Starting phenix.real_space_refine
on Sun Jun 15 15:34:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cvo_27011/06_2025/8cvo_27011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cvo_27011/06_2025/8cvo_27011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cvo_27011/06_2025/8cvo_27011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cvo_27011/06_2025/8cvo_27011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cvo_27011/06_2025/8cvo_27011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cvo_27011/06_2025/8cvo_27011.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.031
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     471      5.49       5
     Mg     12      5.21       5
     S      23      5.16       5
     C    9071      2.51       5
     N    3239      2.21       5
     O    4604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17421
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 10090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 10090
          Classifications: {'RNA': 471}
          Modifications used: {'rna2p_pur': 34, 'rna2p_pyr': 37, 'rna3p': 2, 'rna3p_pur': 219, 'rna3p_pyr': 179}
          Link IDs: {'rna2p': 71, 'rna3p': 399}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 2
    Chain: "E"
      Number of atoms: 482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 482
          Classifications: {'peptide': 64}
          Link IDs: {'PTRANS': 1, 'TRANS': 62}
    Chain: "G"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1670
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 209}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "I"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1225
          Classifications: {'peptide': 155}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 145}
    Chain: "J"
      Number of atoms: 1012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1012
          Classifications: {'peptide': 134}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 125}
    Chain: "M"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 786
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "N"
      Number of atoms: 976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 976
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 2, 'TRANS': 119}
    Chain: "S"
      Number of atoms: 474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 474
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "U"
      Number of atoms: 658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 658
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "A"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 47
          Unusual residues: {' MG': 12, 'V7A': 1}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
    Chain: "S"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  16420  SG  CYS S  24      47.536  67.044  47.555  1.00 68.29           S
  ATOM  16446  SG  CYS S  27      46.769  63.105  48.246  1.00 69.39           S
  ATOM  16552  SG  CYS S  40      50.103  65.280  49.667  1.00 69.26           S
  ATOM  16577  SG  CYS S  43      49.456  64.842  46.134  1.00 70.06           S

  Time building chain proxies: 10.66, per 1000 atoms: 0.61
  Number of scatterers: 17421
  At special positions: 0
  Unit cell: (129.228, 129.228, 124.956, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      23     16.00
     P     471     15.00
     Mg     12     11.99
     O    4604      8.00
     N    3239      7.00
     C    9071      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN S 101 "
        pdb="ZN    ZN S 101 " - pdb=" SG  CYS S  43 "
        pdb="ZN    ZN S 101 " - pdb=" SG  CYS S  40 "
        pdb="ZN    ZN S 101 " - pdb=" SG  CYS S  24 "
        pdb="ZN    ZN S 101 " - pdb=" SG  CYS S  27 "
      Number of angles added : 6


  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1698

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 8 sheets defined
      45.8% alpha, 21.4% beta
      140 base pairs and 251 stacking pairs defined.
    Time for finding SS restraints: 8.22
  Creating SS restraints...
    Processing helix  chain 'E' and resid 78 through 92
      removed outlier: 4.174A  pdb=" N   LYS E  92 " --> pdb=" O   GLU E  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 11
    Processing helix  chain 'G' and resid 27 through 46
    Processing helix  chain 'G' and resid 72 through 77
    Processing helix  chain 'G' and resid 80 through 95
    Processing helix  chain 'G' and resid 111 through 125
    Processing helix  chain 'G' and resid 128 through 144
    Processing helix  chain 'G' and resid 155 through 159
      removed outlier: 3.518A  pdb=" N   ALA G 159 " --> pdb=" O   LEU G 156 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 208 through 215
    Processing helix  chain 'I' and resid 20 through 31
      removed outlier: 3.741A  pdb=" N   SER I  24 " --> pdb=" O   SER I  20 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 32 through 34
      No H-bonds generated for 'chain 'I' and resid 32 through 34'
    Processing helix  chain 'I' and resid 35 through 54
    Processing helix  chain 'I' and resid 57 through 70
    Processing helix  chain 'I' and resid 92 through 111
    Processing helix  chain 'I' and resid 115 through 130
    Processing helix  chain 'I' and resid 132 through 148
    Processing helix  chain 'I' and resid 149 through 155
      removed outlier: 4.752A  pdb=" N   HIS I 153 " --> pdb=" O   ALA I 150 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG I 155 " --> pdb=" O   ALA I 152 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 76 through 81
    Processing helix  chain 'J' and resid 87 through 97
      Proline residue:  J  93  - end of helix
    Processing helix  chain 'J' and resid 113 through 133
    Processing helix  chain 'J' and resid 137 through 144
    Processing helix  chain 'M' and resid 14 through 32
    Processing helix  chain 'M' and resid 80 through 90
    Processing helix  chain 'N' and resid 14 through 19
    Processing helix  chain 'N' and resid 26 through 38
    Processing helix  chain 'N' and resid 49 through 64
    Processing helix  chain 'N' and resid 67 through 85
    Processing helix  chain 'N' and resid 86 through 95
    Processing helix  chain 'N' and resid 107 through 112
    Processing helix  chain 'S' and resid 3 through 12
    Processing helix  chain 'S' and resid 16 through 20
    Processing helix  chain 'S' and resid 40 through 51
    Processing helix  chain 'U' and resid 4 through 8
    Processing helix  chain 'U' and resid 14 through 26
    Processing helix  chain 'U' and resid 41 through 45
    Processing helix  chain 'U' and resid 63 through 69
      removed outlier: 3.727A  pdb=" N   VAL U  67 " --> pdb=" O   GLU U  64 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   GLY U  68 " --> pdb=" O   SER U  65 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 70 through 75
    Processing sheet with id=AA1, first strand: chain 'E' and resid 35 through 47
      removed outlier: 5.218A  pdb=" N   GLU E  36 " --> pdb=" O   GLY E  63 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   GLY E  63 " --> pdb=" O   GLU E  36 " (cutoff:3.500A)
      removed outlier: 5.593A  pdb=" N   VAL E  38 " --> pdb=" O   VAL E  61 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL E  61 " --> pdb=" O   VAL E  38 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 20 through 21
      removed outlier: 3.627A  pdb=" N   ARG G  58 " --> pdb=" O   ARG G  21 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TYR G  68 " --> pdb=" O   SER G  52 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE G  54 " --> pdb=" O   PHE G  66 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   PHE G  66 " --> pdb=" O   ILE G  54 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ILE G  56 " --> pdb=" O   THR G  64 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR G  64 " --> pdb=" O   ILE G  56 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ARG G  58 " --> pdb=" O   ARG G  62 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ARG G  62 " --> pdb=" O   ARG G  58 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL G  63 " --> pdb=" O   GLN G  99 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ASN G 101 " --> pdb=" O   VAL G  63 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   ILE G  65 " --> pdb=" O   ASN G 101 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   LEU G 103 " --> pdb=" O   ILE G  65 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   LEU G  67 " --> pdb=" O   LEU G 103 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 163 through 170
      removed outlier: 3.731A  pdb=" N   GLY G 147 " --> pdb=" O   TYR G 202 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ASP G 180 " --> pdb=" O   LYS G 203 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 73 through 78
    Processing sheet with id=AA5, first strand: chain 'J' and resid 48 through 53
      removed outlier: 6.529A  pdb=" N   LYS J  71 " --> pdb=" O   ALA J 107 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   ILE J 109 " --> pdb=" O   LYS J  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'M' and resid 36 through 52
      removed outlier: 8.548A  pdb=" N   ASP M  75 " --> pdb=" O   PRO M  39 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU M  73 " --> pdb=" O   PRO M  41 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   LYS M  71 " --> pdb=" O   PRO M  43 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASN M  47 " --> pdb=" O   MET M  67 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG M  11 " --> pdb=" O   ASP M  97 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'M' and resid 36 through 52
      removed outlier: 8.548A  pdb=" N   ASP M  75 " --> pdb=" O   PRO M  39 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU M  73 " --> pdb=" O   PRO M  41 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   LYS M  71 " --> pdb=" O   PRO M  43 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASN M  47 " --> pdb=" O   MET M  67 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'U' and resid 30 through 33

    372 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      353 hydrogen bonds
      530 hydrogen bond angles
      0 basepair planarities
      140 basepair parallelities
      251 stacking parallelities
  Total time for adding SS restraints: 8.98

  Time building geometry restraints manager: 5.06 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2732
        1.33 -     1.45: 7103
        1.45 -     1.57: 7908
        1.57 -     1.69: 941
        1.69 -     1.81: 39
  Bond restraints: 18723
  Sorted by residual:
  bond pdb=" CBC V7A A1601 "
       pdb=" NBD V7A A1601 "
    ideal  model  delta    sigma   weight residual
    1.323  1.509 -0.186 2.00e-02 2.50e+03 8.67e+01
  bond pdb=" N   VAL M  36 "
       pdb=" CA  VAL M  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.89e+00
  bond pdb=" N   VAL G 206 "
       pdb=" CA  VAL G 206 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.15e-02 7.56e+03 7.84e+00
  bond pdb=" N   GLU G  25 "
       pdb=" CA  GLU G  25 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.031 1.14e-02 7.69e+03 7.58e+00
  bond pdb=" N   LYS M  35 "
       pdb=" CA  LYS M  35 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.22e-02 6.72e+03 7.33e+00
  ... (remaining 18718 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 27289
        2.75 -     5.50: 272
        5.50 -     8.25: 28
        8.25 -    11.00: 10
       11.00 -    13.75: 3
  Bond angle restraints: 27602
  Sorted by residual:
  angle pdb=" C3'   G A1184 "
        pdb=" O3'   G A1184 "
        pdb=" P     U A1185 "
      ideal   model   delta    sigma   weight residual
     120.20  106.45   13.75 1.50e+00 4.44e-01 8.40e+01
  angle pdb=" C3'   U A1153 "
        pdb=" O3'   U A1153 "
        pdb=" P     C A1154 "
      ideal   model   delta    sigma   weight residual
     120.20  108.99   11.21 1.50e+00 4.44e-01 5.58e+01
  angle pdb=" C3'   U A 958 "
        pdb=" O3'   U A 958 "
        pdb=" P     A A 959 "
      ideal   model   delta    sigma   weight residual
     120.20  109.13   11.07 1.50e+00 4.44e-01 5.44e+01
  angle pdb=" C3'   A A1343 "
        pdb=" O3'   A A1343 "
        pdb=" P     U A1344 "
      ideal   model   delta    sigma   weight residual
     120.20  109.89   10.31 1.50e+00 4.44e-01 4.72e+01
  angle pdb=" C3'   A A 959 "
        pdb=" O3'   A A 959 "
        pdb=" P     G A 960 "
      ideal   model   delta    sigma   weight residual
     120.20  110.11   10.09 1.50e+00 4.44e-01 4.52e+01
  ... (remaining 27597 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 10803
       35.87 -    71.75: 1182
       71.75 -   107.62: 137
      107.62 -   143.49: 3
      143.49 -   179.36: 8
  Dihedral angle restraints: 12133
    sinusoidal: 9489
      harmonic: 2644
  Sorted by residual:
  dihedral pdb=" O4'   C A1013 "
           pdb=" C1'   C A1013 "
           pdb=" N1    C A1013 "
           pdb=" C2    C A1013 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   48.36  151.64     1      1.50e+01 4.44e-03 8.02e+01
  dihedral pdb=" O4'   C A1144 "
           pdb=" C1'   C A1144 "
           pdb=" N1    C A1144 "
           pdb=" C2    C A1144 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   69.94  130.06     1      1.50e+01 4.44e-03 7.01e+01
  dihedral pdb=" O4'   U A1121 "
           pdb=" C1'   U A1121 "
           pdb=" N1    U A1121 "
           pdb=" C2    U A1121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.64  179.36     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 12130 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 3266
       0.085 -    0.170: 149
       0.170 -    0.255: 19
       0.255 -    0.340: 5
       0.340 -    0.425: 15
  Chirality restraints: 3454
  Sorted by residual:
  chirality pdb=" P     G A1184 "
            pdb=" OP1   G A1184 "
            pdb=" OP2   G A1184 "
            pdb=" O5'   G A1184 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.83   -0.42 2.00e-01 2.50e+01 4.51e+00
  chirality pdb=" P     U A1153 "
            pdb=" OP1   U A1153 "
            pdb=" OP2   U A1153 "
            pdb=" O5'   U A1153 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.83   -0.42 2.00e-01 2.50e+01 4.41e+00
  chirality pdb=" P     U A 958 "
            pdb=" OP1   U A 958 "
            pdb=" OP2   U A 958 "
            pdb=" O5'   U A 958 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.82   -0.41 2.00e-01 2.50e+01 4.25e+00
  ... (remaining 3451 not shown)

  Planarity restraints: 1764
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAH V7A A1601 "    0.298 2.00e-02 2.50e+03   2.47e-01 9.13e+02
        pdb=" CAI V7A A1601 "    0.005 2.00e-02 2.50e+03
        pdb=" CAJ V7A A1601 "   -0.293 2.00e-02 2.50e+03
        pdb=" CAL V7A A1601 "   -0.018 2.00e-02 2.50e+03
        pdb=" CAM V7A A1601 "    0.313 2.00e-02 2.50e+03
        pdb=" OAZ V7A A1601 "   -0.304 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A1039 "   -0.045 2.00e-02 2.50e+03   4.06e-02 3.70e+01
        pdb=" N1    C A1039 "    0.027 2.00e-02 2.50e+03
        pdb=" C2    C A1039 "    0.088 2.00e-02 2.50e+03
        pdb=" O2    C A1039 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3    C A1039 "   -0.053 2.00e-02 2.50e+03
        pdb=" C4    C A1039 "   -0.023 2.00e-02 2.50e+03
        pdb=" N4    C A1039 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    C A1039 "    0.027 2.00e-02 2.50e+03
        pdb=" C6    C A1039 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP M  27 "    0.014 2.00e-02 2.50e+03   2.95e-02 8.69e+00
        pdb=" C   ASP M  27 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ASP M  27 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR M  28 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1761 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 525
        2.64 -     3.20: 15170
        3.20 -     3.77: 34652
        3.77 -     4.33: 46716
        4.33 -     4.90: 63682
  Nonbonded interactions: 160745
  Sorted by model distance:
  nonbonded pdb=" OP2   G A1184 "
            pdb="MG    MG A1604 "
     model   vdw
     2.075 2.170
  nonbonded pdb=" OP2   A A1095 "
            pdb="MG    MG A1612 "
     model   vdw
     2.211 2.170
  nonbonded pdb=" O   VAL J  85 "
            pdb=" NE2 GLN J  88 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" N2    G A1163 "
            pdb=" O6    G A1167 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" OP2   U A 945 "
            pdb=" O2'   C A1209 "
     model   vdw
     2.241 3.040
  ... (remaining 160740 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.570
  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:             0.020
  Extract box with map and model:          0.650
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     50.230
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   65.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
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      :  0.005   0.186  18727  Z= 0.244
  Angle     :  0.696  21.698  27608  Z= 0.381
  Chirality :  0.047   0.425   3454
  Planarity :  0.008   0.247   1764
  Dihedral  : 22.824 179.364  10435
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  5.57 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  0.53 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 915
  helix:  1.21 (0.28), residues: 367
  sheet: -0.15 (0.39), residues: 173
  loop : -0.81 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  22 
 HIS   0.004   0.001   HIS J  86 
 PHE   0.018   0.002   PHE S  37 
 TYR   0.024   0.002   TYR N  64 
 ARG   0.008   0.000   ARG N  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18280 (  718)
  hydrogen bonds       : angle       6.51194 ( 1586)
  metal coordination   : bond        0.05865 (    4)
  metal coordination   : angle      11.91809 (    6)
  covalent geometry    : bond        0.00452 (18723)
  covalent geometry    : angle       0.67373 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 284
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   34 TYR cc_start: 0.7211 (m-80) cc_final: 0.6856 (m-80)
REVERT: E   78 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7794 (mt-10)
REVERT: E   85 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8196 (ttpt)
REVERT: G  161 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7940 (mmm)
REVERT: I  123 GLU cc_start: 0.9045 (tp30) cc_final: 0.8834 (mm-30)
REVERT: J   79 ASP cc_start: 0.9016 (t0) cc_final: 0.8655 (t0)
REVERT: J   80 TYR cc_start: 0.9076 (t80) cc_final: 0.8754 (t80)
REVERT: M   20 SER cc_start: 0.9191 (p) cc_final: 0.8970 (p)
REVERT: M   46 LYS cc_start: 0.8416 (tptm) cc_final: 0.8163 (tppp)
REVERT: M   76 ILE cc_start: 0.8875 (mm) cc_final: 0.8551 (mm)
REVERT: S   46 GLU cc_start: 0.8188 (pt0) cc_final: 0.7962 (pt0)
  outliers start: 11
  outliers final: 3
  residues processed: 290
  average time/residue: 1.4097
  time to fit residues: 452.3238
Evaluate side-chains
  221 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 217
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  111 ASP
Chi-restraints excluded: chain G residue  161 MET
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   66 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0060
   chunk 79 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   overall best weight:    0.7802

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

Flipped N/Q/H residues before XYZ refinement:
G  27 GLN
G  97 GLN
** I  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  96 GLN
J  86 HIS
M  47 ASN
N  52 GLN
** U  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.095853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.069754 restraints weight = 39141.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.63
r_work: 0.2813 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  18727  Z= 0.146
  Angle     :  0.619   9.195  27608  Z= 0.318
  Chirality :  0.037   0.246   3454
  Planarity :  0.005   0.042   1764
  Dihedral  : 23.509 178.724   8627
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  5.36 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.45 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.29), residues: 915
  helix:  1.29 (0.28), residues: 373
  sheet: -0.03 (0.40), residues: 178
  loop : -0.67 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 200 
 HIS   0.006   0.001   HIS N  46 
 PHE   0.011   0.001   PHE U  74 
 TYR   0.012   0.001   TYR I  44 
 ARG   0.007   0.001   ARG G 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06184 (  718)
  hydrogen bonds       : angle       3.79897 ( 1586)
  metal coordination   : bond        0.00798 (    4)
  metal coordination   : angle       5.29094 (    6)
  covalent geometry    : bond        0.00294 (18723)
  covalent geometry    : angle       0.61436 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 238
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: E   34 TYR cc_start: 0.7155 (m-80) cc_final: 0.6675 (m-80)
REVERT: E   78 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8424 (mt-10)
REVERT: E   85 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8196 (ttpt)
REVERT: E   89 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8362 (tm-30)
REVERT: G   17 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8296 (m-30)
REVERT: G  138 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8264 (tp40)
REVERT: I   41 ASN cc_start: 0.9028 (t0) cc_final: 0.8815 (t0)
REVERT: I   74 GLU cc_start: 0.8353 (pp20) cc_final: 0.7937 (pp20)
REVERT: I  123 GLU cc_start: 0.9256 (tp30) cc_final: 0.8914 (mm-30)
REVERT: J   79 ASP cc_start: 0.9285 (t0) cc_final: 0.8773 (t0)
REVERT: J   80 TYR cc_start: 0.9183 (t80) cc_final: 0.8906 (t80)
REVERT: J   92 GLU cc_start: 0.8458 (pp20) cc_final: 0.8222 (pp20)
REVERT: J  169 GLN cc_start: 0.9422 (tt0) cc_final: 0.9193 (tt0)
REVERT: M   20 SER cc_start: 0.9162 (p) cc_final: 0.8897 (p)
REVERT: M   76 ILE cc_start: 0.8763 (mm) cc_final: 0.8550 (mm)
REVERT: N   32 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8331 (tm-30)
REVERT: N   58 ASP cc_start: 0.8476 (p0) cc_final: 0.8257 (p0)
  outliers start: 24
  outliers final: 12
  residues processed: 245
  average time/residue: 1.3148
  time to fit residues: 360.4021
Evaluate side-chains
  227 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 213
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain G residue   17 ASP
Chi-restraints excluded: chain G residue   98 ILE
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   62 LEU
Chi-restraints excluded: chain I residue  131 LEU
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  137 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain U residue   39 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 109 optimal weight:    0.8980
   chunk 123 optimal weight:    0.0770
   chunk 24 optimal weight:    9.9990
   chunk 135 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   overall best weight:    1.9942

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

Flipped N/Q/H residues before XYZ refinement:
G  27 GLN
J  86 HIS
** U  23 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 = 0.3399 r_free = 0.3399 target = 0.093748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.067482 restraints weight = 39049.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 1.64
r_work: 0.2763 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  18727  Z= 0.230
  Angle     :  0.622   9.537  27608  Z= 0.322
  Chirality :  0.039   0.262   3454
  Planarity :  0.005   0.044   1764
  Dihedral  : 23.368 177.383   8619
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  5.79 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 20.59 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.29), residues: 915
  helix:  1.29 (0.28), residues: 374
  sheet:  0.10 (0.39), residues: 180
  loop : -0.65 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 200 
 HIS   0.007   0.001   HIS N  46 
 PHE   0.012   0.001   PHE U  74 
 TYR   0.016   0.002   TYR J 170 
 ARG   0.008   0.001   ARG G  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05647 (  718)
  hydrogen bonds       : angle       3.67606 ( 1586)
  metal coordination   : bond        0.00646 (    4)
  metal coordination   : angle       5.36050 (    6)
  covalent geometry    : bond        0.00459 (18723)
  covalent geometry    : angle       0.61737 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 223
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
REVERT: E   34 TYR cc_start: 0.7407 (m-80) cc_final: 0.6790 (m-80)
REVERT: E   85 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8044 (ttpp)
REVERT: G   48 ARG cc_start: 0.8787 (mtp85) cc_final: 0.8555 (mtp85)
REVERT: G  138 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8510 (tp40)
REVERT: G  141 MET cc_start: 0.9258 (mmt) cc_final: 0.8787 (mmt)
REVERT: I   74 GLU cc_start: 0.8364 (pp20) cc_final: 0.8139 (pp20)
REVERT: J   79 ASP cc_start: 0.9301 (t0) cc_final: 0.8793 (t0)
REVERT: J   92 GLU cc_start: 0.8498 (pp20) cc_final: 0.8285 (pp20)
REVERT: J  106 ILE cc_start: 0.9342 (mt) cc_final: 0.9124 (mp)
REVERT: J  169 GLN cc_start: 0.9525 (tt0) cc_final: 0.9234 (tt0)
REVERT: M    5 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5839 (pttp)
REVERT: M   20 SER cc_start: 0.9145 (p) cc_final: 0.8921 (p)
REVERT: M   68 ARG cc_start: 0.9190 (mtp85) cc_final: 0.8971 (mtp85)
REVERT: M   76 ILE cc_start: 0.8720 (mm) cc_final: 0.8474 (mm)
REVERT: N   32 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8405 (tm-30)
REVERT: N   47 GLU cc_start: 0.8142 (pm20) cc_final: 0.7808 (pm20)
  outliers start: 44
  outliers final: 20
  residues processed: 242
  average time/residue: 1.2629
  time to fit residues: 341.7179
Evaluate side-chains
  230 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   17 ASP
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   89 VAL
Chi-restraints excluded: chain I residue  131 LEU
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  132 VAL
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain U residue   38 SER
Chi-restraints excluded: chain U residue   39 MET
Chi-restraints excluded: chain U residue   79 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 115 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
G  97 GLN
J  86 HIS
N  59 HIS
** U  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.093870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.067446 restraints weight = 39184.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 1.64
r_work: 0.2764 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  18727  Z= 0.239
  Angle     :  0.626   8.930  27608  Z= 0.325
  Chirality :  0.039   0.265   3454
  Planarity :  0.005   0.047   1764
  Dihedral  : 23.340 175.301   8619
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.12 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 23.93 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.29), residues: 915
  helix:  1.24 (0.28), residues: 374
  sheet:  0.01 (0.39), residues: 185
  loop : -0.63 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  70 
 HIS   0.007   0.001   HIS N  46 
 PHE   0.011   0.002   PHE I 107 
 TYR   0.019   0.002   TYR J 170 
 ARG   0.006   0.001   ARG I   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05446 (  718)
  hydrogen bonds       : angle       3.68444 ( 1586)
  metal coordination   : bond        0.00582 (    4)
  metal coordination   : angle       4.73191 (    6)
  covalent geometry    : bond        0.00476 (18723)
  covalent geometry    : angle       0.62189 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 216
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   34 TYR cc_start: 0.7564 (m-80) cc_final: 0.7136 (m-80)
REVERT: E   85 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8079 (ttpp)
REVERT: G  138 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8470 (tp40)
REVERT: G  142 ASN cc_start: 0.8903 (m-40) cc_final: 0.8499 (m-40)
REVERT: I   74 GLU cc_start: 0.8396 (pp20) cc_final: 0.8093 (pp20)
REVERT: I   75 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8786 (m)
REVERT: I  123 GLU cc_start: 0.9259 (tp30) cc_final: 0.8952 (mm-30)
REVERT: J   79 ASP cc_start: 0.9305 (t0) cc_final: 0.8800 (t0)
REVERT: J   92 GLU cc_start: 0.8570 (pp20) cc_final: 0.8342 (pp20)
REVERT: J  106 ILE cc_start: 0.9404 (mt) cc_final: 0.9197 (mp)
REVERT: J  108 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8165 (tmt-80)
REVERT: J  169 GLN cc_start: 0.9538 (tt0) cc_final: 0.9239 (tt0)
REVERT: M    5 LYS cc_start: 0.6250 (ttpp) cc_final: 0.5926 (ptmm)
REVERT: M   68 ARG cc_start: 0.9134 (mtp85) cc_final: 0.8885 (mtp85)
REVERT: M   76 ILE cc_start: 0.8755 (mm) cc_final: 0.8401 (mm)
REVERT: M  100 ILE cc_start: 0.8715 (mm) cc_final: 0.8504 (mt)
REVERT: N   16 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8306 (tt0)
REVERT: N   32 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: N   33 THR cc_start: 0.9384 (m) cc_final: 0.9057 (m)
REVERT: N  115 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8108 (ptmm)
REVERT: S   35 ARG cc_start: 0.9027 (mtt180) cc_final: 0.8747 (mtt180)
REVERT: S   37 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8520 (p90)
  outliers start: 45
  outliers final: 26
  residues processed: 237
  average time/residue: 1.4280
  time to fit residues: 378.8217
Evaluate side-chains
  236 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 206
  time to evaluate  : 1.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain G residue   17 ASP
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   77 SER
Chi-restraints excluded: chain I residue  131 LEU
Chi-restraints excluded: chain J residue   51 THR
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  108 ARG
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  132 VAL
Chi-restraints excluded: chain J residue  137 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   18 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   90 LEU
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   16 GLU
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   96 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain S residue   37 PHE
Chi-restraints excluded: chain U residue   38 SER
Chi-restraints excluded: chain U residue   39 MET
Chi-restraints excluded: chain U residue   79 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 115 optimal weight:    0.0470
   chunk 2 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 136 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.7884

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

Flipped N/Q/H residues before XYZ refinement:
G  27 GLN
J  86 HIS
** J  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  23 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.094582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.068512 restraints weight = 39545.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 1.60
r_work: 0.2779 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  18727  Z= 0.211
  Angle     :  0.616   8.217  27608  Z= 0.319
  Chirality :  0.038   0.260   3454
  Planarity :  0.005   0.058   1764
  Dihedral  : 23.320 174.104   8619
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.79 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 26.34 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.29), residues: 915
  helix:  1.27 (0.28), residues: 374
  sheet: -0.02 (0.38), residues: 185
  loop : -0.65 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J  70 
 HIS   0.006   0.001   HIS N  46 
 PHE   0.011   0.001   PHE G 129 
 TYR   0.022   0.002   TYR J 170 
 ARG   0.008   0.000   ARG G  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05276 (  718)
  hydrogen bonds       : angle       3.64552 ( 1586)
  metal coordination   : bond        0.00469 (    4)
  metal coordination   : angle       4.16566 (    6)
  covalent geometry    : bond        0.00422 (18723)
  covalent geometry    : angle       0.61283 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 212
  time to evaluate  : 1.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   34 TYR cc_start: 0.7783 (m-80) cc_final: 0.7352 (m-80)
REVERT: E   85 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8087 (ttpp)
REVERT: G  138 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8453 (tp40)
REVERT: G  142 ASN cc_start: 0.8933 (m-40) cc_final: 0.8479 (m-40)
REVERT: I   74 GLU cc_start: 0.8448 (pp20) cc_final: 0.8114 (pp20)
REVERT: I  123 GLU cc_start: 0.9274 (tp30) cc_final: 0.8952 (mm-30)
REVERT: J   79 ASP cc_start: 0.9308 (t0) cc_final: 0.8781 (t0)
REVERT: J  106 ILE cc_start: 0.9398 (mt) cc_final: 0.9195 (mp)
REVERT: J  108 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8083 (tmt-80)
REVERT: J  130 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8767 (t0)
REVERT: J  150 ASP cc_start: 0.8719 (p0) cc_final: 0.7993 (p0)
REVERT: J  169 GLN cc_start: 0.9529 (tt0) cc_final: 0.9188 (tt0)
REVERT: M    5 LYS cc_start: 0.6223 (ttpp) cc_final: 0.5819 (pttp)
REVERT: M   53 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8516 (mtt-85)
REVERT: M   68 ARG cc_start: 0.9130 (mtp85) cc_final: 0.8823 (mtp85)
REVERT: M   76 ILE cc_start: 0.8793 (mm) cc_final: 0.8519 (mm)
REVERT: M  100 ILE cc_start: 0.8721 (mm) cc_final: 0.8482 (mt)
REVERT: N   16 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8295 (tt0)
REVERT: N   32 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8397 (tm-30)
REVERT: N   33 THR cc_start: 0.9351 (m) cc_final: 0.8995 (m)
REVERT: N   47 GLU cc_start: 0.8011 (pm20) cc_final: 0.7619 (pm20)
REVERT: N  115 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7949 (ptmt)
  outliers start: 48
  outliers final: 29
  residues processed: 235
  average time/residue: 1.5673
  time to fit residues: 411.5461
Evaluate side-chains
  241 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 208
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain G residue   17 ASP
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain G residue  161 MET
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   33 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   89 VAL
Chi-restraints excluded: chain I residue  131 LEU
Chi-restraints excluded: chain J residue   51 THR
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  108 ARG
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  130 ASN
Chi-restraints excluded: chain M residue   18 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   90 LEU
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   16 GLU
Chi-restraints excluded: chain N residue   17 VAL
Chi-restraints excluded: chain N residue   42 ASP
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   96 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain U residue   38 SER
Chi-restraints excluded: chain U residue   39 MET
Chi-restraints excluded: chain U residue   79 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 59 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0470
   chunk 79 optimal weight:    5.9990
   chunk 129 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.2084

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

Flipped N/Q/H residues before XYZ refinement:
G   8 HIS
G  27 GLN
G  97 GLN
J  86 HIS
** J  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.093854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.067572 restraints weight = 39300.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 1.64
r_work: 0.2751 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  18727  Z= 0.249
  Angle     :  0.636   7.894  27608  Z= 0.329
  Chirality :  0.039   0.268   3454
  Planarity :  0.005   0.060   1764
  Dihedral  : 23.308 172.562   8617
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.01 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 27.27 %
    Favored  : 66.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.29), residues: 915
  helix:  1.27 (0.28), residues: 374
  sheet: -0.05 (0.39), residues: 184
  loop : -0.65 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  70 
 HIS   0.007   0.001   HIS N  46 
 PHE   0.011   0.001   PHE I 107 
 TYR   0.016   0.002   TYR J 103 
 ARG   0.008   0.001   ARG G  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05383 (  718)
  hydrogen bonds       : angle       3.65518 ( 1586)
  metal coordination   : bond        0.00438 (    4)
  metal coordination   : angle       4.00086 (    6)
  covalent geometry    : bond        0.00497 (18723)
  covalent geometry    : angle       0.63288 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 217
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   34 TYR cc_start: 0.7719 (m-80) cc_final: 0.7174 (m-80)
REVERT: E   85 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8056 (ttpp)
REVERT: G  138 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8437 (tp40)
REVERT: G  142 ASN cc_start: 0.8915 (m-40) cc_final: 0.8433 (m-40)
REVERT: I   74 GLU cc_start: 0.8415 (pp20) cc_final: 0.8057 (pp20)
REVERT: I  123 GLU cc_start: 0.9270 (tp30) cc_final: 0.8949 (mm-30)
REVERT: J   79 ASP cc_start: 0.9313 (t0) cc_final: 0.8785 (t0)
REVERT: J  108 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8110 (tmt-80)
REVERT: J  130 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8790 (t0)
REVERT: J  150 ASP cc_start: 0.8702 (p0) cc_final: 0.7976 (p0)
REVERT: J  169 GLN cc_start: 0.9540 (tt0) cc_final: 0.9196 (tt0)
REVERT: M    5 LYS cc_start: 0.6229 (ttpp) cc_final: 0.5845 (ptmm)
REVERT: M   53 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8583 (mtt-85)
REVERT: M   68 ARG cc_start: 0.9166 (mtp85) cc_final: 0.8848 (mtp85)
REVERT: N   16 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8277 (tt0)
REVERT: N   32 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8366 (tm-30)
REVERT: N   33 THR cc_start: 0.9365 (m) cc_final: 0.8995 (m)
REVERT: N   57 ARG cc_start: 0.8443 (tmm-80) cc_final: 0.8212 (tmm-80)
REVERT: S   35 ARG cc_start: 0.9018 (mtt180) cc_final: 0.8723 (mtt180)
  outliers start: 48
  outliers final: 32
  residues processed: 239
  average time/residue: 1.5940
  time to fit residues: 426.0032
Evaluate side-chains
  247 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 210
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain G residue   17 ASP
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain G residue  146 LEU
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   13 MET
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   62 LEU
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   77 SER
Chi-restraints excluded: chain I residue   89 VAL
Chi-restraints excluded: chain I residue  131 LEU
Chi-restraints excluded: chain J residue   51 THR
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  108 ARG
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  130 ASN
Chi-restraints excluded: chain J residue  132 VAL
Chi-restraints excluded: chain M residue   18 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   90 LEU
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   16 GLU
Chi-restraints excluded: chain N residue   17 VAL
Chi-restraints excluded: chain N residue   32 GLU
Chi-restraints excluded: chain N residue   42 ASP
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   96 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain U residue   38 SER
Chi-restraints excluded: chain U residue   39 MET
Chi-restraints excluded: chain U residue   79 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 112 optimal weight:    0.2980
   chunk 95 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
G  27 GLN
J  86 HIS
** J  88 GLN ** 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 = 0.3448 r_free = 0.3448 target = 0.094605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.067876 restraints weight = 38789.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.66
r_work: 0.2803 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8847
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  18727  Z= 0.291
  Angle     :  0.666   9.446  27608  Z= 0.345
  Chirality :  0.041   0.277   3454
  Planarity :  0.005   0.062   1764
  Dihedral  : 23.318 172.062   8617
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.23 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 27.81 %
    Favored  : 65.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.29), residues: 915
  helix:  1.19 (0.27), residues: 376
  sheet: -0.14 (0.39), residues: 184
  loop : -0.68 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J  70 
 HIS   0.006   0.001   HIS N  46 
 PHE   0.012   0.002   PHE I 107 
 TYR   0.025   0.002   TYR J 170 
 ARG   0.009   0.001   ARG G  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05543 (  718)
  hydrogen bonds       : angle       3.71757 ( 1586)
  metal coordination   : bond        0.00373 (    4)
  metal coordination   : angle       3.28209 (    6)
  covalent geometry    : bond        0.00581 (18723)
  covalent geometry    : angle       0.66469 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 215
  time to evaluate  : 1.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   34 TYR cc_start: 0.7722 (m-80) cc_final: 0.7084 (m-80)
REVERT: E   85 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8116 (ttpp)
REVERT: G  117 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8068 (tt0)
REVERT: G  138 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8478 (tp40)
REVERT: G  142 ASN cc_start: 0.8886 (m-40) cc_final: 0.8371 (m-40)
REVERT: I   74 GLU cc_start: 0.8463 (pp20) cc_final: 0.8094 (pp20)
REVERT: I  123 GLU cc_start: 0.9164 (tp30) cc_final: 0.8880 (mm-30)
REVERT: J   79 ASP cc_start: 0.9243 (t0) cc_final: 0.8793 (t0)
REVERT: J  108 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8167 (tmt-80)
REVERT: J  130 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8876 (t0)
REVERT: J  150 ASP cc_start: 0.8615 (p0) cc_final: 0.7968 (p0)
REVERT: M    5 LYS cc_start: 0.6487 (ttpp) cc_final: 0.6078 (ptmm)
REVERT: M   53 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8646 (mtt-85)
REVERT: M   68 ARG cc_start: 0.9200 (mtp85) cc_final: 0.8896 (mtp85)
REVERT: M  100 ILE cc_start: 0.8764 (mm) cc_final: 0.8545 (mt)
REVERT: N   16 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8196 (tt0)
REVERT: N   32 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8373 (tm-30)
REVERT: N   33 THR cc_start: 0.9391 (m) cc_final: 0.9037 (m)
REVERT: N   47 GLU cc_start: 0.7980 (pm20) cc_final: 0.7687 (pm20)
REVERT: N   57 ARG cc_start: 0.8458 (tmm-80) cc_final: 0.8230 (tmm-80)
REVERT: N  115 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8154 (ptmm)
REVERT: U   29 ASN cc_start: 0.8502 (t0) cc_final: 0.8179 (t0)
  outliers start: 50
  outliers final: 31
  residues processed: 239
  average time/residue: 1.3237
  time to fit residues: 353.2471
Evaluate side-chains
  246 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 209
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain G residue   17 ASP
Chi-restraints excluded: chain G residue  110 THR
Chi-restraints excluded: chain G residue  117 GLN
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   13 MET
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   62 LEU
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   77 SER
Chi-restraints excluded: chain I residue   89 VAL
Chi-restraints excluded: chain I residue  131 LEU
Chi-restraints excluded: chain J residue   51 THR
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  108 ARG
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  130 ASN
Chi-restraints excluded: chain M residue   18 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   90 LEU
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   16 GLU
Chi-restraints excluded: chain N residue   17 VAL
Chi-restraints excluded: chain N residue   32 GLU
Chi-restraints excluded: chain N residue   42 ASP
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   96 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain U residue   38 SER
Chi-restraints excluded: chain U residue   39 MET
Chi-restraints excluded: chain U residue   79 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 128 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 115 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  97 GLN
** J  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  88 GLN ** 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 = 0.3505 r_free = 0.3505 target = 0.097829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.071391 restraints weight = 38632.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.62
r_work: 0.2883 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  18727  Z= 0.156
  Angle     :  0.618  11.270  27608  Z= 0.319
  Chirality :  0.036   0.249   3454
  Planarity :  0.005   0.054   1764
  Dihedral  : 23.274 173.065   8617
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.36 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 30.48 %
    Favored  : 64.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.29), residues: 915
  helix:  1.27 (0.27), residues: 377
  sheet: -0.02 (0.39), residues: 182
  loop : -0.62 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  70 
 HIS   0.008   0.001   HIS N  46 
 PHE   0.011   0.001   PHE G 129 
 TYR   0.021   0.002   TYR J 170 
 ARG   0.009   0.000   ARG G  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05121 (  718)
  hydrogen bonds       : angle       3.63735 ( 1586)
  metal coordination   : bond        0.00381 (    4)
  metal coordination   : angle       2.81272 (    6)
  covalent geometry    : bond        0.00320 (18723)
  covalent geometry    : angle       0.61649 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 213
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   85 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8192 (ttpp)
REVERT: G  117 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8067 (tt0)
REVERT: G  138 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8366 (tp40)
REVERT: G  142 ASN cc_start: 0.8874 (m-40) cc_final: 0.8379 (m-40)
REVERT: G  180 ASP cc_start: 0.8871 (t0) cc_final: 0.8037 (p0)
REVERT: G  203 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8545 (mmtp)
REVERT: I   74 GLU cc_start: 0.8453 (pp20) cc_final: 0.8063 (pp20)
REVERT: I  123 GLU cc_start: 0.9140 (tp30) cc_final: 0.8925 (mm-30)
REVERT: J   79 ASP cc_start: 0.9251 (t0) cc_final: 0.8798 (t0)
REVERT: J  108 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8095 (tmt-80)
REVERT: J  130 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8824 (t0)
REVERT: M    5 LYS cc_start: 0.6076 (ttpp) cc_final: 0.5775 (ptmm)
REVERT: M   53 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8397 (mtt-85)
REVERT: M   68 ARG cc_start: 0.9136 (mtp85) cc_final: 0.8832 (mtp85)
REVERT: M  100 ILE cc_start: 0.8790 (mm) cc_final: 0.8538 (mt)
REVERT: N   16 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8168 (tt0)
REVERT: N   32 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8428 (tm-30)
REVERT: N   33 THR cc_start: 0.9375 (m) cc_final: 0.9026 (m)
REVERT: N   47 GLU cc_start: 0.7944 (pm20) cc_final: 0.7658 (pm20)
REVERT: N   57 ARG cc_start: 0.8471 (tmm-80) cc_final: 0.8123 (tmm-80)
REVERT: N  115 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8191 (ptmm)
REVERT: S   46 GLU cc_start: 0.8858 (pt0) cc_final: 0.8541 (pt0)
  outliers start: 37
  outliers final: 27
  residues processed: 232
  average time/residue: 1.2753
  time to fit residues: 331.1754
Evaluate side-chains
  237 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 204
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain G residue  110 THR
Chi-restraints excluded: chain G residue  117 GLN
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain G residue  146 LEU
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   66 LEU
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   89 VAL
Chi-restraints excluded: chain I residue  131 LEU
Chi-restraints excluded: chain J residue   51 THR
Chi-restraints excluded: chain J residue   86 HIS
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  108 ARG
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  130 ASN
Chi-restraints excluded: chain M residue   18 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   90 LEU
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   16 GLU
Chi-restraints excluded: chain N residue   32 GLU
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   96 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain U residue   38 SER
Chi-restraints excluded: chain U residue   39 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 109 optimal weight:    0.0040
   chunk 48 optimal weight:   20.0000
   chunk 98 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 107 optimal weight:    0.0060
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7612

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

Flipped N/Q/H residues before XYZ refinement:
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  97 GLN
** J  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  25 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.099357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.072879 restraints weight = 38800.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.62
r_work: 0.2933 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  18727  Z= 0.135
  Angle     :  0.601  10.692  27608  Z= 0.310
  Chirality :  0.035   0.240   3454
  Planarity :  0.004   0.042   1764
  Dihedral  : 23.197 173.679   8617
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.57 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 31.68 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.29), residues: 915
  helix:  1.27 (0.27), residues: 378
  sheet: -0.04 (0.39), residues: 183
  loop : -0.58 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP J  70 
 HIS   0.009   0.001   HIS N  46 
 PHE   0.010   0.001   PHE U  74 
 TYR   0.022   0.002   TYR G 202 
 ARG   0.005   0.000   ARG G  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04960 (  718)
  hydrogen bonds       : angle       3.57530 ( 1586)
  metal coordination   : bond        0.00301 (    4)
  metal coordination   : angle       2.87462 (    6)
  covalent geometry    : bond        0.00277 (18723)
  covalent geometry    : angle       0.59975 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 222
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   85 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8130 (ttpp)
REVERT: E   92 LYS cc_start: 0.8825 (ptpp) cc_final: 0.8479 (pmtt)
REVERT: G  117 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8081 (tt0)
REVERT: G  138 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8330 (tp40)
REVERT: G  180 ASP cc_start: 0.8879 (t0) cc_final: 0.8132 (p0)
REVERT: I   15 ASP cc_start: 0.8128 (t0) cc_final: 0.7531 (m-30)
REVERT: I   74 GLU cc_start: 0.8428 (pp20) cc_final: 0.8031 (pp20)
REVERT: J   51 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.9006 (t)
REVERT: J   56 GLU cc_start: 0.8427 (tp30) cc_final: 0.8202 (tp30)
REVERT: J   79 ASP cc_start: 0.9194 (t0) cc_final: 0.8814 (t0)
REVERT: M   53 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8555 (mtt-85)
REVERT: M   68 ARG cc_start: 0.9143 (mtp85) cc_final: 0.8858 (mtp85)
REVERT: N   16 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8152 (tt0)
REVERT: N   32 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8478 (tm-30)
REVERT: N   47 GLU cc_start: 0.7880 (pm20) cc_final: 0.7638 (pm20)
REVERT: N   57 ARG cc_start: 0.8518 (tmm-80) cc_final: 0.8170 (tmm-80)
REVERT: S   46 GLU cc_start: 0.8841 (pt0) cc_final: 0.8527 (pt0)
  outliers start: 34
  outliers final: 22
  residues processed: 237
  average time/residue: 1.3205
  time to fit residues: 349.2908
Evaluate side-chains
  232 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain G residue  117 GLN
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain G residue  205 ASP
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   66 LEU
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain J residue   51 THR
Chi-restraints excluded: chain J residue   86 HIS
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  132 VAL
Chi-restraints excluded: chain M residue   18 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   90 LEU
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   16 GLU
Chi-restraints excluded: chain N residue   32 GLU
Chi-restraints excluded: chain N residue   66 VAL
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   96 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain U residue   38 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 124 optimal weight:    0.4980
   chunk 76 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 85 optimal weight:    0.3980
   chunk 96 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  59 HIS
U  29 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.097531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.070729 restraints weight = 38633.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.63
r_work: 0.2877 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  18727  Z= 0.197
  Angle     :  0.643  11.352  27608  Z= 0.331
  Chirality :  0.037   0.254   3454
  Planarity :  0.005   0.081   1764
  Dihedral  : 23.174 173.181   8617
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.25 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 33.42 %
    Favored  : 62.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.29), residues: 915
  helix:  1.24 (0.27), residues: 377
  sheet: -0.19 (0.39), residues: 186
  loop : -0.59 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP J  70 
 HIS   0.007   0.001   HIS N  46 
 PHE   0.011   0.001   PHE U  74 
 TYR   0.025   0.002   TYR N  64 
 ARG   0.011   0.001   ARG G 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05104 (  718)
  hydrogen bonds       : angle       3.60051 ( 1586)
  metal coordination   : bond        0.00324 (    4)
  metal coordination   : angle       2.89297 (    6)
  covalent geometry    : bond        0.00402 (18723)
  covalent geometry    : angle       0.64178 (27602)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  117 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8117 (tt0)
REVERT: G  180 ASP cc_start: 0.8901 (t0) cc_final: 0.8142 (p0)
REVERT: I   74 GLU cc_start: 0.8426 (pp20) cc_final: 0.7974 (pp20)
REVERT: I   90 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8466 (tp30)
REVERT: J   51 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9010 (t)
REVERT: M   53 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8456 (mtt-85)
REVERT: M   68 ARG cc_start: 0.9177 (mtp85) cc_final: 0.8892 (mtp85)
REVERT: N   16 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8167 (tt0)
REVERT: N   17 VAL cc_start: 0.9538 (m) cc_final: 0.9247 (p)
REVERT: N   32 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8550 (tm-30)
REVERT: N   57 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.8164 (tmm-80)
REVERT: S   13 LYS cc_start: 0.8667 (tppt) cc_final: 0.8349 (ttpp)
REVERT: S   37 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8294 (p90)
REVERT: S   46 GLU cc_start: 0.8860 (pt0) cc_final: 0.8572 (pt0)
  outliers start: 32
  outliers final: 19
  residues processed: 218
  average time/residue: 1.2391
  time to fit residues: 302.0361
Evaluate side-chains
  222 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain G residue  117 GLN
Chi-restraints excluded: chain G residue  139 SER
Chi-restraints excluded: chain I residue   31 LEU
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain J residue   51 THR
Chi-restraints excluded: chain J residue   86 HIS
Chi-restraints excluded: chain J residue  100 GLU
Chi-restraints excluded: chain J residue  105 VAL
Chi-restraints excluded: chain J residue  125 ILE
Chi-restraints excluded: chain J residue  132 VAL
Chi-restraints excluded: chain M residue   18 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   53 ARG
Chi-restraints excluded: chain M residue   84 VAL
Chi-restraints excluded: chain M residue   90 LEU
Chi-restraints excluded: chain M residue   96 VAL
Chi-restraints excluded: chain N residue    7 VAL
Chi-restraints excluded: chain N residue   16 GLU
Chi-restraints excluded: chain N residue   32 GLU
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain N residue   96 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain S residue   37 PHE
Chi-restraints excluded: chain U residue   38 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 130 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0050
   chunk 131 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.099782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.073501 restraints weight = 38833.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.57
r_work: 0.2929 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  18727  Z= 0.137
  Angle     :  0.624  10.736  27608  Z= 0.322
  Chirality :  0.035   0.241   3454
  Planarity :  0.005   0.044   1764
  Dihedral  : 23.188 173.417   8617
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.25 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 35.16 %
    Favored  : 61.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.29), residues: 915
  helix:  1.12 (0.27), residues: 378
  sheet: -0.04 (0.39), residues: 180
  loop : -0.58 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP J  70 
 HIS   0.006   0.001   HIS M  15 
 PHE   0.010   0.001   PHE U  74 
 TYR   0.025   0.002   TYR J 170 
 ARG   0.011   0.001   ARG G 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05025 (  718)
  hydrogen bonds       : angle       3.62470 ( 1586)
  metal coordination   : bond        0.00338 (    4)
  metal coordination   : angle       2.80889 (    6)
  covalent geometry    : bond        0.00287 (18723)
  covalent geometry    : angle       0.62297 (27602)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13839.05 seconds
wall clock time: 241 minutes 56.21 seconds (14516.21 seconds total)