogen bonds       : angle       3.76751 ( 2388)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4690.14 seconds
wall clock time: 80 minutes 8.47 seconds (4808.47 seconds total)