Starting phenix.real_space_refine
on Mon Jul 28 15:03:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ube_42084/07_2025/8ube_42084.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ube_42084/07_2025/8ube_42084.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ube_42084/07_2025/8ube_42084.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ube_42084/07_2025/8ube_42084.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ube_42084/07_2025/8ube_42084.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ube_42084/07_2025/8ube_42084.cif"
  }
  resolution = 3.05
  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=   0.030
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     167      5.49       5
     S      36      5.16       5
     C    6142      2.51       5
     N    1900      2.21       5
     O    2368      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10613
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2562
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 976
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "C"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "D"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 879
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "E"
      Number of atoms: 876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 876
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "F"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 879
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "G"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 243
          Classifications: {'RNA': 11}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 10}
    Chain: "H"
      Number of atoms: 350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 350
          Classifications: {'RNA': 17}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 4, 'rna3p': 12}
    Chain: "I"
      Number of atoms: 2960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2960
          Classifications: {'RNA': 139}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 17, 'rna3p_pur': 57, 'rna3p_pyr': 53}
          Link IDs: {'rna2p': 29, 'rna3p': 109}
  Time building chain proxies: 7.55, per 1000 atoms: 0.71
  Number of scatterers: 10613
  At special positions: 0
  Unit cell: (86, 105, 130, 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      36     16.00
     P     167     15.00
     O    2368      8.00
     N    1900      7.00
     C    6142      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: 2.54
  Conformation dependent library (CDL) restraints added in 949.3 milliseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      76.8% alpha, 1.5% beta
      34 base pairs and 87 stacking pairs defined.
    Time for finding SS restraints: 4.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 13
    Processing helix  chain 'A' and resid 14 through 27
    Processing helix  chain 'A' and resid 32 through 40
      removed outlier: 3.873A  pdb=" N   GLU A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.576A  pdb=" N   LEU A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 94 through 99
    Processing helix  chain 'A' and resid 114 through 126
    Processing helix  chain 'A' and resid 141 through 146
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.606A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 183 through 191
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 203 through 207
      removed outlier: 3.598A  pdb=" N   LYS A 206 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLN A 207 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 203 through 207'
    Processing helix  chain 'A' and resid 223 through 241
    Processing helix  chain 'A' and resid 275 through 289
    Processing helix  chain 'A' and resid 294 through 307
      removed outlier: 3.906A  pdb=" N   ARG A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 324
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 38 through 50
    Processing helix  chain 'B' and resid 51 through 62
    Processing helix  chain 'B' and resid 64 through 87
      removed outlier: 3.965A  pdb=" N   LEU B  68 " --> pdb=" O   GLN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 122
    Processing helix  chain 'C' and resid 12 through 34
      removed outlier: 3.733A  pdb=" N   ARG C  22 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      Proline residue:  C  29  - end of helix
    Processing helix  chain 'C' and resid 38 through 63
      removed outlier: 3.834A  pdb=" N   VAL C  53 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLU C  54 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 88
      removed outlier: 3.932A  pdb=" N   ALA C  86 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY C  87 " --> pdb=" O   ARG C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 121
    Processing helix  chain 'D' and resid 14 through 34
      removed outlier: 3.790A  pdb=" N   ARG D  22 " --> pdb=" O   GLU D  18 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL D  23 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      Proline residue:  D  29  - end of helix
    Processing helix  chain 'D' and resid 38 through 62
      removed outlier: 3.767A  pdb=" N   VAL D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLU D  54 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 86
      removed outlier: 3.755A  pdb=" N   LEU D  68 " --> pdb=" O   GLN D  64 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA D  70 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA D  71 " --> pdb=" O   LYS D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 121
    Processing helix  chain 'E' and resid 13 through 34
      removed outlier: 3.726A  pdb=" N   ARG E  22 " --> pdb=" O   GLU E  18 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      Proline residue:  E  29  - end of helix
    Processing helix  chain 'E' and resid 35 through 37
      No H-bonds generated for 'chain 'E' and resid 35 through 37'
    Processing helix  chain 'E' and resid 38 through 50
    Processing helix  chain 'E' and resid 51 through 61
    Processing helix  chain 'E' and resid 65 through 86
    Processing helix  chain 'E' and resid 95 through 121
    Processing helix  chain 'F' and resid 14 through 34
      removed outlier: 4.548A  pdb=" N   ARG F  22 " --> pdb=" O   GLU F  18 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL F  23 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      Proline residue:  F  29  - end of helix
    Processing helix  chain 'F' and resid 35 through 37
      No H-bonds generated for 'chain 'F' and resid 35 through 37'
    Processing helix  chain 'F' and resid 38 through 61
      removed outlier: 3.915A  pdb=" N   VAL F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLU F  54 " --> pdb=" O   LEU F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 64 through 87
    Processing helix  chain 'F' and resid 88 through 93
      Proline residue:  F  91  - end of helix
      No H-bonds generated for 'chain 'F' and resid 88 through 93'
    Processing helix  chain 'F' and resid 95 through 122
      removed outlier: 4.410A  pdb=" N   LEU F 105 " --> pdb=" O   THR F 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212
    Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 260

    480 hydrogen bonds defined for protein.
    1425 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      87 hydrogen bonds
      134 hydrogen bond angles
      0 basepair planarities
      34 basepair parallelities
      87 stacking parallelities
  Total time for adding SS restraints: 3.44

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1268
        1.30 -     1.43: 3903
        1.43 -     1.56: 5618
        1.56 -     1.70: 334
        1.70 -     1.83: 61
  Bond restraints: 11184
  Sorted by residual:
  bond pdb=" C   PRO E  35 "
       pdb=" O   PRO E  35 "
    ideal  model  delta    sigma   weight residual
    1.233  1.167  0.066 1.19e-02 7.06e+03 3.06e+01
  bond pdb=" CA  ARG B  36 "
       pdb=" CB  ARG B  36 "
    ideal  model  delta    sigma   weight residual
    1.530  1.603 -0.073 1.57e-02 4.06e+03 2.18e+01
  bond pdb=" CG  HIS E  38 "
       pdb=" CD2 HIS E  38 "
    ideal  model  delta    sigma   weight residual
    1.354  1.305  0.049 1.10e-02 8.26e+03 2.00e+01
  bond pdb=" CA  SER A 186 "
       pdb=" CB  SER A 186 "
    ideal  model  delta    sigma   weight residual
    1.530  1.457  0.073 1.69e-02 3.50e+03 1.85e+01
  bond pdb=" CG  LYS A 278 "
       pdb=" CD  LYS A 278 "
    ideal  model  delta    sigma   weight residual
    1.520  1.401  0.119 3.00e-02 1.11e+03 1.58e+01
  ... (remaining 11179 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.11: 14908
        3.11 -     6.21: 882
        6.21 -     9.32: 115
        9.32 -    12.42: 12
       12.42 -    15.53: 6
  Bond angle restraints: 15923
  Sorted by residual:
  angle pdb=" C3'   C I  28 "
        pdb=" O3'   C I  28 "
        pdb=" P     G I  29 "
      ideal   model   delta    sigma   weight residual
     120.20  104.67   15.53 1.50e+00 4.44e-01 1.07e+02
  angle pdb=" C3'   U I 106 "
        pdb=" O3'   U I 106 "
        pdb=" P     C I 107 "
      ideal   model   delta    sigma   weight residual
     120.20  105.15   15.05 1.50e+00 4.44e-01 1.01e+02
  angle pdb=" C3'   C I 107 "
        pdb=" O3'   C I 107 "
        pdb=" P     G I 108 "
      ideal   model   delta    sigma   weight residual
     120.20  106.00   14.20 1.50e+00 4.44e-01 8.96e+01
  angle pdb=" C3'   G I  26 "
        pdb=" O3'   G I  26 "
        pdb=" P     G I  27 "
      ideal   model   delta    sigma   weight residual
     120.20  106.94   13.26 1.50e+00 4.44e-01 7.82e+01
  angle pdb=" C3'   C I  78 "
        pdb=" O3'   C I  78 "
        pdb=" P     G I  79 "
      ideal   model   delta    sigma   weight residual
     120.20  107.01   13.19 1.50e+00 4.44e-01 7.73e+01
  ... (remaining 15918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.75: 6003
       35.75 -    71.50: 855
       71.50 -   107.25: 100
      107.25 -   143.00: 4
      143.00 -   178.75: 5
  Dihedral angle restraints: 6967
    sinusoidal: 4421
      harmonic: 2546
  Sorted by residual:
  dihedral pdb=" O4'   C I  82 "
           pdb=" C1'   C I  82 "
           pdb=" N1    C I  82 "
           pdb=" C2    C I  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.25  178.75     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U I  94 "
           pdb=" C1'   U I  94 "
           pdb=" N1    U I  94 "
           pdb=" C2    U I  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   54.32  177.68     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C I  59 "
           pdb=" C1'   C I  59 "
           pdb=" N1    C I  59 "
           pdb=" C2    C I  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   58.83  173.17     1      1.70e+01 3.46e-03 6.62e+01
  ... (remaining 6964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1392
       0.111 -    0.223: 434
       0.223 -    0.334: 39
       0.334 -    0.445: 33
       0.445 -    0.557: 10
  Chirality restraints: 1908
  Sorted by residual:
  chirality pdb=" P     G G 371 "
            pdb=" OP1   G G 371 "
            pdb=" OP2   G G 371 "
            pdb=" O5'   G G 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.97   -0.56 2.00e-01 2.50e+01 7.75e+00
  chirality pdb=" P     G G 372 "
            pdb=" OP1   G G 372 "
            pdb=" OP2   G G 372 "
            pdb=" O5'   G G 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.94   -0.53 2.00e-01 2.50e+01 7.11e+00
  chirality pdb=" P     U H 118 "
            pdb=" OP1   U H 118 "
            pdb=" OP2   U H 118 "
            pdb=" O5'   U H 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.94   -0.53 2.00e-01 2.50e+01 6.96e+00
  ... (remaining 1905 not shown)

  Planarity restraints: 1395
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  28 "    0.089 2.00e-02 2.50e+03   4.58e-02 4.20e+01
        pdb=" CG  TYR C  28 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  28 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  28 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  28 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  28 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  28 "    0.027 2.00e-02 2.50e+03
        pdb=" OH  TYR C  28 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  28 "   -0.062 2.00e-02 2.50e+03   3.54e-02 2.50e+01
        pdb=" CG  TYR D  28 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  28 "    0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  28 "    0.059 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  28 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  28 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR D  28 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 163 "    0.024 2.00e-02 2.50e+03   4.84e-02 2.34e+01
        pdb=" C   ALA A 163 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   ALA A 163 "    0.032 2.00e-02 2.50e+03
        pdb=" N   THR A 164 "    0.028 2.00e-02 2.50e+03
  ... (remaining 1392 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.26: 2
        2.26 -     2.92: 5253
        2.92 -     3.58: 18827
        3.58 -     4.24: 33867
        4.24 -     4.90: 48219
  Nonbonded interactions: 106168
  Sorted by model distance:
  nonbonded pdb=" O3'   G H 134 "
            pdb=" P     C I   1 "
     model   vdw
     1.606 3.400
  nonbonded pdb=" NE2 GLN E  98 "
            pdb=" O3'   C I  17 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NZ  LYS D  47 "
            pdb=" OE2 GLU E  43 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   ILE B  34 "
            pdb=" O   PRO B  35 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   SER A 140 "
            pdb=" N   PHE A 142 "
     model   vdw
     2.305 3.120
  ... (remaining 106163 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 13 through 121)
  selection = (chain 'C' and resid 13 through 121)
  selection = (chain 'D' and resid 13 through 121)
  selection = (chain 'E' and resid 13 through 121)
  selection = (chain 'F' and resid 13 through 121)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.270
  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:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     29.960
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6229
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      :  0.012   0.119  11184  Z= 0.701
  Angle     :  1.654  15.531  15923  Z= 1.022
  Chirality :  0.116   0.557   1908
  Planarity :  0.011   0.091   1395
  Dihedral  : 26.943 178.748   5325
  Min Nonbonded Distance : 1.606

Molprobity Statistics.
  All-atom Clashscore : 51.54
  Ramachandran Plot:
    Outliers :  3.94 %
    Allowed  : 11.48 %
    Favored  : 84.57 %
  Rotamer:
    Outliers : 23.26 %
    Allowed  : 12.31 %
    Favored  : 64.43 %
  Cbeta Deviations :  0.12 %
  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: -4.56 (0.22), residues: 862
  helix: -2.25 (0.16), residues: 619
  sheet: -5.97 (0.64), residues: 10
  loop : -4.67 (0.29), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.009   TRP C 116 
 HIS   0.016   0.004   HIS A 248 
 PHE   0.050   0.010   PHE C  84 
 TYR   0.089   0.011   TYR C  28 
 ARG   0.029   0.003   ARG A   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23218 (  567)
  hydrogen bonds       : angle      10.41068 ( 1559)
  covalent geometry    : bond        0.01209 (11184)
  covalent geometry    : angle       1.65392 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  463 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 170
    poor density    : 293
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4776 (mmt) cc_final: 0.4575 (mpp)
REVERT: A   16 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8158 (mp0)
REVERT: A   22 TYR cc_start: 0.7939 (t80) cc_final: 0.7714 (t80)
REVERT: A   27 HIS cc_start: 0.7733 (t70) cc_final: 0.7475 (t70)
REVERT: A   39 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5271 (ttpt)
REVERT: A   58 TYR cc_start: 0.7603 (t80) cc_final: 0.7300 (t80)
REVERT: A   59 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8201 (tm-30)
REVERT: A   84 ARG cc_start: 0.6745 (mtm110) cc_final: 0.6534 (mtm110)
REVERT: A  107 TYR cc_start: 0.8281 (m-80) cc_final: 0.7937 (m-80)
REVERT: A  116 HIS cc_start: 0.8549 (m-70) cc_final: 0.8235 (t70)
REVERT: A  127 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6982 (mtp180)
REVERT: A  156 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7244 (m-30)
REVERT: A  165 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6194 (mtp180)
REVERT: A  220 LEU cc_start: 0.7642 (mt) cc_final: 0.7308 (mt)
REVERT: A  263 TYR cc_start: 0.6669 (m-80) cc_final: 0.6422 (m-10)
REVERT: A  270 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7239 (pttp)
REVERT: B    1 MET cc_start: 0.5546 (tmm) cc_final: 0.5132 (ttp)
REVERT: B   54 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6788 (tt0)
REVERT: B   65 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7745 (p)
REVERT: B   94 MET cc_start: 0.8043 (mtp) cc_final: 0.7762 (mtm)
REVERT: B  108 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6859 (tp30)
REVERT: B  116 TRP cc_start: 0.8115 (t60) cc_final: 0.7391 (t60)
REVERT: C   21 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6722 (tt0)
REVERT: C   44 MET cc_start: 0.6906 (mtp) cc_final: 0.6472 (mtp)
REVERT: C   91 PRO cc_start: 0.7729 (OUTLIER) cc_final: 0.7521 (Cg_endo)
REVERT: C   94 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8155 (ttm)
REVERT: D   18 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5775 (tp30)
REVERT: D   62 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.6983 (p)
REVERT: D   64 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6932 (pm20)
REVERT: D   77 MET cc_start: 0.8234 (tpt) cc_final: 0.7915 (tpp)
REVERT: D   89 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6633 (tp40)
REVERT: D  100 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6429 (mm-30)
REVERT: D  103 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.6047 (mt0)
REVERT: D  111 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6753 (mtt180)
REVERT: E   14 MET cc_start: 0.5087 (mmt) cc_final: 0.4433 (mpp)
REVERT: E   22 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7253 (mtp85)
REVERT: E   54 GLU cc_start: 0.7532 (tt0) cc_final: 0.7017 (tt0)
REVERT: E   83 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7047 (ttp-110)
REVERT: F   14 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.3848 (ttt)
REVERT: F   21 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: F   26 TYR cc_start: 0.6499 (t80) cc_final: 0.6146 (t80)
REVERT: F   54 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6371 (tp30)
REVERT: F   77 MET cc_start: 0.7206 (tpt) cc_final: 0.6445 (tpt)
REVERT: F   88 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7337 (tt)
REVERT: F   94 MET cc_start: 0.7789 (ttm) cc_final: 0.7586 (ttp)
  outliers start: 170
  outliers final: 48
  residues processed: 385
  average time/residue: 0.3224
  time to fit residues: 158.0859
Evaluate side-chains
  296 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 227
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue   16 GLU
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   91 PRO
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   94 MET
Chi-restraints excluded: chain D residue   18 GLU
Chi-restraints excluded: chain D residue   37 LYS
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   64 GLN
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain D residue  122 ARG
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   83 ARG
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue   89 GLN
Chi-restraints excluded: chain E residue   95 THR
Chi-restraints excluded: chain F residue   14 MET
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   95 THR
Chi-restraints excluded: chain F residue  113 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 77 optimal weight:    0.2980
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:   10.0000
   chunk 52 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0980
   chunk 30 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  13 GLN
C  97 HIS
C 121 ASN
D  32 GLN
E  97 HIS
E 103 GLN
E 121 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.223856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.164878 restraints weight = 13355.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 1.94
r_work: 0.3785 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.099  11184  Z= 0.212
  Angle     :  0.827   9.885  15923  Z= 0.420
  Chirality :  0.044   0.212   1908
  Planarity :  0.007   0.078   1395
  Dihedral  : 26.187 178.005   3794
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 25.13
  Ramachandran Plot:
    Outliers :  1.16 %
    Allowed  :  8.00 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  8.89 %
    Allowed  : 18.60 %
    Favored  : 72.50 %
  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: -1.77 (0.27), residues: 862
  helix: -0.34 (0.19), residues: 655
  sheet: -4.90 (0.97), residues: 10
  loop : -3.57 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 303 
 HIS   0.008   0.002   HIS A 313 
 PHE   0.029   0.004   PHE A 143 
 TYR   0.026   0.003   TYR C  28 
 ARG   0.009   0.001   ARG E 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06568 (  567)
  hydrogen bonds       : angle       5.65450 ( 1559)
  covalent geometry    : bond        0.00474 (11184)
  covalent geometry    : angle       0.82741 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 234
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6905 (ttpt)
REVERT: A   57 ASN cc_start: 0.7175 (t0) cc_final: 0.6962 (t0)
REVERT: A  123 GLN cc_start: 0.7522 (tt0) cc_final: 0.6970 (tt0)
REVERT: A  141 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6841 (pttp)
REVERT: A  181 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7335 (mp)
REVERT: A  209 HIS cc_start: 0.7086 (m-70) cc_final: 0.6883 (m-70)
REVERT: A  250 GLN cc_start: 0.7795 (pt0) cc_final: 0.7541 (pt0)
REVERT: B  119 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7165 (ptt90)
REVERT: C   21 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7108 (tt0)
REVERT: C   26 TYR cc_start: 0.7668 (t80) cc_final: 0.7405 (t80)
REVERT: D  103 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6916 (mt0)
REVERT: E   14 MET cc_start: 0.6371 (mmt) cc_final: 0.5622 (mpp)
REVERT: E   50 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7389 (mt)
REVERT: F   21 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7414 (mt-10)
REVERT: F   22 ARG cc_start: 0.7916 (ptm160) cc_final: 0.7713 (ptm-80)
  outliers start: 65
  outliers final: 29
  residues processed: 271
  average time/residue: 0.2824
  time to fit residues: 101.1878
Evaluate side-chains
  232 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain D residue  122 ARG
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   97 HIS
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   62 SER
Chi-restraints excluded: chain F residue   95 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0980
   chunk 49 optimal weight:    0.5980
   chunk 83 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0170
   chunk 50 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.2618

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 191 ASN
A 259 ASN
A 290 HIS
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 121 ASN
F  92 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.226917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.166809 restraints weight = 13719.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 1.85
r_work: 0.3876 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  11184  Z= 0.172
  Angle     :  0.711   7.704  15923  Z= 0.364
  Chirality :  0.040   0.216   1908
  Planarity :  0.006   0.090   1395
  Dihedral  : 25.390 177.640   3679
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 21.88
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  7.54 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 19.70 %
    Favored  : 73.87 %
  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: -1.20 (0.28), residues: 862
  helix:  0.06 (0.20), residues: 657
  sheet: -3.29 (1.40), residues: 10
  loop : -3.45 (0.41), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 303 
 HIS   0.021   0.002   HIS E  97 
 PHE   0.022   0.003   PHE A 143 
 TYR   0.019   0.002   TYR C  28 
 ARG   0.010   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05739 (  567)
  hydrogen bonds       : angle       5.18789 ( 1559)
  covalent geometry    : bond        0.00375 (11184)
  covalent geometry    : angle       0.71114 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 212
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.4910 (tp30)
REVERT: A  191 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6689 (m-40)
REVERT: A  250 GLN cc_start: 0.7724 (pt0) cc_final: 0.7393 (pt0)
REVERT: B    1 MET cc_start: 0.7104 (tmm) cc_final: 0.6697 (ttp)
REVERT: B  119 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7229 (ptt90)
REVERT: C   21 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6770 (tt0)
REVERT: C   26 TYR cc_start: 0.7577 (t80) cc_final: 0.7368 (t80)
REVERT: C   69 TYR cc_start: 0.7904 (m-80) cc_final: 0.7699 (m-80)
REVERT: C  103 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6805 (mt0)
REVERT: D   43 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7307 (mt-10)
REVERT: E   14 MET cc_start: 0.6309 (mmt) cc_final: 0.5656 (mpp)
REVERT: E   50 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7513 (mt)
REVERT: F   43 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6681 (tp30)
  outliers start: 47
  outliers final: 19
  residues processed: 241
  average time/residue: 0.2907
  time to fit residues: 92.3949
Evaluate side-chains
  212 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 187
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  191 ASN
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  259 ASN
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  117 ILE
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   95 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0980
   chunk 91 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 88 optimal weight:   30.0000
   chunk 65 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 99 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 297 GLN
D  64 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.224772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.162755 restraints weight = 13393.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 1.88
r_work: 0.3796 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.5577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11184  Z= 0.198
  Angle     :  0.728   8.414  15923  Z= 0.368
  Chirality :  0.041   0.371   1908
  Planarity :  0.006   0.106   1395
  Dihedral  : 24.994 177.661   3654
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 22.40
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  :  6.96 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 20.25 %
    Favored  : 72.78 %
  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: -0.87 (0.28), residues: 862
  helix:  0.19 (0.20), residues: 655
  sheet: -1.56 (1.89), residues: 10
  loop : -2.99 (0.45), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 303 
 HIS   0.012   0.002   HIS A 133 
 PHE   0.026   0.003   PHE B  80 
 TYR   0.024   0.002   TYR C  28 
 ARG   0.005   0.001   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05661 (  567)
  hydrogen bonds       : angle       5.12888 ( 1559)
  covalent geometry    : bond        0.00453 (11184)
  covalent geometry    : angle       0.72815 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 204
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 LYS cc_start: 0.7341 (pttp) cc_final: 0.7012 (pttp)
REVERT: A  165 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7470 (mtt180)
REVERT: A  232 TYR cc_start: 0.7666 (m-80) cc_final: 0.7440 (m-80)
REVERT: A  287 PHE cc_start: 0.6230 (m-80) cc_final: 0.6029 (m-80)
REVERT: B    1 MET cc_start: 0.6936 (tmm) cc_final: 0.6707 (ttp)
REVERT: B  119 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6942 (ptm160)
REVERT: C   21 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6851 (tt0)
REVERT: C   26 TYR cc_start: 0.7746 (t80) cc_final: 0.7407 (t80)
REVERT: C  103 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7031 (mt0)
REVERT: D   19 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7327 (mmm-85)
REVERT: D  103 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7080 (mt0)
REVERT: E   14 MET cc_start: 0.6407 (mmt) cc_final: 0.5700 (mpp)
REVERT: E   50 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7713 (mt)
REVERT: F   26 TYR cc_start: 0.6716 (t80) cc_final: 0.6163 (t80)
REVERT: F   43 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6755 (tp30)
  outliers start: 51
  outliers final: 27
  residues processed: 236
  average time/residue: 0.2876
  time to fit residues: 88.8916
Evaluate side-chains
  220 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 187
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue   95 THR
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  105 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 95 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  27 HIS
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 HIS
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 GLN
F  97 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.223669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.162865 restraints weight = 13369.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.4023 rms_B_bonded: 1.75
r_work: 0.3780 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.5961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11184  Z= 0.204
  Angle     :  0.712   8.847  15923  Z= 0.360
  Chirality :  0.040   0.258   1908
  Planarity :  0.006   0.090   1395
  Dihedral  : 24.693 178.001   3652
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 22.45
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.19 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 21.89 %
    Favored  : 72.23 %
  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: -0.73 (0.29), residues: 862
  helix:  0.25 (0.20), residues: 659
  sheet: -1.48 (1.89), residues: 10
  loop : -2.79 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 303 
 HIS   0.011   0.002   HIS A 133 
 PHE   0.024   0.003   PHE B  80 
 TYR   0.024   0.002   TYR C  28 
 ARG   0.010   0.001   ARG A 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05638 (  567)
  hydrogen bonds       : angle       5.06854 ( 1559)
  covalent geometry    : bond        0.00469 (11184)
  covalent geometry    : angle       0.71226 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 191
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4238 (mpp) cc_final: 0.3619 (mpp)
REVERT: A  141 LYS cc_start: 0.7373 (pttp) cc_final: 0.7012 (pttp)
REVERT: A  165 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7405 (mtt180)
REVERT: A  287 PHE cc_start: 0.6257 (m-80) cc_final: 0.5978 (m-80)
REVERT: B   37 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8349 (ptmm)
REVERT: B  119 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6963 (ptt90)
REVERT: C   21 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6890 (tt0)
REVERT: C   26 TYR cc_start: 0.7776 (t80) cc_final: 0.7410 (t80)
REVERT: C  103 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7169 (mt0)
REVERT: D  103 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7099 (mt0)
REVERT: E   14 MET cc_start: 0.6458 (mmt) cc_final: 0.5676 (mpp)
REVERT: E   50 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7647 (mt)
REVERT: E   78 LEU cc_start: 0.7776 (tp) cc_final: 0.7562 (tp)
REVERT: F   43 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6779 (tp30)
  outliers start: 43
  outliers final: 26
  residues processed: 219
  average time/residue: 0.2908
  time to fit residues: 84.5280
Evaluate side-chains
  216 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 183
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue   37 LYS
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue   95 THR
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  105 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 43 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0870
   chunk 95 optimal weight:   20.0000
   chunk 38 optimal weight:    0.5980
   chunk 27 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0670
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
A 286 ASN
A 290 HIS
A 322 GLN
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 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 = 0.4695 r_free = 0.4695 target = 0.226262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.167214 restraints weight = 13604.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 1.74
r_work: 0.3828 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.6402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11184  Z= 0.161
  Angle     :  0.688  14.071  15923  Z= 0.346
  Chirality :  0.038   0.223   1908
  Planarity :  0.006   0.095   1395
  Dihedral  : 24.450 177.955   3649
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 20.85
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  6.84 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 22.85 %
    Favored  : 71.68 %
  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: -0.67 (0.29), residues: 862
  helix:  0.25 (0.20), residues: 661
  sheet: -0.91 (2.03), residues: 10
  loop : -2.67 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 303 
 HIS   0.021   0.002   HIS B  97 
 PHE   0.022   0.003   PHE B  80 
 TYR   0.022   0.002   TYR C  28 
 ARG   0.007   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05436 (  567)
  hydrogen bonds       : angle       5.00658 ( 1559)
  covalent geometry    : bond        0.00361 (11184)
  covalent geometry    : angle       0.68770 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 196
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 LYS cc_start: 0.7391 (pttp) cc_final: 0.7125 (pttp)
REVERT: A  154 MET cc_start: 0.7285 (ptp) cc_final: 0.6949 (ptp)
REVERT: A  165 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7332 (mtt180)
REVERT: A  191 ASN cc_start: 0.8301 (m-40) cc_final: 0.8020 (m-40)
REVERT: A  232 TYR cc_start: 0.7632 (m-80) cc_final: 0.7410 (m-80)
REVERT: A  287 PHE cc_start: 0.6599 (m-80) cc_final: 0.6345 (m-80)
REVERT: B  119 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6877 (ptm160)
REVERT: C   21 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6676 (tt0)
REVERT: C   26 TYR cc_start: 0.7675 (t80) cc_final: 0.7418 (t80)
REVERT: C  103 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7061 (mt0)
REVERT: D   19 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6532 (mmm-85)
REVERT: D   44 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7842 (mtp)
REVERT: D  103 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7058 (mt0)
REVERT: E   14 MET cc_start: 0.6403 (mmt) cc_final: 0.5634 (mpp)
REVERT: E   50 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7687 (mt)
REVERT: F   26 TYR cc_start: 0.6817 (t80) cc_final: 0.6330 (t80)
REVERT: F   43 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6673 (tp30)
REVERT: F   47 LYS cc_start: 0.8133 (mttm) cc_final: 0.7736 (mmtt)
  outliers start: 40
  outliers final: 18
  residues processed: 222
  average time/residue: 0.2924
  time to fit residues: 86.2415
Evaluate side-chains
  211 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue   44 MET
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue  105 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 96 optimal weight:   30.0000
   chunk 72 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 68 optimal weight:    0.1980
   chunk 79 optimal weight:    0.0980
   chunk 95 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9990
   chunk 88 optimal weight:   20.0000
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.227931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.168727 restraints weight = 13737.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 1.88
r_work: 0.3863 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.6859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11184  Z= 0.155
  Angle     :  0.688  11.890  15923  Z= 0.346
  Chirality :  0.039   0.224   1908
  Planarity :  0.006   0.094   1395
  Dihedral  : 24.247 177.809   3644
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 19.77
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  6.38 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.90 %
    Favored  : 70.59 %
  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: -0.46 (0.29), residues: 862
  helix:  0.39 (0.20), residues: 662
  sheet: -1.09 (1.94), residues: 10
  loop : -2.53 (0.48), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 303 
 HIS   0.011   0.002   HIS A 133 
 PHE   0.022   0.002   PHE B  80 
 TYR   0.018   0.002   TYR C  28 
 ARG   0.007   0.001   ARG F  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05314 (  567)
  hydrogen bonds       : angle       4.92251 ( 1559)
  covalent geometry    : bond        0.00341 (11184)
  covalent geometry    : angle       0.68770 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6979 (ttpt)
REVERT: A  141 LYS cc_start: 0.7407 (pttp) cc_final: 0.7185 (pttp)
REVERT: A  154 MET cc_start: 0.7349 (ptp) cc_final: 0.7111 (ptp)
REVERT: A  165 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7310 (mtt180)
REVERT: A  191 ASN cc_start: 0.8268 (m-40) cc_final: 0.8023 (m-40)
REVERT: A  287 PHE cc_start: 0.6498 (m-80) cc_final: 0.6111 (m-80)
REVERT: A  300 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6899 (pp)
REVERT: B   66 SER cc_start: 0.8424 (m) cc_final: 0.8078 (p)
REVERT: B  119 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6834 (ptm160)
REVERT: C   21 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6434 (tt0)
REVERT: C   82 LEU cc_start: 0.8313 (mt) cc_final: 0.8052 (mt)
REVERT: C  103 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7002 (mt0)
REVERT: D   28 TYR cc_start: 0.8269 (t80) cc_final: 0.8020 (t80)
REVERT: D   44 MET cc_start: 0.8133 (mtp) cc_final: 0.7795 (mtp)
REVERT: D  103 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7082 (mt0)
REVERT: E   14 MET cc_start: 0.6525 (mmt) cc_final: 0.5746 (mpp)
REVERT: E   50 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7424 (mt)
REVERT: F   26 TYR cc_start: 0.6710 (t80) cc_final: 0.6174 (t80)
REVERT: F   43 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6694 (tp30)
REVERT: F   44 MET cc_start: 0.7816 (ttp) cc_final: 0.7435 (ptm)
REVERT: F   47 LYS cc_start: 0.8118 (mttm) cc_final: 0.7800 (mmtt)
  outliers start: 33
  outliers final: 16
  residues processed: 208
  average time/residue: 0.3031
  time to fit residues: 83.1946
Evaluate side-chains
  209 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   43 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 23 optimal weight:    0.0470
   chunk 9 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 90 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 97 optimal weight:   30.0000
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 HIS
** D  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  97 HIS
** F  98 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 = 0.4689 r_free = 0.4689 target = 0.225621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.165461 restraints weight = 13496.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 1.74
r_work: 0.3814 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.6900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  11184  Z= 0.188
  Angle     :  0.707  10.865  15923  Z= 0.359
  Chirality :  0.040   0.238   1908
  Planarity :  0.006   0.091   1395
  Dihedral  : 24.182 178.042   3643
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 21.42
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.73 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 25.72 %
    Favored  : 70.31 %
  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: -0.58 (0.29), residues: 862
  helix:  0.29 (0.20), residues: 662
  sheet: -1.44 (1.87), residues: 10
  loop : -2.51 (0.48), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 303 
 HIS   0.021   0.002   HIS B  97 
 PHE   0.024   0.002   PHE B  80 
 TYR   0.023   0.002   TYR C  28 
 ARG   0.009   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05471 (  567)
  hydrogen bonds       : angle       5.01617 ( 1559)
  covalent geometry    : bond        0.00432 (11184)
  covalent geometry    : angle       0.70656 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6960 (ttpt)
REVERT: A  141 LYS cc_start: 0.7416 (pttp) cc_final: 0.7203 (pttp)
REVERT: A  154 MET cc_start: 0.7466 (ptp) cc_final: 0.7136 (ptp)
REVERT: A  165 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7327 (mtt180)
REVERT: A  191 ASN cc_start: 0.8308 (m-40) cc_final: 0.8045 (m-40)
REVERT: A  232 TYR cc_start: 0.7647 (m-80) cc_final: 0.7393 (m-80)
REVERT: A  287 PHE cc_start: 0.6505 (m-80) cc_final: 0.6185 (m-80)
REVERT: A  300 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6924 (pp)
REVERT: B  119 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6765 (ptm160)
REVERT: C   21 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6644 (tt0)
REVERT: C   26 TYR cc_start: 0.7621 (t80) cc_final: 0.7320 (t80)
REVERT: C   42 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7625 (ttp-170)
REVERT: C  103 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7019 (mt0)
REVERT: D   28 TYR cc_start: 0.8238 (t80) cc_final: 0.7960 (t80)
REVERT: D  103 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7076 (mt0)
REVERT: E   14 MET cc_start: 0.6566 (mmt) cc_final: 0.5755 (mpp)
REVERT: E   50 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7712 (mt)
REVERT: F   22 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.7617 (ptm-80)
REVERT: F   43 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6670 (tp30)
REVERT: F   47 LYS cc_start: 0.8101 (mttm) cc_final: 0.7742 (mmtt)
  outliers start: 29
  outliers final: 15
  residues processed: 202
  average time/residue: 0.4306
  time to fit residues: 113.8818
Evaluate side-chains
  201 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   43 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 58 optimal weight:    0.1980
   chunk 83 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 57 optimal weight:    0.1980
   chunk 34 optimal weight:    0.7980
   chunk 88 optimal weight:   20.0000
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 HIS
** D  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 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 = 0.4701 r_free = 0.4701 target = 0.226992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.169230 restraints weight = 13709.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 1.82
r_work: 0.3815 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.7107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11184  Z= 0.175
  Angle     :  0.703  10.198  15923  Z= 0.356
  Chirality :  0.040   0.249   1908
  Planarity :  0.006   0.092   1395
  Dihedral  : 24.095 177.998   3637
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 21.42
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  7.08 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 26.27 %
    Favored  : 69.77 %
  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: -0.58 (0.29), residues: 862
  helix:  0.30 (0.20), residues: 663
  sheet: -1.46 (1.86), residues: 10
  loop : -2.57 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 303 
 HIS   0.020   0.002   HIS B  97 
 PHE   0.023   0.002   PHE B  80 
 TYR   0.020   0.002   TYR C  28 
 ARG   0.007   0.001   ARG D  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05432 (  567)
  hydrogen bonds       : angle       4.99715 ( 1559)
  covalent geometry    : bond        0.00403 (11184)
  covalent geometry    : angle       0.70343 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 179
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6984 (ttpt)
REVERT: A  154 MET cc_start: 0.7413 (ptp) cc_final: 0.7078 (ptp)
REVERT: A  165 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7322 (mtt180)
REVERT: A  191 ASN cc_start: 0.8294 (m-40) cc_final: 0.8038 (m-40)
REVERT: A  232 TYR cc_start: 0.7633 (m-80) cc_final: 0.7408 (m-80)
REVERT: A  287 PHE cc_start: 0.6506 (m-80) cc_final: 0.6186 (m-80)
REVERT: A  300 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6914 (pp)
REVERT: B   95 THR cc_start: 0.7710 (m) cc_final: 0.7370 (m)
REVERT: B  119 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6882 (ptm160)
REVERT: C   21 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6263 (tt0)
REVERT: C  103 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7012 (mt0)
REVERT: D   26 TYR cc_start: 0.6909 (t80) cc_final: 0.6493 (t80)
REVERT: D   28 TYR cc_start: 0.8177 (t80) cc_final: 0.7924 (t80)
REVERT: D  103 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7063 (mt0)
REVERT: E   14 MET cc_start: 0.6532 (mmt) cc_final: 0.5707 (mpp)
REVERT: E   50 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7684 (mt)
REVERT: F   22 ARG cc_start: 0.7900 (ptm-80) cc_final: 0.7657 (ptm-80)
REVERT: F   26 TYR cc_start: 0.6878 (t80) cc_final: 0.6400 (t80)
REVERT: F   43 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6660 (tp30)
REVERT: F   44 MET cc_start: 0.7878 (ttp) cc_final: 0.7587 (ptm)
REVERT: F   47 LYS cc_start: 0.8067 (mttm) cc_final: 0.7720 (mmtt)
  outliers start: 29
  outliers final: 17
  residues processed: 195
  average time/residue: 0.2881
  time to fit residues: 74.8725
Evaluate side-chains
  201 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue   16 ILE
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  105 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 96 optimal weight:   20.0000
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   chunk 44 optimal weight:    0.0970
   chunk 8 optimal weight:    0.4980
   chunk 82 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0010
   overall best weight:    0.3384

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 HIS
** D  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 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 = 0.4710 r_free = 0.4710 target = 0.228025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.171480 restraints weight = 13688.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.4116 rms_B_bonded: 1.78
r_work: 0.3855 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.7376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11184  Z= 0.159
  Angle     :  0.701  10.006  15923  Z= 0.355
  Chirality :  0.039   0.234   1908
  Planarity :  0.006   0.090   1395
  Dihedral  : 24.014 177.879   3637
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 21.16
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  6.61 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 26.68 %
    Favored  : 69.77 %
  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: -0.54 (0.29), residues: 862
  helix:  0.32 (0.20), residues: 662
  sheet: -1.78 (1.65), residues: 12
  loop : -2.49 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 303 
 HIS   0.026   0.002   HIS B  97 
 PHE   0.022   0.002   PHE C  80 
 TYR   0.019   0.002   TYR C  28 
 ARG   0.007   0.001   ARG F  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05385 (  567)
  hydrogen bonds       : angle       4.97440 ( 1559)
  covalent geometry    : bond        0.00357 (11184)
  covalent geometry    : angle       0.70105 (15923)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6963 (ttpt)
REVERT: A  154 MET cc_start: 0.7265 (ptp) cc_final: 0.6961 (ptp)
REVERT: A  165 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7264 (mtt180)
REVERT: A  191 ASN cc_start: 0.8273 (m-40) cc_final: 0.8031 (m-40)
REVERT: A  287 PHE cc_start: 0.6538 (m-80) cc_final: 0.6168 (m-80)
REVERT: B   66 SER cc_start: 0.8465 (m) cc_final: 0.8128 (p)
REVERT: B  119 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6783 (ptm160)
REVERT: C   20 TYR cc_start: 0.7330 (t80) cc_final: 0.7116 (t80)
REVERT: C   21 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6007 (tt0)
REVERT: C  103 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6949 (mt0)
REVERT: D   26 TYR cc_start: 0.6813 (t80) cc_final: 0.6506 (t80)
REVERT: D   28 TYR cc_start: 0.8095 (t80) cc_final: 0.7867 (t80)
REVERT: D  103 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7013 (mt0)
REVERT: E   14 MET cc_start: 0.6521 (mmt) cc_final: 0.5745 (mpp)
REVERT: E   50 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7586 (mt)
REVERT: E   67 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7836 (tppt)
REVERT: F   22 ARG cc_start: 0.7922 (ptm-80) cc_final: 0.7683 (ptm-80)
REVERT: F   26 TYR cc_start: 0.6811 (t80) cc_final: 0.6324 (t80)
REVERT: F   43 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6632 (tp30)
REVERT: F   44 MET cc_start: 0.7891 (ttp) cc_final: 0.7539 (ptm)
REVERT: F   47 LYS cc_start: 0.7998 (mttm) cc_final: 0.7665 (mmtt)
  outliers start: 26
  outliers final: 15
  residues processed: 201
  average time/residue: 0.2675
  time to fit residues: 72.2856
Evaluate side-chains
  202 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  266 TRP
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain D residue   16 ILE
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   97 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 43 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 HIS
** D  38 HIS ** 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 = 0.4703 r_free = 0.4703 target = 0.227243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.169031 restraints weight = 13537.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 1.98
r_work: 0.3783 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.7363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11184  Z= 0.183
  Angle     :  0.707   9.680  15923  Z= 0.360
  Chirality :  0.040   0.260   1908
  Planarity :  0.006   0.087   1395
  Dihedral  : 23.991 178.055   3637
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 21.37
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.26 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 26.13 %
    Favored  : 70.18 %
  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: -0.59 (0.29), residues: 862
  helix:  0.29 (0.20), residues: 663
  sheet: -2.06 (1.56), residues: 12
  loop : -2.52 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 303 
 HIS   0.024   0.002   HIS B  97 
 PHE   0.024   0.002   PHE B  80 
 TYR   0.023   0.002   TYR C  28 
 ARG   0.007   0.001   ARG D  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05491 (  567)
  hydrogen bonds       : angle       5.03240 ( 1559)
  covalent geometry    : bond        0.00421 (11184)
  covalent geometry    : angle       0.70736 (15923)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6022.46 seconds
wall clock time: 106 minutes 23.59 seconds (6383.59 seconds total)