Starting phenix.real_space_refine
on Mon Jun 23 16:27:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c99_16506/06_2025/8c99_16506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c99_16506/06_2025/8c99_16506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c99_16506/06_2025/8c99_16506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c99_16506/06_2025/8c99_16506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c99_16506/06_2025/8c99_16506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c99_16506/06_2025/8c99_16506.cif"
  }
  resolution = 3.29
  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=   0.005 sd=   0.091
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     945      5.49       5
     S      18      5.16       5
     C   13888      2.51       5
     N    5234      2.21       5
     O    7903      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 27988
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "2"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 286
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
    Chain: "E"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1454
          Classifications: {'peptide': 189}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 184}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1055
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 125}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 676
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "S"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 734
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 93}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 509
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
    Chain: "Z"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 439
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 2, 'TRANS': 54}
    Chain: "A"
      Number of atoms: 20293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 945, 20293
          Classifications: {'DNA': 1, 'RNA': 944}
          Modifications used: {'rna2p_pur': 92, 'rna2p_pyr': 44, 'rna3p_pur': 465, 'rna3p_pyr': 343}
          Incomplete info: {'p_only': 1}
          Link IDs: {'rna2p': 136, 'rna3p': 808}
          Unresolved chain links: 1
          Chain breaks: 4
          Unresolved chain link angles: 7
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'  G:plan2': 1, '  G:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 16.37, per 1000 atoms: 0.58
  Number of scatterers: 27988
  At special positions: 0
  Unit cell: (132.5, 176.25, 168.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P     945     15.00
     O    7903      8.00
     N    5234      7.00
     C   13888      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: 7.13
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
Warning! O4 atom is missing from residue    U A 358  
  Was trying to link:    A A 282 N6 with    U A 358 O4, Saenger class: 20
Warning! O4 atom is missing from residue    U A 358  
  Was trying to link:    A A 282 N6 with    U A 358 O4, Saenger class: 23
    Secondary structure from input PDB file:
      34 helices and 11 sheets defined
      41.6% alpha, 12.4% beta
      310 base pairs and 465 stacking pairs defined.
    Time for finding SS restraints: 14.06
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 17
      removed outlier: 3.535A  pdb=" N   SER 2  15 " --> pdb=" O   LYS 2  11 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 3.976A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 39
      removed outlier: 3.516A  pdb=" N   ALA E  39 " --> pdb=" O   TYR E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
      removed outlier: 3.513A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 164
      removed outlier: 4.416A  pdb=" N   ASN E 163 " --> pdb=" O   LEU E 159 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU E 164 " --> pdb=" O   ALA E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 173 through 175
      No H-bonds generated for 'chain 'E' and resid 173 through 175'
    Processing helix  chain 'E' and resid 178 through 183
      removed outlier: 3.548A  pdb=" N   PHE E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 201
    Processing helix  chain 'J' and resid 7 through 11
      removed outlier: 3.681A  pdb=" N   VAL J  11 " --> pdb=" O   PRO J   8 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 24 through 37
    Processing helix  chain 'J' and resid 58 through 62
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 88 through 96
    Processing helix  chain 'J' and resid 96 through 108
      removed outlier: 4.151A  pdb=" N   VAL J 100 " --> pdb=" O   ARG J  96 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE J 101 " --> pdb=" O   PRO J  97 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 122
      removed outlier: 3.786A  pdb=" N   LYS J 121 " --> pdb=" O   ALA J 117 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU J 122 " --> pdb=" O   MET J 118 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 130 through 136
      removed outlier: 4.028A  pdb=" N   ALA J 134 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 135
      removed outlier: 4.419A  pdb=" N   ALA L 134 " --> pdb=" O   GLY L 130 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 5 through 19
      removed outlier: 3.919A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 25 through 30
    Processing helix  chain 'Q' and resid 30 through 71
      removed outlier: 4.351A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ARG Q  50 " --> pdb=" O   TYR Q  46 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASN Q  71 " --> pdb=" O   ALA Q  67 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 74 through 85
    Processing helix  chain 'Q' and resid 90 through 101
    Processing helix  chain 'Q' and resid 101 through 117
      removed outlier: 3.890A  pdb=" N   PHE Q 105 " --> pdb=" O   ASP Q 101 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA Q 117 " --> pdb=" O   LYS Q 113 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 13 through 22
      removed outlier: 3.512A  pdb=" N   VAL S  20 " --> pdb=" O   LYS S  16 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 4.106A  pdb=" N   ASP S  34 " --> pdb=" O   SER S  30 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 62
      removed outlier: 4.193A  pdb=" N   VAL S  45 " --> pdb=" O   LYS S  41 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 3 through 8
      removed outlier: 4.108A  pdb=" N   ARG Y   7 " --> pdb=" O   LYS Y   4 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 9 through 34
      removed outlier: 4.351A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 3.590A  pdb=" N   LYS Y  44 " --> pdb=" O   SER Y  40 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 16 through 27
    Processing helix  chain 'Z' and resid 40 through 50
    Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3
      removed outlier: 3.648A  pdb=" N   LEU E   3 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 121
      removed outlier: 3.924A  pdb=" N   VAL E 121 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU E 147 " --> pdb=" O   VAL E 187 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   THR E 189 " --> pdb=" O   LEU E 147 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   ILE E 149 " --> pdb=" O   THR E 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 123 through 124
    Processing sheet with id=AA4, first strand: chain 'R' and resid 2 through 6
    Processing sheet with id=AA5, first strand: chain 'R' and resid 20 through 22
      removed outlier: 6.556A  pdb=" N   PHE R  93 " --> pdb=" O   HIS R  66 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   HIS R  66 " --> pdb=" O   PHE R  93 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ASP R  95 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   LYS R  60 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 72 through 74
    Processing sheet with id=AA7, first strand: chain 'S' and resid 3 through 10
      removed outlier: 3.624A  pdb=" N   HIS S   9 " --> pdb=" O   SER S 101 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   SER S 101 " --> pdb=" O   HIS S   9 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS S  73 " --> pdb=" O   VAL S 106 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'U' and resid 64 through 65
      removed outlier: 6.887A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'U' and resid 40 through 44
    Processing sheet with id=AB1, first strand: chain 'U' and resid 82 through 86
    Processing sheet with id=AB2, first strand: chain 'Z' and resid 34 through 37

    317 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      790 hydrogen bonds
      1254 hydrogen bond angles
      0 basepair planarities
      310 basepair parallelities
      465 stacking parallelities
  Total time for adding SS restraints: 19.01

  Time building geometry restraints manager: 8.55 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: 4015
        1.33 -     1.45: 12679
        1.45 -     1.57: 11893
        1.57 -     1.69: 1884
        1.69 -     1.81: 36
  Bond restraints: 30507
  Sorted by residual:
  bond pdb=" C1'   U A 827 "
       pdb=" N1    U A 827 "
    ideal  model  delta    sigma   weight residual
    1.480  1.573 -0.093 1.50e-02 4.44e+03 3.87e+01
  bond pdb=" C1'   A A 526 "
       pdb=" N9    A A 526 "
    ideal  model  delta    sigma   weight residual
    1.475  1.391  0.084 1.50e-02 4.44e+03 3.14e+01
  bond pdb=" N   MET Y   1 "
       pdb=" CA  MET Y   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   MET J   1 "
       pdb=" CA  MET J   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   MET S   1 "
       pdb=" CA  MET S   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  ... (remaining 30502 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 45386
        1.40 -     2.80: 422
        2.80 -     4.20: 49
        4.20 -     5.60: 5
        5.60 -     6.99: 4
  Bond angle restraints: 45866
  Sorted by residual:
  angle pdb=" N   VAL Q  33 "
        pdb=" CA  VAL Q  33 "
        pdb=" C   VAL Q  33 "
      ideal   model   delta    sigma   weight residual
     112.96  109.37    3.59 1.00e+00 1.00e+00 1.29e+01
  angle pdb=" N   ILE L 103 "
        pdb=" CA  ILE L 103 "
        pdb=" C   ILE L 103 "
      ideal   model   delta    sigma   weight residual
     111.62  108.83    2.79 7.90e-01 1.60e+00 1.25e+01
  angle pdb=" C   SER U  97 "
        pdb=" N   ASN U  98 "
        pdb=" CA  ASN U  98 "
      ideal   model   delta    sigma   weight residual
     121.54  128.08   -6.54 1.91e+00 2.74e-01 1.17e+01
  angle pdb=" N   ILE U  38 "
        pdb=" CA  ILE U  38 "
        pdb=" C   ILE U  38 "
      ideal   model   delta    sigma   weight residual
     112.12  109.29    2.83 8.40e-01 1.42e+00 1.14e+01
  angle pdb=" C4'   A A 404 "
        pdb=" C3'   A A 404 "
        pdb=" O3'   A A 404 "
      ideal   model   delta    sigma   weight residual
     109.40  112.84   -3.44 1.50e+00 4.44e-01 5.25e+00
  ... (remaining 45861 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.09: 17159
       35.09 -    70.19: 2066
       70.19 -   105.28: 248
      105.28 -   140.38: 6
      140.38 -   175.47: 3
  Dihedral angle restraints: 19482
    sinusoidal: 16664
      harmonic: 2818
  Sorted by residual:
  dihedral pdb=" O4'   U A 545 "
           pdb=" C1'   U A 545 "
           pdb=" N1    U A 545 "
           pdb=" C2    U A 545 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   15.06 -175.06     1      1.50e+01 4.44e-03 8.52e+01
  dihedral pdb=" O4'   C A 323 "
           pdb=" C1'   C A 323 "
           pdb=" N1    C A 323 "
           pdb=" C2    C A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   36.76 -164.76     1      1.70e+01 3.46e-03 6.53e+01
  dihedral pdb=" C4'   G A 271 "
           pdb=" C3'   G A 271 "
           pdb=" O3'   G A 271 "
           pdb=" P     A A 272 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   65.47 -175.47     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 19479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 4776
       0.033 -    0.065: 962
       0.065 -    0.098: 120
       0.098 -    0.131: 63
       0.131 -    0.163: 4
  Chirality restraints: 5925
  Sorted by residual:
  chirality pdb=" C1'   U A 827 "
            pdb=" O4'   U A 827 "
            pdb=" C2'   U A 827 "
            pdb=" N1    U A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.63   -0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" C1'   A A 526 "
            pdb=" O4'   A A 526 "
            pdb=" C2'   A A 526 "
            pdb=" N9    A A 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" C3'   G A 271 "
            pdb=" C4'   G A 271 "
            pdb=" O3'   G A 271 "
            pdb=" C2'   G A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.15 2.00e-01 2.50e+01 5.56e-01
  ... (remaining 5922 not shown)

  Planarity restraints: 2271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A1138 "   -0.028 2.00e-02 2.50e+03   1.20e-02 4.35e+00
        pdb=" N9    G A1138 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    G A1138 "    0.005 2.00e-02 2.50e+03
        pdb=" N7    G A1138 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G A1138 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G A1138 "   -0.008 2.00e-02 2.50e+03
        pdb=" O6    G A1138 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G A1138 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G A1138 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G A1138 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G A1138 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G A1138 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 481 "    0.024 2.00e-02 2.50e+03   1.09e-02 3.54e+00
        pdb=" N9    G A 481 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8    G A 481 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G A 481 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G A 481 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G A 481 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G A 481 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G A 481 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G A 481 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G A 481 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G A 481 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G A 481 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 308 "   -0.023 2.00e-02 2.50e+03   1.03e-02 3.21e+00
        pdb=" N9    G A 308 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    G A 308 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G A 308 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G A 308 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G A 308 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G A 308 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G A 308 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G A 308 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G A 308 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G A 308 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G A 308 "    0.002 2.00e-02 2.50e+03
  ... (remaining 2268 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 229
        2.55 -     3.13: 21171
        3.13 -     3.72: 53007
        3.72 -     4.31: 72752
        4.31 -     4.90: 101233
  Nonbonded interactions: 248392
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP Q  48 "
            pdb=" O2'   U A 534 "
     model   vdw
     1.957 3.040
  nonbonded pdb=" OP2   G A 117 "
            pdb=" O2'   A A 119 "
     model   vdw
     1.962 3.040
  nonbonded pdb=" O2'   A A 126 "
            pdb=" O4'   A A 127 "
     model   vdw
     1.968 3.040
  nonbonded pdb=" O2'   U A 369 "
            pdb=" OP2   A A 422 "
     model   vdw
     2.002 3.040
  nonbonded pdb=" O2'   C A 957 "
            pdb=" OP1   A A 959 "
     model   vdw
     2.011 3.040
  ... (remaining 248387 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:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          1.200
  Check model and map are aligned:         0.240
  Set scattering table:                    0.260
  Process input model:                     78.250
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.080
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   85.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
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      :  0.002   0.093  30507  Z= 0.106
  Angle     :  0.392   6.995  45866  Z= 0.210
  Chirality :  0.027   0.163   5925
  Planarity :  0.003   0.039   2271
  Dihedral  : 22.330 175.471  17654
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  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:  0.97 (0.28), residues: 959
  helix:  2.46 (0.29), residues: 337
  sheet:  0.07 (0.50), residues: 120
  loop : -0.48 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP R  92 
 HIS   0.002   0.001   HIS E  29 
 PHE   0.016   0.001   PHE R  53 
 TYR   0.023   0.001   TYR Q  24 
 ARG   0.004   0.000   ARG Q  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08803 ( 1107)
  hydrogen bonds       : angle       3.87751 ( 2151)
  covalent geometry    : bond        0.00190 (30507)
  covalent geometry    : angle       0.39221 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
REVERT: J   16 TYR cc_start: 0.8401 (m-80) cc_final: 0.8156 (m-10)
REVERT: J  138 GLN cc_start: 0.7310 (tt0) cc_final: 0.7022 (tt0)
REVERT: L  126 ARG cc_start: 0.4765 (mtm180) cc_final: 0.3627 (tpt-90)
REVERT: Q   96 ASP cc_start: 0.7714 (t70) cc_final: 0.7457 (t70)
REVERT: Z   44 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7705 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.4372
  time to fit residues: 76.3127
Evaluate side-chains
  74 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 158 optimal weight:   10.0000
   chunk 142 optimal weight:    7.9990
   chunk 79 optimal weight:    0.0170
   chunk 48 optimal weight:    4.9990
   chunk 96 optimal weight:    8.9990
   chunk 76 optimal weight:    0.0470
   chunk 147 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 109 optimal weight:   40.0000
   chunk 170 optimal weight:   10.0000
   overall best weight:    2.6122

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

Flipped N/Q/H residues before XYZ refinement:
Q  80 ASN
R  18 GLN
S  57 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  31 GLN
Z  19 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.078641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.054639 restraints weight = 124777.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.71
r_work: 0.3116 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  30507  Z= 0.174
  Angle     :  0.531   9.261  45866  Z= 0.271
  Chirality :  0.030   0.180   5925
  Planarity :  0.004   0.042   2271
  Dihedral  : 22.862 177.620  15736
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  6.38 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.28), residues: 959
  helix:  1.57 (0.28), residues: 355
  sheet: -0.19 (0.46), residues: 145
  loop : -0.68 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R  92 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.014   0.002   PHE Q 105 
 TYR   0.014   0.001   TYR J  74 
 ARG   0.006   0.001   ARG Q   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06313 ( 1107)
  hydrogen bonds       : angle       3.21258 ( 2151)
  covalent geometry    : bond        0.00337 (30507)
  covalent geometry    : angle       0.53077 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 1.622 
Fit side-chains
   revert: symmetry clash
REVERT: J    1 MET cc_start: 0.7525 (ppp) cc_final: 0.7124 (tpp)
REVERT: J   16 TYR cc_start: 0.8333 (m-80) cc_final: 0.7906 (m-80)
REVERT: J  138 GLN cc_start: 0.7655 (tt0) cc_final: 0.7136 (tt0)
REVERT: J  142 ILE cc_start: 0.5483 (mt) cc_final: 0.5160 (mm)
REVERT: Q   96 ASP cc_start: 0.8077 (t70) cc_final: 0.7830 (t70)
REVERT: S   31 GLN cc_start: 0.8394 (mt0) cc_final: 0.8143 (mm-40)
REVERT: U  100 GLU cc_start: 0.8257 (tp30) cc_final: 0.7760 (tt0)
REVERT: Y    2 LYS cc_start: 0.7768 (mttm) cc_final: 0.6689 (mttp)
REVERT: Y   23 ARG cc_start: 0.8316 (mmt90) cc_final: 0.7860 (mmt-90)
REVERT: Y   26 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8257 (t80)
REVERT: Z   44 ARG cc_start: 0.7755 (mmp80) cc_final: 0.7372 (mmp80)
  outliers start: 8
  outliers final: 4
  residues processed: 87
  average time/residue: 0.4292
  time to fit residues: 61.6014
Evaluate side-chains
  78 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain Y residue   26 PHE
Chi-restraints excluded: chain Z residue    9 THR
Chi-restraints excluded: chain Z residue   34 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 132 optimal weight:   40.0000
   chunk 171 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 117 optimal weight:   20.0000
   chunk 112 optimal weight:   20.0000
   chunk 143 optimal weight:    7.9990
   chunk 129 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   overall best weight:    5.5992

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

Flipped N/Q/H residues before XYZ refinement:
J 132 HIS
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  18 GLN
** U  53 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 = 0.3788 r_free = 0.3788 target = 0.075756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.051478 restraints weight = 124817.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.91
r_work: 0.3018 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  30507  Z= 0.351
  Angle     :  0.683   9.799  45866  Z= 0.344
  Chirality :  0.038   0.223   5925
  Planarity :  0.005   0.046   2271
  Dihedral  : 23.081 177.664  15736
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.26 %
    Favored  : 87.61 %
  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: -0.39 (0.26), residues: 959
  helix:  0.94 (0.27), residues: 350
  sheet: -0.55 (0.45), residues: 141
  loop : -1.08 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R  92 
 HIS   0.005   0.001   HIS J 132 
 PHE   0.019   0.002   PHE E  23 
 TYR   0.018   0.002   TYR J  74 
 ARG   0.007   0.001   ARG 2  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07736 ( 1107)
  hydrogen bonds       : angle       3.49049 ( 2151)
  covalent geometry    : bond        0.00687 (30507)
  covalent geometry    : angle       0.68281 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 2.030 
Fit side-chains
   revert: symmetry clash
REVERT: J  138 GLN cc_start: 0.7583 (tt0) cc_final: 0.7199 (tt0)
REVERT: J  142 ILE cc_start: 0.6207 (mt) cc_final: 0.5858 (mm)
REVERT: S   31 GLN cc_start: 0.8400 (mt0) cc_final: 0.8178 (mm-40)
REVERT: U  100 GLU cc_start: 0.8525 (tp30) cc_final: 0.8097 (tt0)
REVERT: Y    2 LYS cc_start: 0.7688 (mttm) cc_final: 0.6611 (mttp)
REVERT: Y   13 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7495 (mm-30)
REVERT: Y   26 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (t80)
REVERT: Z   44 ARG cc_start: 0.7912 (mmp80) cc_final: 0.7657 (mmp80)
  outliers start: 17
  outliers final: 8
  residues processed: 96
  average time/residue: 0.4691
  time to fit residues: 77.4080
Evaluate side-chains
  82 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 1.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain Y residue   26 PHE
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 14 optimal weight:    0.2980
   chunk 112 optimal weight:   20.0000
   chunk 136 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 185 optimal weight:    6.9990
   chunk 122 optimal weight:    6.9990
   chunk 142 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 128 optimal weight:   20.0000
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
E  97 ASN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 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 = 0.3836 r_free = 0.3836 target = 0.078096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.053724 restraints weight = 130552.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.80
r_work: 0.3082 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  30507  Z= 0.146
  Angle     :  0.501  10.140  45866  Z= 0.258
  Chirality :  0.030   0.223   5925
  Planarity :  0.004   0.040   2271
  Dihedral  : 23.016 176.284  15736
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 12.64 %
    Favored  : 85.98 %
  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: -0.12 (0.27), residues: 959
  helix:  1.23 (0.28), residues: 359
  sheet: -0.34 (0.44), residues: 142
  loop : -1.05 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  92 
 HIS   0.003   0.001   HIS S  60 
 PHE   0.011   0.001   PHE 2  18 
 TYR   0.011   0.001   TYR J  74 
 ARG   0.002   0.000   ARG Q  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05732 ( 1107)
  hydrogen bonds       : angle       3.12152 ( 2151)
  covalent geometry    : bond        0.00284 (30507)
  covalent geometry    : angle       0.50051 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 1.916 
Fit side-chains
REVERT: E  188 MET cc_start: 0.8803 (ttm) cc_final: 0.8502 (ttp)
REVERT: J  138 GLN cc_start: 0.7739 (tt0) cc_final: 0.7347 (tt0)
REVERT: J  142 ILE cc_start: 0.5927 (mt) cc_final: 0.5606 (mm)
REVERT: Y    2 LYS cc_start: 0.7705 (mttm) cc_final: 0.6646 (mttp)
REVERT: Y   23 ARG cc_start: 0.8355 (mmt90) cc_final: 0.8138 (mmt-90)
REVERT: Y   31 GLN cc_start: 0.8624 (mp10) cc_final: 0.8349 (mt0)
REVERT: Z   44 ARG cc_start: 0.7906 (mmp80) cc_final: 0.7501 (mmp80)
  outliers start: 11
  outliers final: 7
  residues processed: 92
  average time/residue: 0.4014
  time to fit residues: 60.5608
Evaluate side-chains
  84 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 100 optimal weight:   10.0000
   chunk 187 optimal weight:   10.0000
   chunk 92 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 177 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 136 optimal weight:    8.9990
   chunk 167 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.076671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.052022 restraints weight = 130622.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 1.90
r_work: 0.3029 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  30507  Z= 0.267
  Angle     :  0.591   9.848  45866  Z= 0.301
  Chirality :  0.034   0.224   5925
  Planarity :  0.004   0.041   2271
  Dihedral  : 23.061 179.549  15736
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.77 %
    Favored  : 84.86 %
  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 (0.27), residues: 959
  helix:  1.18 (0.28), residues: 349
  sheet: -0.71 (0.45), residues: 136
  loop : -1.09 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  92 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.013   0.002   PHE E  23 
 TYR   0.011   0.002   TYR J  74 
 ARG   0.005   0.001   ARG 2  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06742 ( 1107)
  hydrogen bonds       : angle       3.28111 ( 2151)
  covalent geometry    : bond        0.00523 (30507)
  covalent geometry    : angle       0.59117 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
REVERT: E  105 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7815 (mp)
REVERT: J   90 GLU cc_start: 0.7721 (mp0) cc_final: 0.7259 (mp0)
REVERT: J  138 GLN cc_start: 0.7779 (tt0) cc_final: 0.7370 (tt0)
REVERT: J  142 ILE cc_start: 0.6071 (mt) cc_final: 0.5650 (mm)
REVERT: U  100 GLU cc_start: 0.8281 (tp30) cc_final: 0.7956 (tt0)
REVERT: Y    2 LYS cc_start: 0.7675 (mttm) cc_final: 0.6585 (mttp)
  outliers start: 19
  outliers final: 13
  residues processed: 95
  average time/residue: 0.3821
  time to fit residues: 59.2005
Evaluate side-chains
  88 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  105 LEU
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 164 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9980
   chunk 158 optimal weight:   10.0000
   chunk 138 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 171 optimal weight:   10.0000
   chunk 37 optimal weight:   20.0000
   chunk 98 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.076345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.051871 restraints weight = 129967.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.85
r_work: 0.3022 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  30507  Z= 0.273
  Angle     :  0.601  10.010  45866  Z= 0.306
  Chirality :  0.035   0.241   5925
  Planarity :  0.004   0.040   2271
  Dihedral  : 23.152 179.797  15736
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.89 %
    Favored  : 83.73 %
  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: -0.56 (0.27), residues: 959
  helix:  0.95 (0.28), residues: 355
  sheet: -0.66 (0.43), residues: 143
  loop : -1.33 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R  92 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.015   0.002   PHE Q  56 
 TYR   0.016   0.002   TYR J  74 
 ARG   0.004   0.001   ARG 2  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06993 ( 1107)
  hydrogen bonds       : angle       3.32162 ( 2151)
  covalent geometry    : bond        0.00537 (30507)
  covalent geometry    : angle       0.60112 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 1.475 
Fit side-chains
   revert: symmetry clash
REVERT: E  188 MET cc_start: 0.8908 (ttm) cc_final: 0.8622 (mtp)
REVERT: J   90 GLU cc_start: 0.7374 (mp0) cc_final: 0.7161 (mp0)
REVERT: J  138 GLN cc_start: 0.7680 (tt0) cc_final: 0.7267 (tt0)
REVERT: J  142 ILE cc_start: 0.5964 (mt) cc_final: 0.5661 (mm)
REVERT: U  100 GLU cc_start: 0.8347 (tp30) cc_final: 0.8143 (tt0)
REVERT: Y    2 LYS cc_start: 0.7701 (mttm) cc_final: 0.6627 (mttp)
REVERT: Y   23 ARG cc_start: 0.8456 (mmt90) cc_final: 0.8173 (mmt-90)
  outliers start: 19
  outliers final: 13
  residues processed: 94
  average time/residue: 0.3799
  time to fit residues: 58.5090
Evaluate side-chains
  84 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 157 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 155 optimal weight:   50.0000
   chunk 118 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 181 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 170 optimal weight:   10.0000
   chunk 176 optimal weight:   10.0000
   chunk 121 optimal weight:   20.0000
   chunk 17 optimal weight:    3.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.076024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.051631 restraints weight = 129510.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.85
r_work: 0.3014 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  30507  Z= 0.298
  Angle     :  0.623  10.044  45866  Z= 0.316
  Chirality :  0.035   0.240   5925
  Planarity :  0.004   0.039   2271
  Dihedral  : 23.195 178.798  15736
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.77 %
    Favored  : 82.73 %
  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: -0.68 (0.27), residues: 959
  helix:  0.89 (0.28), residues: 355
  sheet: -0.85 (0.43), residues: 148
  loop : -1.39 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R  92 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.031   0.002   PHE R  53 
 TYR   0.013   0.002   TYR J  74 
 ARG   0.005   0.001   ARG R  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07235 ( 1107)
  hydrogen bonds       : angle       3.37353 ( 2151)
  covalent geometry    : bond        0.00587 (30507)
  covalent geometry    : angle       0.62263 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 1.844 
Fit side-chains
   revert: symmetry clash
REVERT: J  138 GLN cc_start: 0.7694 (tt0) cc_final: 0.7252 (tt0)
REVERT: J  142 ILE cc_start: 0.6014 (mt) cc_final: 0.5769 (mm)
REVERT: Y    2 LYS cc_start: 0.7722 (mttm) cc_final: 0.6606 (mttp)
  outliers start: 20
  outliers final: 15
  residues processed: 92
  average time/residue: 0.4478
  time to fit residues: 68.8750
Evaluate side-chains
  87 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 1.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 183 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 94 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 116 optimal weight:   10.0000
   chunk 138 optimal weight:    6.9990
   chunk 170 optimal weight:   10.0000
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.077452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.053215 restraints weight = 129471.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.78
r_work: 0.3067 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  30507  Z= 0.164
  Angle     :  0.523  11.626  45866  Z= 0.268
  Chirality :  0.031   0.239   5925
  Planarity :  0.004   0.035   2271
  Dihedral  : 23.154 176.657  15736
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.52 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.47 (0.27), residues: 959
  helix:  1.24 (0.28), residues: 356
  sheet: -1.13 (0.43), residues: 139
  loop : -1.29 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  92 
 HIS   0.003   0.001   HIS S  60 
 PHE   0.012   0.001   PHE R  77 
 TYR   0.010   0.001   TYR E 101 
 ARG   0.003   0.000   ARG Z  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05991 ( 1107)
  hydrogen bonds       : angle       3.15578 ( 2151)
  covalent geometry    : bond        0.00322 (30507)
  covalent geometry    : angle       0.52298 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 1.521 
Fit side-chains
   revert: symmetry clash
REVERT: J   90 GLU cc_start: 0.7377 (mp0) cc_final: 0.7119 (mp0)
REVERT: J  138 GLN cc_start: 0.7827 (tt0) cc_final: 0.7417 (tt0)
REVERT: J  142 ILE cc_start: 0.5994 (mt) cc_final: 0.5700 (mm)
REVERT: Q   96 ASP cc_start: 0.8264 (t70) cc_final: 0.7955 (t0)
REVERT: R   48 LYS cc_start: 0.7582 (tptp) cc_final: 0.7158 (tptp)
REVERT: Y    2 LYS cc_start: 0.7668 (mttm) cc_final: 0.6591 (mttp)
  outliers start: 16
  outliers final: 13
  residues processed: 95
  average time/residue: 0.3843
  time to fit residues: 59.6637
Evaluate side-chains
  90 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 131 optimal weight:   30.0000
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 115 optimal weight:   20.0000
   chunk 40 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 90 optimal weight:    1.9990
   chunk 124 optimal weight:   10.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.077318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.053244 restraints weight = 128411.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.75
r_work: 0.3069 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  30507  Z= 0.165
  Angle     :  0.520  12.614  45866  Z= 0.266
  Chirality :  0.031   0.231   5925
  Planarity :  0.004   0.034   2271
  Dihedral  : 23.134 176.841  15736
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.65 %
    Favored  : 81.85 %
  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: -0.41 (0.27), residues: 959
  helix:  1.29 (0.28), residues: 356
  sheet: -1.06 (0.43), residues: 139
  loop : -1.27 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  92 
 HIS   0.003   0.001   HIS E  29 
 PHE   0.012   0.001   PHE R  77 
 TYR   0.025   0.002   TYR R  83 
 ARG   0.003   0.000   ARG 2  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06025 ( 1107)
  hydrogen bonds       : angle       3.15487 ( 2151)
  covalent geometry    : bond        0.00324 (30507)
  covalent geometry    : angle       0.52001 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 1.644 
Fit side-chains
   revert: symmetry clash
REVERT: J  138 GLN cc_start: 0.7830 (tt0) cc_final: 0.7403 (tt0)
REVERT: J  142 ILE cc_start: 0.5938 (mt) cc_final: 0.5637 (mm)
REVERT: Q   96 ASP cc_start: 0.8259 (t70) cc_final: 0.7951 (t0)
REVERT: R   48 LYS cc_start: 0.7525 (tptp) cc_final: 0.7126 (tptp)
REVERT: Y    2 LYS cc_start: 0.7692 (mttm) cc_final: 0.6607 (mttp)
  outliers start: 12
  outliers final: 11
  residues processed: 88
  average time/residue: 0.3934
  time to fit residues: 57.4823
Evaluate side-chains
  88 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0470
   chunk 115 optimal weight:   20.0000
   chunk 120 optimal weight:   30.0000
   chunk 36 optimal weight:    9.9990
   chunk 130 optimal weight:   30.0000
   chunk 170 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 161 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    2.4082

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.077343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.053310 restraints weight = 128212.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.74
r_work: 0.3070 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  30507  Z= 0.166
  Angle     :  0.521  11.766  45866  Z= 0.267
  Chirality :  0.031   0.231   5925
  Planarity :  0.004   0.034   2271
  Dihedral  : 23.132 176.632  15736
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.52 %
    Favored  : 81.73 %
  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: -0.39 (0.27), residues: 959
  helix:  1.31 (0.28), residues: 356
  sheet: -1.00 (0.44), residues: 137
  loop : -1.28 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R  92 
 HIS   0.003   0.001   HIS E  29 
 PHE   0.012   0.001   PHE R  77 
 TYR   0.015   0.001   TYR R  83 
 ARG   0.005   0.000   ARG Z  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06009 ( 1107)
  hydrogen bonds       : angle       3.14465 ( 2151)
  covalent geometry    : bond        0.00324 (30507)
  covalent geometry    : angle       0.52140 (45866)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 1.465 
Fit side-chains
   revert: symmetry clash
REVERT: J  138 GLN cc_start: 0.7814 (tt0) cc_final: 0.7404 (tt0)
REVERT: J  142 ILE cc_start: 0.5870 (mt) cc_final: 0.5596 (mm)
REVERT: Q   96 ASP cc_start: 0.8276 (t70) cc_final: 0.7966 (t0)
REVERT: R   32 THR cc_start: 0.9118 (m) cc_final: 0.8680 (t)
  outliers start: 14
  outliers final: 13
  residues processed: 89
  average time/residue: 0.3724
  time to fit residues: 55.4630
Evaluate side-chains
  88 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 1.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 112 optimal weight:   20.0000
   chunk 67 optimal weight:    3.9990
   chunk 149 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 168 optimal weight:   20.0000
   chunk 45 optimal weight:    0.0670
   chunk 25 optimal weight:    7.9990
   chunk 146 optimal weight:   10.0000
   chunk 115 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   overall best weight:    5.0126

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

Flipped N/Q/H residues before XYZ refinement:
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.075571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.051501 restraints weight = 124177.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.83
r_work: 0.3020 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  30507  Z= 0.311
  Angle     :  0.636  11.717  45866  Z= 0.321
  Chirality :  0.036   0.237   5925
  Planarity :  0.004   0.037   2271
  Dihedral  : 23.208 178.480  15736
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.77 %
    Favored  : 81.10 %
  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: -0.66 (0.27), residues: 959
  helix:  0.98 (0.28), residues: 355
  sheet: -1.16 (0.44), residues: 140
  loop : -1.33 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  92 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.022   0.002   PHE Q  56 
 TYR   0.014   0.002   TYR J  74 
 ARG   0.008   0.001   ARG Z  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07332 ( 1107)
  hydrogen bonds       : angle       3.36966 ( 2151)
  covalent geometry    : bond        0.00612 (30507)
  covalent geometry    : angle       0.63578 (45866)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14706.18 seconds
wall clock time: 255 minutes 44.11 seconds (15344.11 seconds total)