Starting phenix.real_space_refine
on Sun Jun 15 05:29:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pfb_17645/06_2025/8pfb_17645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pfb_17645/06_2025/8pfb_17645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pfb_17645/06_2025/8pfb_17645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pfb_17645/06_2025/8pfb_17645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pfb_17645/06_2025/8pfb_17645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pfb_17645/06_2025/8pfb_17645.cif"
  }
  resolution = 3.67
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       9      5.16       5
     C    5343      2.51       5
     N    1477      2.21       5
     O    1710      1.98       5
     H    8598      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17137
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "G"
      Number of atoms: 1841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 1841
          Classifications: {'peptide': 121}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 1915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1915
          Classifications: {'peptide': 125}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 119}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1977
          Classifications: {'peptide': 131}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 125}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1966
          Classifications: {'peptide': 130}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1966
          Classifications: {'peptide': 130}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1966
          Classifications: {'peptide': 130}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1955
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1835
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 1716
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 5, 'TRANS': 110}
          Chain breaks: 1
  Time building chain proxies: 8.56, per 1000 atoms: 0.50
  Number of scatterers: 17137
  At special positions: 0
  Unit cell: (77.19, 80.91, 170.19, 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       9     16.00
     O    1710      8.00
     N    1477      7.00
     C    5343      6.00
     H    8598      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.95
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 9 sheets defined
      44.5% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'G' and resid 2 through 17
      removed outlier: 4.815A  pdb=" N   VAL G   8 " --> pdb=" O   VAL G   4 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   VAL G   9 " --> pdb=" O   GLU G   5 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE G  10 " --> pdb=" O   LEU G   6 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 23 through 51
      removed outlier: 4.019A  pdb=" N   PHE G  27 " --> pdb=" O   ALA G  23 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASN G  30 " --> pdb=" O   SER G  26 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   SER G  34 " --> pdb=" O   ASN G  30 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG G  35 " --> pdb=" O   ALA G  31 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ARG G  41 " --> pdb=" O   GLN G  37 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU G  42 " --> pdb=" O   SER G  38 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 65 through 69
    Processing helix  chain 'G' and resid 70 through 72
      No H-bonds generated for 'chain 'G' and resid 70 through 72'
    Processing helix  chain 'G' and resid 81 through 85
    Processing helix  chain 'F' and resid 2 through 17
      removed outlier: 3.717A  pdb=" N   LEU F   6 " --> pdb=" O   THR F   2 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE F  10 " --> pdb=" O   LEU F   6 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE F  13 " --> pdb=" O   VAL F   9 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA F  14 " --> pdb=" O   ILE F  10 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ILE F  15 " --> pdb=" O   ILE F  11 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 51
      removed outlier: 3.612A  pdb=" N   LYS F  33 " --> pdb=" O   ASP F  29 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN F  37 " --> pdb=" O   LYS F  33 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE F  51 " --> pdb=" O   ILE F  47 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 64 through 69
    Processing helix  chain 'F' and resid 70 through 72
      No H-bonds generated for 'chain 'F' and resid 70 through 72'
    Processing helix  chain 'F' and resid 81 through 85
    Processing helix  chain 'C' and resid 2 through 17
      removed outlier: 3.547A  pdb=" N   LEU C   6 " --> pdb=" O   THR C   2 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE C  10 " --> pdb=" O   LEU C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 52
      removed outlier: 4.218A  pdb=" N   ALA C  31 " --> pdb=" O   PHE C  27 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY C  52 " --> pdb=" O   GLN C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 72
    Processing helix  chain 'C' and resid 81 through 85
    Processing helix  chain 'C' and resid 107 through 109
      No H-bonds generated for 'chain 'C' and resid 107 through 109'
    Processing helix  chain 'C' and resid 132 through 136
    Processing helix  chain 'A' and resid 2 through 10
      removed outlier: 4.070A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 18
      removed outlier: 3.686A  pdb=" N   ALA A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 27
      No H-bonds generated for 'chain 'A' and resid 25 through 27'
    Processing helix  chain 'A' and resid 28 through 51
      removed outlier: 3.569A  pdb=" N   GLN A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 54
      No H-bonds generated for 'chain 'A' and resid 52 through 54'
    Processing helix  chain 'A' and resid 64 through 69
    Processing helix  chain 'A' and resid 70 through 72
      No H-bonds generated for 'chain 'A' and resid 70 through 72'
    Processing helix  chain 'A' and resid 81 through 86
      removed outlier: 3.707A  pdb=" N   SER A  85 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 17
      removed outlier: 4.440A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B   4 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   VAL B   9 " --> pdb=" O   GLU B   5 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE B  10 " --> pdb=" O   LEU B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 54
      removed outlier: 3.928A  pdb=" N   PHE B  27 " --> pdb=" O   ALA B  23 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ASN B  30 " --> pdb=" O   SER B  26 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA B  31 " --> pdb=" O   PHE B  27 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   SER B  34 " --> pdb=" O   ASN B  30 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG B  41 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY B  52 " --> pdb=" O   GLN B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 69
    Processing helix  chain 'B' and resid 70 through 72
      No H-bonds generated for 'chain 'B' and resid 70 through 72'
    Processing helix  chain 'B' and resid 81 through 86
      removed outlier: 3.819A  pdb=" N   SER B  85 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 17
      removed outlier: 3.595A  pdb=" N   ALA I  14 " --> pdb=" O   ILE I  10 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA I  17 " --> pdb=" O   ILE I  13 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 29 through 54
      removed outlier: 3.964A  pdb=" N   LYS I  33 " --> pdb=" O   ASP I  29 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ARG I  41 " --> pdb=" O   GLN I  37 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU I  42 " --> pdb=" O   SER I  38 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY I  52 " --> pdb=" O   GLN I  48 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 72 through 77
      removed outlier: 4.098A  pdb=" N   ASN I  75 " --> pdb=" O   MET I  72 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ALA I  76 " --> pdb=" O   SER I  73 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LYS I  77 " --> pdb=" O   LYS I  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 72 through 77'
    Processing helix  chain 'I' and resid 81 through 85
    Processing helix  chain 'H' and resid 3 through 17
      removed outlier: 3.776A  pdb=" N   ILE H  10 " --> pdb=" O   LEU H   6 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE H  11 " --> pdb=" O   ILE H   7 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 28
    Processing helix  chain 'H' and resid 29 through 51
      removed outlier: 4.226A  pdb=" N   LYS H  33 " --> pdb=" O   ASP H  29 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER H  34 " --> pdb=" O   ASN H  30 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG H  35 " --> pdb=" O   ALA H  31 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER H  38 " --> pdb=" O   SER H  34 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ARG H  41 " --> pdb=" O   GLN H  37 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 64 through 69
    Processing helix  chain 'H' and resid 70 through 72
      No H-bonds generated for 'chain 'H' and resid 70 through 72'
    Processing helix  chain 'H' and resid 81 through 85
    Processing helix  chain 'H' and resid 107 through 109
      No H-bonds generated for 'chain 'H' and resid 107 through 109'
    Processing helix  chain 'D' and resid 11 through 17
      removed outlier: 3.804A  pdb=" N   ILE D  15 " --> pdb=" O   ILE D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 27
    Processing helix  chain 'D' and resid 28 through 51
      removed outlier: 3.666A  pdb=" N   SER D  34 " --> pdb=" O   ASN D  30 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLU D  39 " --> pdb=" O   ARG D  35 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLU D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 69
    Processing helix  chain 'D' and resid 70 through 72
      No H-bonds generated for 'chain 'D' and resid 70 through 72'
    Processing helix  chain 'D' and resid 107 through 109
      No H-bonds generated for 'chain 'D' and resid 107 through 109'
    Processing helix  chain 'E' and resid 23 through 54
      removed outlier: 4.521A  pdb=" N   PHE E  27 " --> pdb=" O   ALA E  23 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASN E  30 " --> pdb=" O   SER E  26 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER E  34 " --> pdb=" O   ASN E  30 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN E  37 " --> pdb=" O   LYS E  33 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ARG E  41 " --> pdb=" O   GLN E  37 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   SER E  45 " --> pdb=" O   ARG E  41 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN E  48 " --> pdb=" O   VAL E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 69
    Processing helix  chain 'E' and resid 70 through 72
      No H-bonds generated for 'chain 'E' and resid 70 through 72'
    Processing helix  chain 'E' and resid 81 through 85
    Processing helix  chain 'E' and resid 107 through 109
      No H-bonds generated for 'chain 'E' and resid 107 through 109'
    Processing sheet with id=AA1, first strand: chain 'G' and resid 103 through 106
      removed outlier: 3.641A  pdb=" N   SER G 114 " --> pdb=" O   LEU G 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 103 through 105
    Processing sheet with id=AA3, first strand: chain 'C' and resid 103 through 106
      removed outlier: 3.747A  pdb=" N   LYS C 111 " --> pdb=" O   ASP C 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106
    Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 106
    Processing sheet with id=AA6, first strand: chain 'I' and resid 103 through 106
    Processing sheet with id=AA7, first strand: chain 'H' and resid 103 through 106
      removed outlier: 4.040A  pdb=" N   LYS H 111 " --> pdb=" O   ASP H 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 106
    Processing sheet with id=AA9, first strand: chain 'E' and resid 103 through 105

    347 hydrogen bonds defined for protein.
    942 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.21

  Time building geometry restraints manager: 4.88 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8598
        1.03 -     1.23: 1
        1.23 -     1.42: 3476
        1.42 -     1.61: 5164
        1.61 -     1.81: 18
  Bond restraints: 17257
  Sorted by residual:
  bond pdb=" CB  GLU E  62 "
       pdb=" CG  GLU E  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.94e+00
  bond pdb=" N   PHE H  27 "
       pdb=" CA  PHE H  27 "
    ideal  model  delta    sigma   weight residual
    1.458  1.477 -0.019 1.42e-02 4.96e+03 1.86e+00
  bond pdb=" CA  PHE C  27 "
       pdb=" C   PHE C  27 "
    ideal  model  delta    sigma   weight residual
    1.524  1.545 -0.021 1.57e-02 4.06e+03 1.83e+00
  bond pdb=" CB  LYS D  77 "
       pdb=" CG  LYS D  77 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.65e+00
  bond pdb=" C   GLN B  28 "
       pdb=" O   GLN B  28 "
    ideal  model  delta    sigma   weight residual
    1.236  1.251 -0.015 1.15e-02 7.56e+03 1.61e+00
  ... (remaining 17252 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 30159
        1.82 -     3.65: 999
        3.65 -     5.47: 70
        5.47 -     7.29: 12
        7.29 -     9.11: 4
  Bond angle restraints: 31244
  Sorted by residual:
  angle pdb=" N   ILE H  24 "
        pdb=" CA  ILE H  24 "
        pdb=" C   ILE H  24 "
      ideal   model   delta    sigma   weight residual
     112.50  117.89   -5.39 1.39e+00 5.18e-01 1.51e+01
  angle pdb=" N   ASP I  29 "
        pdb=" CA  ASP I  29 "
        pdb=" C   ASP I  29 "
      ideal   model   delta    sigma   weight residual
     111.28  115.45   -4.17 1.09e+00 8.42e-01 1.47e+01
  angle pdb=" CA  LYS D  77 "
        pdb=" CB  LYS D  77 "
        pdb=" CG  LYS D  77 "
      ideal   model   delta    sigma   weight residual
     114.10  121.62   -7.52 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" N   PHE C  27 "
        pdb=" CA  PHE C  27 "
        pdb=" CB  PHE C  27 "
      ideal   model   delta    sigma   weight residual
     112.41  106.81    5.60 1.55e+00 4.16e-01 1.30e+01
  angle pdb=" CB  GLU E  62 "
        pdb=" CG  GLU E  62 "
        pdb=" CD  GLU E  62 "
      ideal   model   delta    sigma   weight residual
     112.60  118.72   -6.12 1.70e+00 3.46e-01 1.30e+01
  ... (remaining 31239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 7391
       17.84 -    35.68: 497
       35.68 -    53.52: 151
       53.52 -    71.36: 69
       71.36 -    89.20: 20
  Dihedral angle restraints: 8128
    sinusoidal: 4469
      harmonic: 3659
  Sorted by residual:
  dihedral pdb=" CA  ILE H  24 "
           pdb=" C   ILE H  24 "
           pdb=" N   THR H  25 "
           pdb=" CA  THR H  25 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.92  -29.08     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASP I 130 "
           pdb=" C   ASP I 130 "
           pdb=" N   TRP I 131 "
           pdb=" CA  TRP I 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.97  -28.03     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  GLU E  79 "
           pdb=" C   GLU E  79 "
           pdb=" N   ASP E  80 "
           pdb=" CA  ASP E  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.21  -27.79     0      5.00e+00 4.00e-02 3.09e+01
  ... (remaining 8125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 773
       0.033 -    0.065: 414
       0.065 -    0.098: 173
       0.098 -    0.131: 61
       0.131 -    0.163: 11
  Chirality restraints: 1432
  Sorted by residual:
  chirality pdb=" CA  TYR D  71 "
            pdb=" N   TYR D  71 "
            pdb=" C   TYR D  71 "
            pdb=" CB  TYR D  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CB  ILE A  47 "
            pdb=" CA  ILE A  47 "
            pdb=" CG1 ILE A  47 "
            pdb=" CG2 ILE A  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.08e-01
  chirality pdb=" CA  TYR B  71 "
            pdb=" N   TYR B  71 "
            pdb=" C   TYR B  71 "
            pdb=" CB  TYR B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.86e-01
  ... (remaining 1429 not shown)

  Planarity restraints: 2585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  69 "   -0.075 5.00e-02 4.00e+02   1.14e-01 2.07e+01
        pdb=" N   PRO F  70 "    0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO F  70 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO F  70 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  34 "    0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   SER B  34 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   SER B  34 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ARG B  35 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  41 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.78e+00
        pdb=" C   ARG B  41 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ARG B  41 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU B  42 "    0.018 2.00e-02 2.50e+03
  ... (remaining 2582 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 870
        2.19 -     2.79: 32944
        2.79 -     3.39: 43679
        3.39 -     4.00: 52443
        4.00 -     4.60: 81675
  Nonbonded interactions: 211611
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C  75 "
            pdb=" H   LYS C  77 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" OD1 ASP D  29 "
            pdb=" H   ASN D  30 "
     model   vdw
     1.599 2.450
  nonbonded pdb=" OD2 ASP D 106 "
            pdb="HD21 ASN D 109 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" OD1 ASN E 120 "
            pdb=" H   GLY E 122 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" OD2 ASP E  29 "
            pdb=" HG  SER E 119 "
     model   vdw
     1.637 2.450
  ... (remaining 211606 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 'A' and (resid 16 through 54 or resid 64 through 91 or resid 101 through  \ 
134))
  selection = (chain 'B' and (resid 16 through 54 or resid 64 through 91 or resid 101 through  \ 
134))
  selection = (chain 'C' and (resid 16 through 54 or resid 64 through 91 or resid 101 through  \ 
134))
  selection = (chain 'D' and (resid 16 through 54 or resid 64 through 91 or resid 101 through  \ 
134))
  selection = (chain 'E' and (resid 16 through 54 or resid 64 through 91 or resid 101 through  \ 
134))
  selection = (chain 'F' and (resid 16 through 54 or resid 64 through 134))
  selection = (chain 'G' and (resid 16 through 91 or resid 101 through 134))
  selection = (chain 'H' and (resid 16 through 54 or resid 64 through 91 or resid 101 through  \ 
134))
  selection = (chain 'I' and (resid 16 through 54 or resid 64 through 91 or resid 101 through  \ 
134))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  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:             0.290
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.120
  Set scattering table:                    0.140
  Process input model:                     35.350
  Find NCS groups from input model:        0.610
  Set up NCS constraints:                  0.060
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
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      :  0.004   0.042   8659  Z= 0.223
  Angle     :  0.899   9.114  11767  Z= 0.528
  Chirality :  0.048   0.163   1432
  Planarity :  0.007   0.114   1511
  Dihedral  : 14.616  89.204   3111
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 13.80 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.08 (0.23), residues: 1098
  helix: -1.89 (0.24), residues: 362
  sheet:  0.89 (0.38), residues: 169
  loop : -0.26 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP I 131 
 HIS   0.005   0.001   HIS F  40 
 PHE   0.021   0.002   PHE H  27 
 TYR   0.018   0.003   TYR H  71 
 ARG   0.008   0.001   ARG E  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17685 (  347)
  hydrogen bonds       : angle       6.75878 (  942)
  covalent geometry    : bond        0.00417 ( 8659)
  covalent geometry    : angle       0.89931 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 215
  time to evaluate  : 1.331 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   56 ASP cc_start: 0.8637 (m-30) cc_final: 0.8245 (p0)
REVERT: H    5 GLU cc_start: 0.8751 (pt0) cc_final: 0.8510 (tm-30)
REVERT: E   30 ASN cc_start: 0.9263 (m-40) cc_final: 0.9040 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 218
  average time/residue: 0.4632
  time to fit residues: 137.0750
Evaluate side-chains
  134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    2 THR
Chi-restraints excluded: chain F residue   16 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
F  59 ASN
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 104 GLN
H  37 GLN
H 110 HIS
** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 134 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.067455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.054532 restraints weight = 115162.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.056969 restraints weight = 51365.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.058717 restraints weight = 30599.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8659  Z= 0.158
  Angle     :  0.660   6.461  11767  Z= 0.367
  Chirality :  0.043   0.151   1432
  Planarity :  0.005   0.068   1511
  Dihedral  :  6.347  25.533   1174
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 16.45 %
    Favored  : 82.27 %
  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: -0.57 (0.24), residues: 1098
  helix: -0.58 (0.26), residues: 381
  sheet:  0.58 (0.37), residues: 174
  loop : -0.42 (0.25), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP I 131 
 HIS   0.005   0.001   HIS E 103 
 PHE   0.010   0.001   PHE G  27 
 TYR   0.007   0.001   TYR C  71 
 ARG   0.004   0.000   ARG D  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06736 (  347)
  hydrogen bonds       : angle       5.48285 (  942)
  covalent geometry    : bond        0.00346 ( 8659)
  covalent geometry    : angle       0.66009 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 1.479 
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: symmetry clash
REVERT: G   28 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8454 (tm-30)
REVERT: G   37 GLN cc_start: 0.9358 (tt0) cc_final: 0.8969 (tm-30)
REVERT: C  106 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.9021 (t70)
REVERT: I   54 GLN cc_start: 0.9212 (tp40) cc_final: 0.8244 (tt0)
REVERT: I   55 ASP cc_start: 0.9255 (m-30) cc_final: 0.8901 (t0)
REVERT: I   56 ASP cc_start: 0.9015 (m-30) cc_final: 0.7686 (p0)
REVERT: I  106 ASP cc_start: 0.8332 (t0) cc_final: 0.8086 (t0)
REVERT: H    5 GLU cc_start: 0.9114 (pt0) cc_final: 0.8663 (tm-30)
REVERT: H   42 GLU cc_start: 0.9097 (tp30) cc_final: 0.8794 (tp30)
REVERT: H   61 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9016 (t)
REVERT: D   39 GLU cc_start: 0.8908 (tt0) cc_final: 0.8683 (tt0)
REVERT: E  120 ASN cc_start: 0.9313 (t0) cc_final: 0.9074 (p0)
  outliers start: 12
  outliers final: 5
  residues processed: 159
  average time/residue: 0.3584
  time to fit residues: 83.7239
Evaluate side-chains
  129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain I residue  104 GLN
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   86 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 99 optimal weight:    0.0570
   chunk 70 optimal weight:    4.9990
   chunk 37 optimal weight:    0.1980
   chunk 102 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.4504

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

Flipped N/Q/H residues before XYZ refinement:
C  78 ASN
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 GLN
** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.066958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.053997 restraints weight = 116035.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.056459 restraints weight = 52271.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.058191 restraints weight = 31267.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8659  Z= 0.169
  Angle     :  0.610   5.921  11767  Z= 0.337
  Chirality :  0.041   0.147   1432
  Planarity :  0.004   0.055   1511
  Dihedral  :  5.779  23.556   1171
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 17.62 %
    Favored  : 81.63 %
  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: -0.42 (0.24), residues: 1098
  helix: -0.01 (0.26), residues: 404
  sheet:  0.40 (0.36), residues: 174
  loop : -0.62 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I 131 
 HIS   0.004   0.001   HIS E 103 
 PHE   0.008   0.001   PHE H  27 
 TYR   0.008   0.001   TYR G 129 
 ARG   0.001   0.000   ARG D  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05908 (  347)
  hydrogen bonds       : angle       5.15234 (  942)
  covalent geometry    : bond        0.00365 ( 8659)
  covalent geometry    : angle       0.61047 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 1.956 
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: G   28 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: G   37 GLN cc_start: 0.9350 (tt0) cc_final: 0.9069 (tm-30)
REVERT: I   42 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7664 (tm-30)
REVERT: I   44 VAL cc_start: 0.9056 (t) cc_final: 0.8831 (t)
REVERT: I   54 GLN cc_start: 0.9250 (tp40) cc_final: 0.8050 (tt0)
REVERT: I   55 ASP cc_start: 0.9163 (m-30) cc_final: 0.8848 (t0)
REVERT: I   56 ASP cc_start: 0.8931 (m-30) cc_final: 0.7502 (p0)
REVERT: I  106 ASP cc_start: 0.8205 (t0) cc_final: 0.7960 (t0)
REVERT: H    5 GLU cc_start: 0.9150 (pt0) cc_final: 0.8670 (tm-30)
REVERT: H   61 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.9009 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 126
  average time/residue: 0.4316
  time to fit residues: 79.4004
Evaluate side-chains
  121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   65 LEU
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain I residue   90 LYS
Chi-restraints excluded: chain H residue   61 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9980
   chunk 69 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** F  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 ASN
A  54 GLN
I 104 GLN
H  37 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.068107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.055094 restraints weight = 114543.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.057598 restraints weight = 51455.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.059402 restraints weight = 30707.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8659  Z= 0.109
  Angle     :  0.562   5.797  11767  Z= 0.301
  Chirality :  0.040   0.145   1432
  Planarity :  0.004   0.048   1511
  Dihedral  :  5.181  20.540   1171
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 18.15 %
    Favored  : 80.68 %
  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:  0.08 (0.24), residues: 1098
  helix:  0.62 (0.26), residues: 403
  sheet:  0.68 (0.36), residues: 174
  loop : -0.55 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 131 
 HIS   0.003   0.001   HIS B 110 
 PHE   0.007   0.001   PHE H  27 
 TYR   0.007   0.001   TYR E  50 
 ARG   0.001   0.000   ARG H  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04657 (  347)
  hydrogen bonds       : angle       4.54854 (  942)
  covalent geometry    : bond        0.00245 ( 8659)
  covalent geometry    : angle       0.56186 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 3.429 
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: G   28 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: G   29 ASP cc_start: 0.8610 (p0) cc_final: 0.8365 (p0)
REVERT: G   37 GLN cc_start: 0.9322 (tt0) cc_final: 0.9020 (tm-30)
REVERT: G  111 LYS cc_start: 0.8866 (tttt) cc_final: 0.8475 (ttmt)
REVERT: F   80 ASP cc_start: 0.7583 (p0) cc_final: 0.7371 (p0)
REVERT: I    6 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9310 (mm)
REVERT: I   44 VAL cc_start: 0.8984 (t) cc_final: 0.8744 (t)
REVERT: I   56 ASP cc_start: 0.8882 (m-30) cc_final: 0.7743 (p0)
REVERT: I   59 ASN cc_start: 0.9354 (t0) cc_final: 0.9036 (t0)
REVERT: I  106 ASP cc_start: 0.8199 (t0) cc_final: 0.7931 (t0)
REVERT: H    5 GLU cc_start: 0.9134 (pt0) cc_final: 0.8714 (tt0)
REVERT: H   42 GLU cc_start: 0.9094 (tp30) cc_final: 0.8823 (tt0)
REVERT: E  120 ASN cc_start: 0.9373 (t0) cc_final: 0.9028 (p0)
  outliers start: 11
  outliers final: 3
  residues processed: 142
  average time/residue: 0.4621
  time to fit residues: 97.9074
Evaluate side-chains
  127 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 1.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   65 LEU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain I residue    6 LEU
Chi-restraints excluded: chain H residue  107 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0270
   chunk 48 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0040
   chunk 32 optimal weight:   10.0000
   overall best weight:    2.2056

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

Flipped N/Q/H residues before XYZ refinement:
** F  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN
H  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.067160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.054520 restraints weight = 114982.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.056890 restraints weight = 55035.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.058529 restraints weight = 33914.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.4259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8659  Z= 0.155
  Angle     :  0.568   5.666  11767  Z= 0.310
  Chirality :  0.040   0.145   1432
  Planarity :  0.004   0.042   1511
  Dihedral  :  5.068  20.421   1171
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.15 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.24), residues: 1098
  helix:  0.82 (0.26), residues: 398
  sheet:  0.65 (0.35), residues: 174
  loop : -0.60 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F 131 
 HIS   0.004   0.001   HIS E 103 
 PHE   0.006   0.001   PHE C  27 
 TYR   0.009   0.001   TYR G 129 
 ARG   0.002   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04747 (  347)
  hydrogen bonds       : angle       4.63594 (  942)
  covalent geometry    : bond        0.00348 ( 8659)
  covalent geometry    : angle       0.56829 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 1.520 
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: G   28 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: G   29 ASP cc_start: 0.8591 (p0) cc_final: 0.8322 (p0)
REVERT: G   37 GLN cc_start: 0.9312 (tt0) cc_final: 0.9084 (tm-30)
REVERT: G  111 LYS cc_start: 0.8963 (tttt) cc_final: 0.8610 (ttmt)
REVERT: I   42 GLU cc_start: 0.8441 (tt0) cc_final: 0.8052 (tm-30)
REVERT: I   56 ASP cc_start: 0.8734 (m-30) cc_final: 0.7603 (p0)
REVERT: I  106 ASP cc_start: 0.8149 (t0) cc_final: 0.7938 (t0)
REVERT: H    5 GLU cc_start: 0.9120 (pt0) cc_final: 0.8702 (tt0)
REVERT: H   39 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8293 (tt0)
REVERT: H   42 GLU cc_start: 0.8995 (tp30) cc_final: 0.8781 (tt0)
REVERT: E  120 ASN cc_start: 0.9339 (t0) cc_final: 0.9065 (p0)
  outliers start: 12
  outliers final: 7
  residues processed: 129
  average time/residue: 0.3688
  time to fit residues: 69.9929
Evaluate side-chains
  123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain B residue    5 GLU
Chi-restraints excluded: chain I residue   90 LYS
Chi-restraints excluded: chain H residue   39 GLU
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  107 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** F  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN
H  37 GLN
** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.066343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.053888 restraints weight = 114286.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.056246 restraints weight = 54797.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.057846 restraints weight = 33683.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.4576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8659  Z= 0.164
  Angle     :  0.566   5.155  11767  Z= 0.308
  Chirality :  0.040   0.145   1432
  Planarity :  0.004   0.041   1511
  Dihedral  :  4.965  20.113   1171
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 18.58 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.24), residues: 1098
  helix:  0.84 (0.26), residues: 405
  sheet:  0.65 (0.36), residues: 175
  loop : -0.63 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 131 
 HIS   0.005   0.001   HIS E 103 
 PHE   0.007   0.001   PHE C  27 
 TYR   0.009   0.001   TYR G 129 
 ARG   0.002   0.000   ARG E  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04675 (  347)
  hydrogen bonds       : angle       4.61743 (  942)
  covalent geometry    : bond        0.00362 ( 8659)
  covalent geometry    : angle       0.56571 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 1.461 
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: G   37 GLN cc_start: 0.9321 (tt0) cc_final: 0.9106 (tm-30)
REVERT: G  111 LYS cc_start: 0.9029 (tttt) cc_final: 0.8687 (ttmt)
REVERT: I   42 GLU cc_start: 0.8412 (tt0) cc_final: 0.8090 (tm-30)
REVERT: I   56 ASP cc_start: 0.8728 (m-30) cc_final: 0.7641 (p0)
REVERT: I   72 MET cc_start: 0.8961 (mmm) cc_final: 0.8711 (mmm)
REVERT: H    5 GLU cc_start: 0.9124 (pt0) cc_final: 0.8736 (tt0)
REVERT: H   28 GLN cc_start: 0.9127 (pt0) cc_final: 0.8647 (pm20)
REVERT: H   39 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8449 (tt0)
  outliers start: 11
  outliers final: 5
  residues processed: 123
  average time/residue: 0.3667
  time to fit residues: 66.2677
Evaluate side-chains
  116 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain B residue    5 GLU
Chi-restraints excluded: chain H residue   39 GLU
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain D residue  134 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 95 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 110 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
** F  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  30 ASN
I 134 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.065472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.053074 restraints weight = 115315.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.055395 restraints weight = 56050.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.056988 restraints weight = 34758.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8659  Z= 0.201
  Angle     :  0.592   6.579  11767  Z= 0.324
  Chirality :  0.041   0.147   1432
  Planarity :  0.004   0.039   1511
  Dihedral  :  5.016  20.260   1171
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 19.53 %
    Favored  : 79.41 %
  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:  0.07 (0.24), residues: 1098
  helix:  0.87 (0.26), residues: 405
  sheet:  0.60 (0.37), residues: 170
  loop : -0.76 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 131 
 HIS   0.005   0.001   HIS E 103 
 PHE   0.010   0.001   PHE F   1 
 TYR   0.010   0.001   TYR G 129 
 ARG   0.003   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04824 (  347)
  hydrogen bonds       : angle       4.76131 (  942)
  covalent geometry    : bond        0.00441 ( 8659)
  covalent geometry    : angle       0.59168 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   37 GLN cc_start: 0.9368 (tt0) cc_final: 0.9108 (tm-30)
REVERT: G  111 LYS cc_start: 0.8957 (tttt) cc_final: 0.8644 (ttmt)
REVERT: I   42 GLU cc_start: 0.8535 (tt0) cc_final: 0.8173 (tm-30)
REVERT: I   56 ASP cc_start: 0.8761 (m-30) cc_final: 0.7621 (p0)
REVERT: I   72 MET cc_start: 0.9018 (mmm) cc_final: 0.8752 (mmm)
REVERT: H    5 GLU cc_start: 0.9141 (pt0) cc_final: 0.8766 (tt0)
REVERT: H   28 GLN cc_start: 0.9163 (pt0) cc_final: 0.8645 (pm20)
REVERT: H   39 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8581 (tt0)
REVERT: H   42 GLU cc_start: 0.8974 (tp30) cc_final: 0.8742 (tt0)
  outliers start: 10
  outliers final: 8
  residues processed: 115
  average time/residue: 0.3517
  time to fit residues: 59.8024
Evaluate side-chains
  112 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   65 LEU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain B residue    5 GLU
Chi-restraints excluded: chain H residue   39 GLU
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue  134 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** F  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.065107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.052545 restraints weight = 115194.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.054882 restraints weight = 55601.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.056518 restraints weight = 34207.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.4971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8659  Z= 0.177
  Angle     :  0.578   6.578  11767  Z= 0.315
  Chirality :  0.040   0.145   1432
  Planarity :  0.004   0.041   1511
  Dihedral  :  4.936  19.657   1171
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 19.43 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.13 (0.24), residues: 1098
  helix:  0.95 (0.26), residues: 405
  sheet:  0.64 (0.38), residues: 170
  loop : -0.77 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 131 
 HIS   0.005   0.001   HIS E 103 
 PHE   0.008   0.001   PHE C  27 
 TYR   0.008   0.001   TYR G 129 
 ARG   0.001   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04684 (  347)
  hydrogen bonds       : angle       4.71010 (  942)
  covalent geometry    : bond        0.00389 ( 8659)
  covalent geometry    : angle       0.57803 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   37 GLN cc_start: 0.9367 (tt0) cc_final: 0.9107 (tm-30)
REVERT: G  111 LYS cc_start: 0.8932 (tttt) cc_final: 0.8631 (ttmt)
REVERT: I   42 GLU cc_start: 0.8515 (tt0) cc_final: 0.8157 (tm-30)
REVERT: I   56 ASP cc_start: 0.8737 (m-30) cc_final: 0.7604 (p0)
REVERT: I   59 ASN cc_start: 0.9354 (t0) cc_final: 0.9107 (t0)
REVERT: I   72 MET cc_start: 0.8992 (mmm) cc_final: 0.8736 (mmm)
REVERT: H    5 GLU cc_start: 0.9156 (pt0) cc_final: 0.8775 (tt0)
REVERT: H   28 GLN cc_start: 0.9148 (pt0) cc_final: 0.8622 (pm20)
REVERT: H   39 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8511 (tt0)
  outliers start: 14
  outliers final: 12
  residues processed: 118
  average time/residue: 0.3630
  time to fit residues: 62.8401
Evaluate side-chains
  115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    9 VAL
Chi-restraints excluded: chain F residue   65 LEU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain B residue    5 GLU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain I residue   67 LYS
Chi-restraints excluded: chain H residue   39 GLU
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue  134 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0870
   chunk 103 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
** F  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.065307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.052801 restraints weight = 115024.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.055142 restraints weight = 55004.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.056806 restraints weight = 33756.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.5115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8659  Z= 0.140
  Angle     :  0.568   6.519  11767  Z= 0.306
  Chirality :  0.040   0.144   1432
  Planarity :  0.003   0.041   1511
  Dihedral  :  4.761  18.965   1171
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 19.96 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.25), residues: 1098
  helix:  1.17 (0.27), residues: 405
  sheet:  0.70 (0.38), residues: 165
  loop : -0.71 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 131 
 HIS   0.003   0.001   HIS B 110 
 PHE   0.008   0.001   PHE F   1 
 TYR   0.007   0.001   TYR B  50 
 ARG   0.001   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  347)
  hydrogen bonds       : angle       4.47134 (  942)
  covalent geometry    : bond        0.00317 ( 8659)
  covalent geometry    : angle       0.56841 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 1.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   37 GLN cc_start: 0.9373 (tt0) cc_final: 0.9113 (tm-30)
REVERT: G  111 LYS cc_start: 0.8912 (tttt) cc_final: 0.8611 (ttmt)
REVERT: F   15 ILE cc_start: 0.9093 (pt) cc_final: 0.8884 (tp)
REVERT: I   42 GLU cc_start: 0.8516 (tt0) cc_final: 0.8148 (tm-30)
REVERT: I   56 ASP cc_start: 0.8762 (m-30) cc_final: 0.7592 (p0)
REVERT: I   59 ASN cc_start: 0.9365 (t0) cc_final: 0.9113 (t0)
REVERT: I   72 MET cc_start: 0.8945 (mmm) cc_final: 0.8715 (mmm)
REVERT: H    5 GLU cc_start: 0.9142 (pt0) cc_final: 0.8758 (tt0)
REVERT: H   28 GLN cc_start: 0.9139 (pt0) cc_final: 0.8620 (pm20)
REVERT: H   39 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8415 (tt0)
  outliers start: 13
  outliers final: 10
  residues processed: 115
  average time/residue: 0.3514
  time to fit residues: 60.3603
Evaluate side-chains
  110 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    9 VAL
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   65 LEU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain H residue   39 GLU
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue  134 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0050
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    0.4980
   chunk 102 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
F  78 ASN
A  75 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.066519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.054081 restraints weight = 114706.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.056487 restraints weight = 54368.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.058135 restraints weight = 33195.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.5283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8659  Z= 0.109
  Angle     :  0.563   6.489  11767  Z= 0.298
  Chirality :  0.040   0.139   1432
  Planarity :  0.003   0.038   1511
  Dihedral  :  4.474  18.698   1171
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 20.91 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1098
  helix:  1.50 (0.27), residues: 411
  sheet:  0.90 (0.38), residues: 165
  loop : -0.67 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 131 
 HIS   0.004   0.001   HIS D  40 
 PHE   0.004   0.001   PHE C  27 
 TYR   0.008   0.001   TYR D 129 
 ARG   0.002   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  347)
  hydrogen bonds       : angle       4.11451 (  942)
  covalent geometry    : bond        0.00254 ( 8659)
  covalent geometry    : angle       0.56282 (11767)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   37 GLN cc_start: 0.9344 (tt0) cc_final: 0.9095 (tm-30)
REVERT: G   42 GLU cc_start: 0.9069 (tt0) cc_final: 0.8261 (tm-30)
REVERT: G  111 LYS cc_start: 0.8903 (tttt) cc_final: 0.8591 (ttmt)
REVERT: F   15 ILE cc_start: 0.9110 (pt) cc_final: 0.8908 (tp)
REVERT: A   75 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8501 (p0)
REVERT: I   42 GLU cc_start: 0.8469 (tt0) cc_final: 0.8069 (tm-30)
REVERT: I   56 ASP cc_start: 0.8746 (m-30) cc_final: 0.7587 (p0)
REVERT: I   59 ASN cc_start: 0.9338 (t0) cc_final: 0.9114 (t0)
REVERT: I   72 MET cc_start: 0.8885 (mmm) cc_final: 0.8685 (mmm)
REVERT: H    5 GLU cc_start: 0.9123 (pt0) cc_final: 0.8749 (tt0)
REVERT: H   28 GLN cc_start: 0.9062 (pt0) cc_final: 0.8517 (pm20)
REVERT: H   39 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8334 (tt0)
  outliers start: 9
  outliers final: 5
  residues processed: 123
  average time/residue: 0.3730
  time to fit residues: 69.1412
Evaluate side-chains
  114 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain I residue    6 LEU
Chi-restraints excluded: chain H residue   39 GLU
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0000
   chunk 56 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.066414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.053936 restraints weight = 115105.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.056338 restraints weight = 54653.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.057994 restraints weight = 33445.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.5298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.179   8659  Z= 0.184
  Angle     :  0.887  59.193  11767  Z= 0.530
  Chirality :  0.046   0.895   1432
  Planarity :  0.003   0.038   1511
  Dihedral  :  4.522  21.674   1171
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.83 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 20.49 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.09 %
  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:  0.60 (0.25), residues: 1098
  helix:  1.51 (0.27), residues: 411
  sheet:  0.92 (0.37), residues: 165
  loop : -0.67 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 131 
 HIS   0.004   0.001   HIS D  40 
 PHE   0.004   0.000   PHE C  27 
 TYR   0.007   0.001   TYR D 129 
 ARG   0.001   0.000   ARG D  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  347)
  hydrogen bonds       : angle       4.11524 (  942)
  covalent geometry    : bond        0.00382 ( 8659)
  covalent geometry    : angle       0.88720 (11767)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4991.67 seconds
wall clock time: 88 minutes 5.03 seconds (5285.03 seconds total)