Starting phenix.real_space_refine
on Fri Aug 22 21:04:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ouw_70883/08_2025/9ouw_70883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ouw_70883/08_2025/9ouw_70883.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ouw_70883/08_2025/9ouw_70883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ouw_70883/08_2025/9ouw_70883.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ouw_70883/08_2025/9ouw_70883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ouw_70883/08_2025/9ouw_70883.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.044
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: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    4938      2.51       5
     N    1278      2.21       5
     O    1442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7706
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1100
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 135, 1100
          Classifications: {'peptide': 135}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 130}
    Chain: "B"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 160, 1290
          Classifications: {'peptide': 160}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 154}
    Chain: "H"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 173
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 21}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 160, 1290
          Classifications: {'peptide': 160}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 154}
    Chain: "F"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 160, 1290
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 4, 'TRANS': 155}
    Chain: "I"
      Number of atoms: 1100
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 135, 1100
          Classifications: {'peptide': 135}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 130}
    Chain: "J"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 160, 1290
          Classifications: {'peptide': 160}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 154}
    Chain: "L"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 173
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 21}
          Chain breaks: 1
  Time building chain proxies: 2.00, per 1000 atoms: 0.26
  Number of scatterers: 7706
  At special positions: 0
  Unit cell: (90.902, 140.581, 58.135, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1442      8.00
     N    1278      7.00
     C    4938      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 517.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1804

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 10 sheets defined
      8.7% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 138 through 144
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.726A  pdb=" N   ASP A 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.753A  pdb=" N   LYS B  81 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 144
    Processing helix  chain 'B' and resid 150 through 154
      removed outlier: 3.564A  pdb=" N   ASP B 153 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 81
      removed outlier: 3.940A  pdb=" N   LYS D  81 " --> pdb=" O   GLU D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 144
    Processing helix  chain 'D' and resid 150 through 154
      removed outlier: 3.561A  pdb=" N   ASP D 153 " --> pdb=" O   LEU D 150 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 81
      removed outlier: 3.700A  pdb=" N   LYS F  81 " --> pdb=" O   GLU F  78 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 144
    Processing helix  chain 'F' and resid 150 through 154
      removed outlier: 3.733A  pdb=" N   ASP F 153 " --> pdb=" O   LEU F 150 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 138 through 144
      removed outlier: 3.567A  pdb=" N   ASP I 144 " --> pdb=" O   ASP I 140 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 150 through 154
      removed outlier: 3.734A  pdb=" N   ASP I 153 " --> pdb=" O   LEU I 150 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 139 through 144
    Processing helix  chain 'J' and resid 150 through 154
      removed outlier: 3.657A  pdb=" N   ASP J 153 " --> pdb=" O   LEU J 150 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 34 through 38
    current: chain 'A' and resid 113 through 118
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 113 through 118
    current: chain 'B' and resid 113 through 118
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 113 through 118
    current: chain 'F' and resid 168 through 169
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53
      removed outlier: 6.520A  pdb=" N   LYS A  66 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER A  85 " --> pdb=" O   ASN A  72 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 53
      removed outlier: 3.623A  pdb=" N   VAL B  71 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   LYS B  66 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER B  85 " --> pdb=" O   ASN B  72 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 137 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   LEU B  86 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LYS B 135 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   LEU B  88 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   PHE B 133 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   LEU B  90 " --> pdb=" O   TRP B 131 " (cutoff:3.500A)
      removed outlier: 8.898A  pdb=" N   TRP B 131 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   SER B  92 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 9.226A  pdb=" N   LYS B 129 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 26
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 168 through 169
    current: chain 'D' and resid 113 through 118
    Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 26
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 168 through 169
    current: chain 'I' and resid 113 through 118
  WARNING: can't find start of bonding for strands!
    previous: chain 'I' and resid 113 through 118
    current: chain 'J' and resid 113 through 118
    Processing sheet with id=AA6, first strand: chain 'D' and resid 52 through 53
      removed outlier: 6.637A  pdb=" N   LYS D  66 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   LEU D  84 " --> pdb=" O   LYS D 135 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   LYS D 135 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU D  88 " --> pdb=" O   TRP D 131 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LYS D 129 " --> pdb=" O   LEU D  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 29 through 39
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 29 through 39
    current: chain 'F' and resid 113 through 118
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 113 through 118
    current: chain 'L' and resid 168 through 169
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'F' and resid 52 through 53
      removed outlier: 6.480A  pdb=" N   LYS F  66 " --> pdb=" O   VAL F  91 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE F 137 " --> pdb=" O   LEU F  84 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   LEU F  86 " --> pdb=" O   LYS F 135 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   LYS F 135 " --> pdb=" O   LEU F  86 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   LEU F  88 " --> pdb=" O   PHE F 133 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   PHE F 133 " --> pdb=" O   LEU F  88 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   LEU F  90 " --> pdb=" O   TRP F 131 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   TRP F 131 " --> pdb=" O   LEU F  90 " (cutoff:3.500A)
      removed outlier: 8.527A  pdb=" N   SER F  92 " --> pdb=" O   LYS F 129 " (cutoff:3.500A)
      removed outlier: 9.215A  pdb=" N   LYS F 129 " --> pdb=" O   SER F  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 66 through 71
      removed outlier: 6.634A  pdb=" N   LYS I  66 " --> pdb=" O   VAL I  91 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS I 129 " --> pdb=" O   LEU I  90 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53
      removed outlier: 3.690A  pdb=" N   VAL J  71 " --> pdb=" O   ILE J  52 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LYS J  66 " --> pdb=" O   VAL J  91 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER J  85 " --> pdb=" O   ASN J  72 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU J  84 " --> pdb=" O   LYS J 135 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LYS J 135 " --> pdb=" O   LEU J  84 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU J  90 " --> pdb=" O   LYS J 129 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LYS J 129 " --> pdb=" O   LEU J  90 " (cutoff:3.500A)

    90 hydrogen bonds defined for protein.
    219 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: 0.95

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2428
        1.34 -     1.46: 1911
        1.46 -     1.58: 3458
        1.58 -     1.70: 1
        1.70 -     1.82: 66
  Bond restraints: 7864
  Sorted by residual:
  bond pdb=" CB  ARG I  45 "
       pdb=" CG  ARG I  45 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.064 3.00e-02 1.11e+03 4.51e+00
  bond pdb=" CA  ARG I  45 "
       pdb=" C   ARG I  45 "
    ideal  model  delta    sigma   weight residual
    1.523  1.546 -0.023 1.34e-02 5.57e+03 2.84e+00
  bond pdb=" CB  ASP F 144 "
       pdb=" CG  ASP F 144 "
    ideal  model  delta    sigma   weight residual
    1.516  1.557 -0.041 2.50e-02 1.60e+03 2.66e+00
  bond pdb=" CB  ASP B 140 "
       pdb=" CG  ASP B 140 "
    ideal  model  delta    sigma   weight residual
    1.516  1.555 -0.039 2.50e-02 1.60e+03 2.49e+00
  bond pdb=" CB  ASP D  77 "
       pdb=" CG  ASP D  77 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.24e+00
  ... (remaining 7859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 10441
        3.24 -     6.48: 110
        6.48 -     9.72: 14
        9.72 -    12.96: 1
       12.96 -    16.20: 2
  Bond angle restraints: 10568
  Sorted by residual:
  angle pdb=" CA  ARG I  45 "
        pdb=" CB  ARG I  45 "
        pdb=" CG  ARG I  45 "
      ideal   model   delta    sigma   weight residual
     114.10  128.80  -14.70 2.00e+00 2.50e-01 5.40e+01
  angle pdb=" CB  MET I  48 "
        pdb=" CG  MET I  48 "
        pdb=" SD  MET I  48 "
      ideal   model   delta    sigma   weight residual
     112.70  128.90  -16.20 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" N   ARG A  45 "
        pdb=" CA  ARG A  45 "
        pdb=" CB  ARG A  45 "
      ideal   model   delta    sigma   weight residual
     114.17  108.13    6.04 1.14e+00 7.69e-01 2.80e+01
  angle pdb=" CB  ARG I  45 "
        pdb=" CG  ARG I  45 "
        pdb=" CD  ARG I  45 "
      ideal   model   delta    sigma   weight residual
     111.30  121.14   -9.84 2.30e+00 1.89e-01 1.83e+01
  angle pdb=" CA  ARG A  45 "
        pdb=" CB  ARG A  45 "
        pdb=" CG  ARG A  45 "
      ideal   model   delta    sigma   weight residual
     114.10  122.41   -8.31 2.00e+00 2.50e-01 1.73e+01
  ... (remaining 10563 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4057
       17.97 -    35.95: 544
       35.95 -    53.92: 105
       53.92 -    71.90: 13
       71.90 -    89.87: 7
  Dihedral angle restraints: 4726
    sinusoidal: 1946
      harmonic: 2780
  Sorted by residual:
  dihedral pdb=" CA  CYS B  44 "
           pdb=" C   CYS B  44 "
           pdb=" N   ARG B  45 "
           pdb=" CA  ARG B  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.35   20.65     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  CYS A  44 "
           pdb=" C   CYS A  44 "
           pdb=" N   ARG A  45 "
           pdb=" CA  ARG A  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.92   18.08     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  CYS J  44 "
           pdb=" C   CYS J  44 "
           pdb=" N   ARG J  45 "
           pdb=" CA  ARG J  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.05   17.95     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 4723 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 773
       0.039 -    0.078: 230
       0.078 -    0.117: 107
       0.117 -    0.156: 24
       0.156 -    0.194: 2
  Chirality restraints: 1136
  Sorted by residual:
  chirality pdb=" CB  ILE B  52 "
            pdb=" CA  ILE B  52 "
            pdb=" CG1 ILE B  52 "
            pdb=" CG2 ILE B  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.45e-01
  chirality pdb=" CA  VAL I 126 "
            pdb=" N   VAL I 126 "
            pdb=" C   VAL I 126 "
            pdb=" CB  VAL I 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.27e-01
  chirality pdb=" CA  VAL J 126 "
            pdb=" N   VAL J 126 "
            pdb=" C   VAL J 126 "
            pdb=" CB  VAL J 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 1133 not shown)

  Planarity restraints: 1332
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  22 "   -0.020 2.00e-02 2.50e+03   2.28e-02 1.30e+01
        pdb=" CG  TRP D  22 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  22 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  22 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  22 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  22 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  22 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  22 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  22 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  22 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG I  45 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.06e+01
        pdb=" C   ARG I  45 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ARG I  45 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU I  46 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP J 130 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.78e+00
        pdb=" CG  ASP J 130 "   -0.042 2.00e-02 2.50e+03
        pdb=" OD1 ASP J 130 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP J 130 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1329 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1307
        2.77 -     3.30: 7277
        3.30 -     3.84: 12777
        3.84 -     4.37: 15139
        4.37 -     4.90: 25879
  Nonbonded interactions: 62379
  Sorted by model distance:
  nonbonded pdb=" O   ASP A  77 "
            pdb=" OG  SER A  80 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NZ  LYS J 129 "
            pdb=" O   ASP J 130 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG1 THR B  25 "
            pdb=" OD1 ASN B 169 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   VAL I  91 "
            pdb=" NE2 GLN I 127 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OD1 ASP B  77 "
            pdb=" N   GLU B  78 "
     model   vdw
     2.278 3.120
  ... (remaining 62374 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'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.500
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
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   0.064   7864  Z= 0.183
  Angle     :  0.862  16.198  10568  Z= 0.478
  Chirality :  0.047   0.194   1136
  Planarity :  0.004   0.043   1332
  Dihedral  : 16.355  89.873   2922
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.95 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.77 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.26), residues: 936
  helix: -2.27 (0.66), residues: 42
  sheet: -0.14 (0.30), residues: 350
  loop : -1.71 (0.22), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 138 
 TYR   0.025   0.002   TYR A  83 
 PHE   0.031   0.002   PHE J 141 
 TRP   0.061   0.003   TRP D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7864)
  covalent geometry    : angle       0.86181 (10568)
  hydrogen bonds       : bond        0.21798 (   90)
  hydrogen bonds       : angle       8.82214 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8075 (tmm) cc_final: 0.7823 (tmm)
REVERT: A   99 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7765 (mpt-90)
REVERT: H  174 ASN cc_start: 0.6902 (t0) cc_final: 0.6637 (t0)
REVERT: D   27 ILE cc_start: 0.7576 (mt) cc_final: 0.7324 (mt)
REVERT: D  123 TYR cc_start: 0.8281 (m-80) cc_final: 0.8046 (m-80)
REVERT: D  160 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6859 (mp0)
REVERT: F  138 ARG cc_start: 0.8535 (mmm160) cc_final: 0.8332 (mmm-85)
REVERT: I   35 MET cc_start: 0.8567 (ttp) cc_final: 0.8273 (ttt)
REVERT: I   82 ASP cc_start: 0.6342 (t0) cc_final: 0.5578 (t0)
REVERT: I  112 GLU cc_start: 0.8274 (mp0) cc_final: 0.7571 (pm20)
REVERT: I  117 MET cc_start: 0.6811 (ttm) cc_final: 0.6587 (ttm)
REVERT: I  118 GLU cc_start: 0.8068 (tp30) cc_final: 0.7850 (tm-30)
REVERT: I  140 ASP cc_start: 0.7974 (p0) cc_final: 0.7763 (p0)
REVERT: J  123 TYR cc_start: 0.7775 (m-80) cc_final: 0.7438 (m-80)
REVERT: J  126 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8566 (m)
  outliers start: 30
  outliers final: 25
  residues processed: 142
  average time/residue: 0.0984
  time to fit residues: 18.4087
Evaluate side-chains
  139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  175 THR
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  147 ASN
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  147 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 165 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.119034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.092770 restraints weight = 13934.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 3.77
r_work: 0.3416 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   7864  Z= 0.157
  Angle     :  0.569   7.323  10568  Z= 0.304
  Chirality :  0.043   0.145   1136
  Planarity :  0.003   0.018   1332
  Dihedral  :  6.958  58.552   1056
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.49 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 22.44 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.26), residues: 936
  helix: -1.57 (0.75), residues: 42
  sheet: -0.23 (0.30), residues: 350
  loop : -1.69 (0.22), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 138 
 TYR   0.009   0.001   TYR A  34 
 PHE   0.013   0.001   PHE D 158 
 TRP   0.028   0.002   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7864)
  covalent geometry    : angle       0.56885 (10568)
  hydrogen bonds       : bond        0.03182 (   90)
  hydrogen bonds       : angle       5.98863 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 117
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 ASP cc_start: 0.8248 (t0) cc_final: 0.7802 (t0)
REVERT: A   97 GLU cc_start: 0.6664 (tt0) cc_final: 0.6224 (tt0)
REVERT: A   99 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7752 (mpt-90)
REVERT: A  140 ASP cc_start: 0.8570 (p0) cc_final: 0.8299 (p0)
REVERT: B  135 LYS cc_start: 0.8941 (mttm) cc_final: 0.8647 (mmtt)
REVERT: D  123 TYR cc_start: 0.8401 (m-80) cc_final: 0.8113 (m-80)
REVERT: D  138 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8314 (mmm160)
REVERT: F   45 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6347 (mmt180)
REVERT: F   77 ASP cc_start: 0.7414 (p0) cc_final: 0.7208 (p0)
REVERT: I   35 MET cc_start: 0.8582 (ttp) cc_final: 0.8291 (ttt)
REVERT: I   82 ASP cc_start: 0.7069 (t0) cc_final: 0.6808 (t0)
REVERT: I   97 GLU cc_start: 0.7640 (tt0) cc_final: 0.7417 (tt0)
REVERT: I  117 MET cc_start: 0.6756 (ttm) cc_final: 0.6467 (ttm)
REVERT: I  118 GLU cc_start: 0.8049 (tp30) cc_final: 0.7817 (tm-30)
REVERT: I  138 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.7706 (mmm-85)
REVERT: J  123 TYR cc_start: 0.7858 (m-80) cc_final: 0.7534 (m-80)
REVERT: J  126 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8525 (m)
REVERT: J  138 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7711 (mmm-85)
REVERT: J  160 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7864 (tp30)
REVERT: L   28 LYS cc_start: 0.5291 (OUTLIER) cc_final: 0.4215 (pmtt)
  outliers start: 46
  outliers final: 31
  residues processed: 156
  average time/residue: 0.0946
  time to fit residues: 19.4077
Evaluate side-chains
  141 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   54 SER
Chi-restraints excluded: chain F residue  175 THR
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   50 GLU
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain I residue  159 CYS
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  137 ILE
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain J residue  160 GLU
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 79 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 165 GLN
L 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.119260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.092972 restraints weight = 13715.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 3.74
r_work: 0.3424 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7864  Z= 0.131
  Angle     :  0.524   7.276  10568  Z= 0.284
  Chirality :  0.042   0.146   1136
  Planarity :  0.002   0.022   1332
  Dihedral  :  6.389  59.901   1042
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.95 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.40 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.26), residues: 936
  helix: -1.11 (0.78), residues: 42
  sheet: -0.27 (0.30), residues: 350
  loop : -1.58 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 138 
 TYR   0.009   0.001   TYR A  34 
 PHE   0.012   0.001   PHE D 158 
 TRP   0.025   0.002   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7864)
  covalent geometry    : angle       0.52386 (10568)
  hydrogen bonds       : bond        0.02780 (   90)
  hydrogen bonds       : angle       5.42699 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 116
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 ASP cc_start: 0.8230 (t0) cc_final: 0.7945 (t0)
REVERT: B   83 TYR cc_start: 0.8296 (m-80) cc_final: 0.7461 (m-10)
REVERT: B  135 LYS cc_start: 0.9043 (mttm) cc_final: 0.8629 (mmtm)
REVERT: D  123 TYR cc_start: 0.8363 (m-80) cc_final: 0.8131 (m-80)
REVERT: F   45 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6113 (tpp80)
REVERT: F  123 TYR cc_start: 0.8590 (m-80) cc_final: 0.8351 (m-80)
REVERT: F  138 ARG cc_start: 0.8505 (mmt-90) cc_final: 0.8052 (mmm-85)
REVERT: F  153 ASP cc_start: 0.7557 (t0) cc_final: 0.7194 (t0)
REVERT: I   35 MET cc_start: 0.8590 (ttp) cc_final: 0.8288 (ttt)
REVERT: I   82 ASP cc_start: 0.7034 (t0) cc_final: 0.6593 (t0)
REVERT: I  112 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7436 (pm20)
REVERT: I  113 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: I  117 MET cc_start: 0.6857 (ttm) cc_final: 0.6436 (ttm)
REVERT: I  118 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7817 (tm-30)
REVERT: I  138 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.7656 (mmm-85)
REVERT: J   82 ASP cc_start: 0.8088 (p0) cc_final: 0.7814 (p0)
REVERT: J  123 TYR cc_start: 0.7808 (m-80) cc_final: 0.7496 (m-80)
REVERT: J  126 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8479 (m)
REVERT: J  160 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7865 (tp30)
REVERT: L   28 LYS cc_start: 0.5346 (OUTLIER) cc_final: 0.3984 (pmtt)
  outliers start: 44
  outliers final: 31
  residues processed: 152
  average time/residue: 0.1055
  time to fit residues: 20.9390
Evaluate side-chains
  142 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain I residue  159 CYS
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  137 ILE
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain J residue  160 GLU
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0970
   chunk 38 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 30 optimal weight:    0.1980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
J 165 GLN
L 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.119704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.093428 restraints weight = 13962.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 3.78
r_work: 0.3413 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7864  Z= 0.116
  Angle     :  0.516   8.330  10568  Z= 0.278
  Chirality :  0.042   0.131   1136
  Planarity :  0.002   0.021   1332
  Dihedral  :  6.151  59.659   1041
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.27 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 21.05 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.26), residues: 936
  helix: -0.84 (0.79), residues: 42
  sheet: -0.24 (0.30), residues: 350
  loop : -1.54 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 138 
 TYR   0.009   0.001   TYR I  83 
 PHE   0.012   0.001   PHE J 141 
 TRP   0.022   0.001   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7864)
  covalent geometry    : angle       0.51631 (10568)
  hydrogen bonds       : bond        0.02574 (   90)
  hydrogen bonds       : angle       5.12164 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 110
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8091 (tmm) cc_final: 0.7718 (tmm)
REVERT: A   82 ASP cc_start: 0.8259 (t0) cc_final: 0.7902 (t0)
REVERT: B   83 TYR cc_start: 0.8242 (m-80) cc_final: 0.7393 (m-10)
REVERT: B  135 LYS cc_start: 0.9084 (mttm) cc_final: 0.8654 (mmtt)
REVERT: H  174 ASN cc_start: 0.7045 (t0) cc_final: 0.6741 (t0)
REVERT: D  123 TYR cc_start: 0.8421 (m-80) cc_final: 0.8182 (m-80)
REVERT: F   45 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6139 (tpp80)
REVERT: F   82 ASP cc_start: 0.5716 (t70) cc_final: 0.5463 (t0)
REVERT: F  123 TYR cc_start: 0.8626 (m-80) cc_final: 0.8379 (m-80)
REVERT: F  140 ASP cc_start: 0.8757 (p0) cc_final: 0.8453 (p0)
REVERT: I   35 MET cc_start: 0.8582 (ttp) cc_final: 0.8252 (ttt)
REVERT: I   82 ASP cc_start: 0.7224 (t0) cc_final: 0.6191 (t0)
REVERT: I  112 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7461 (pm20)
REVERT: I  113 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7681 (mm-30)
REVERT: I  117 MET cc_start: 0.6789 (ttm) cc_final: 0.6380 (ttm)
REVERT: I  118 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7787 (tm-30)
REVERT: I  138 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.7554 (mmm-85)
REVERT: I  140 ASP cc_start: 0.8317 (p0) cc_final: 0.6648 (p0)
REVERT: J   82 ASP cc_start: 0.8107 (p0) cc_final: 0.7902 (p0)
REVERT: J  123 TYR cc_start: 0.7785 (m-80) cc_final: 0.7485 (m-80)
REVERT: J  126 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8457 (m)
REVERT: L   28 LYS cc_start: 0.5264 (OUTLIER) cc_final: 0.3967 (pmtt)
  outliers start: 47
  outliers final: 35
  residues processed: 149
  average time/residue: 0.0891
  time to fit residues: 17.6758
Evaluate side-chains
  144 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 104
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain I residue  159 CYS
Chi-restraints excluded: chain J residue   35 MET
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   85 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  137 ILE
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue  175 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0770
   chunk 73 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7944

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.116886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.090979 restraints weight = 14188.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 3.84
r_work: 0.3370 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3383
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3383
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7864  Z= 0.152
  Angle     :  0.536   7.717  10568  Z= 0.287
  Chirality :  0.042   0.133   1136
  Planarity :  0.003   0.025   1332
  Dihedral  :  6.321  59.886   1041
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.91 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 21.74 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.26), residues: 936
  helix: -0.49 (0.83), residues: 42
  sheet: -0.34 (0.30), residues: 350
  loop : -1.54 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 138 
 TYR   0.013   0.001   TYR D  83 
 PHE   0.014   0.001   PHE D  43 
 TRP   0.025   0.002   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7864)
  covalent geometry    : angle       0.53602 (10568)
  hydrogen bonds       : bond        0.02532 (   90)
  hydrogen bonds       : angle       5.18193 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 105
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8215 (tmm) cc_final: 0.7958 (tmm)
REVERT: A   82 ASP cc_start: 0.8323 (t0) cc_final: 0.7982 (t0)
REVERT: B   83 TYR cc_start: 0.8408 (m-80) cc_final: 0.7586 (m-10)
REVERT: B  135 LYS cc_start: 0.9079 (mttm) cc_final: 0.8580 (mmtt)
REVERT: H  174 ASN cc_start: 0.7134 (t0) cc_final: 0.6828 (t0)
REVERT: D   22 TRP cc_start: 0.6869 (p-90) cc_final: 0.6662 (p-90)
REVERT: D  123 TYR cc_start: 0.8460 (m-80) cc_final: 0.8208 (m-80)
REVERT: F   45 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5992 (tpp80)
REVERT: F   82 ASP cc_start: 0.6256 (t70) cc_final: 0.6046 (t0)
REVERT: F  123 TYR cc_start: 0.8680 (m-80) cc_final: 0.8451 (m-80)
REVERT: I   35 MET cc_start: 0.8673 (ttp) cc_final: 0.8325 (ttt)
REVERT: I   50 GLU cc_start: 0.7267 (pm20) cc_final: 0.7038 (pm20)
REVERT: I   82 ASP cc_start: 0.7191 (t0) cc_final: 0.6102 (t0)
REVERT: I  112 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7495 (pm20)
REVERT: I  113 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7645 (mm-30)
REVERT: I  117 MET cc_start: 0.6884 (ttm) cc_final: 0.6369 (ttm)
REVERT: I  118 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7708 (tm-30)
REVERT: I  119 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7070 (t)
REVERT: I  138 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7448 (mmm-85)
REVERT: I  140 ASP cc_start: 0.8326 (p0) cc_final: 0.7047 (p0)
REVERT: J  123 TYR cc_start: 0.7896 (m-80) cc_final: 0.7550 (m-80)
REVERT: J  126 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8437 (m)
REVERT: L   28 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.3597 (pmtt)
  outliers start: 45
  outliers final: 36
  residues processed: 143
  average time/residue: 0.0833
  time to fit residues: 16.0195
Evaluate side-chains
  145 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain I residue  159 CYS
Chi-restraints excluded: chain J residue   35 MET
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   85 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  137 ILE
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  175 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 73 optimal weight:    0.2980
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0870
   chunk 53 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0070
   chunk 69 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.118973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.092654 restraints weight = 14206.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 3.97
r_work: 0.3408 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3419
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7864  Z= 0.099
  Angle     :  0.510   9.175  10568  Z= 0.270
  Chirality :  0.042   0.137   1136
  Planarity :  0.002   0.026   1332
  Dihedral  :  5.854  58.938   1040
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.06 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 22.79 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.26), residues: 936
  helix: -0.56 (0.82), residues: 42
  sheet: -0.23 (0.30), residues: 350
  loop : -1.43 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 138 
 TYR   0.013   0.001   TYR D  83 
 PHE   0.012   0.001   PHE D  43 
 TRP   0.019   0.001   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 7864)
  covalent geometry    : angle       0.51017 (10568)
  hydrogen bonds       : bond        0.02377 (   90)
  hydrogen bonds       : angle       4.79924 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 ASP cc_start: 0.8362 (t0) cc_final: 0.8000 (t0)
REVERT: A  117 MET cc_start: 0.7764 (ppp) cc_final: 0.7147 (ppp)
REVERT: B   22 TRP cc_start: 0.8251 (OUTLIER) cc_final: 0.7995 (p-90)
REVERT: B   83 TYR cc_start: 0.8265 (m-80) cc_final: 0.7443 (m-10)
REVERT: B  135 LYS cc_start: 0.9099 (mttm) cc_final: 0.8570 (mmtt)
REVERT: H  174 ASN cc_start: 0.7259 (t0) cc_final: 0.6916 (t0)
REVERT: D  123 TYR cc_start: 0.8396 (m-80) cc_final: 0.8142 (m-80)
REVERT: F   45 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5662 (tpp80)
REVERT: F   77 ASP cc_start: 0.7466 (p0) cc_final: 0.5827 (p0)
REVERT: F  123 TYR cc_start: 0.8661 (m-80) cc_final: 0.8413 (m-80)
REVERT: F  153 ASP cc_start: 0.7290 (t0) cc_final: 0.6894 (t0)
REVERT: I   35 MET cc_start: 0.8614 (ttp) cc_final: 0.8279 (ttt)
REVERT: I   77 ASP cc_start: 0.7374 (p0) cc_final: 0.7013 (p0)
REVERT: I   82 ASP cc_start: 0.7156 (t0) cc_final: 0.5940 (t0)
REVERT: I  112 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7467 (pm20)
REVERT: I  117 MET cc_start: 0.6849 (ttm) cc_final: 0.6332 (ttm)
REVERT: I  118 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7677 (tm-30)
REVERT: I  119 SER cc_start: 0.7697 (OUTLIER) cc_final: 0.7008 (t)
REVERT: I  138 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.7474 (mmm-85)
REVERT: I  140 ASP cc_start: 0.8309 (p0) cc_final: 0.7005 (p0)
REVERT: J   82 ASP cc_start: 0.8230 (p0) cc_final: 0.7848 (p0)
REVERT: J  123 TYR cc_start: 0.7817 (m-80) cc_final: 0.7463 (m-80)
REVERT: J  138 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.8197 (mmm-85)
REVERT: L   28 LYS cc_start: 0.5140 (OUTLIER) cc_final: 0.3544 (pmtt)
  outliers start: 41
  outliers final: 33
  residues processed: 145
  average time/residue: 0.0879
  time to fit residues: 17.3476
Evaluate side-chains
  146 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   22 TRP
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   44 CYS
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   85 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.114333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.088326 restraints weight = 14223.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 3.76
r_work: 0.3333 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7864  Z= 0.231
  Angle     :  0.586   9.055  10568  Z= 0.312
  Chirality :  0.043   0.137   1136
  Planarity :  0.003   0.038   1332
  Dihedral  :  6.614  59.501   1039
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.56 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 23.26 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.26), residues: 936
  helix: -0.11 (0.87), residues: 42
  sheet: -0.55 (0.30), residues: 350
  loop : -1.58 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 124 
 TYR   0.014   0.002   TYR D  83 
 PHE   0.014   0.002   PHE D  43 
 TRP   0.027   0.002   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 7864)
  covalent geometry    : angle       0.58629 (10568)
  hydrogen bonds       : bond        0.02620 (   90)
  hydrogen bonds       : angle       5.35382 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 107
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 ASP cc_start: 0.8200 (t0) cc_final: 0.7866 (t0)
REVERT: B   22 TRP cc_start: 0.8303 (OUTLIER) cc_final: 0.8025 (p-90)
REVERT: B   83 TYR cc_start: 0.8426 (m-80) cc_final: 0.7721 (m-10)
REVERT: B  135 LYS cc_start: 0.9066 (mttm) cc_final: 0.8531 (mmtt)
REVERT: H  174 ASN cc_start: 0.7316 (t0) cc_final: 0.6974 (t0)
REVERT: D  123 TYR cc_start: 0.8578 (m-80) cc_final: 0.8356 (m-80)
REVERT: F   45 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5965 (tpp80)
REVERT: F  123 TYR cc_start: 0.8655 (m-80) cc_final: 0.8441 (m-80)
REVERT: I   35 MET cc_start: 0.8712 (ttp) cc_final: 0.8386 (ttt)
REVERT: I   77 ASP cc_start: 0.7626 (p0) cc_final: 0.7303 (p0)
REVERT: I   82 ASP cc_start: 0.7436 (t0) cc_final: 0.6708 (t0)
REVERT: I  112 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7522 (pm20)
REVERT: I  117 MET cc_start: 0.6939 (ttm) cc_final: 0.6557 (ttm)
REVERT: I  118 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7689 (tm-30)
REVERT: I  119 SER cc_start: 0.7739 (OUTLIER) cc_final: 0.6932 (t)
REVERT: J  123 TYR cc_start: 0.7925 (m-80) cc_final: 0.7620 (m-80)
REVERT: J  126 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8432 (m)
REVERT: L   28 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.3681 (pmtt)
  outliers start: 50
  outliers final: 38
  residues processed: 149
  average time/residue: 0.0780
  time to fit residues: 15.7864
Evaluate side-chains
  146 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 101
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   22 TRP
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   44 CYS
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  175 THR
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   84 LEU
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   85 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  114 THR
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  175 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0370
   chunk 22 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0010
   chunk 77 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.5064

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

Flipped N/Q/H residues before XYZ refinement:
B 169 ASN
** D  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 120 GLN
J 165 GLN
L 174 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.117590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.091271 restraints weight = 14224.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 3.88
r_work: 0.3378 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7864  Z= 0.120
  Angle     :  0.539   8.697  10568  Z= 0.290
  Chirality :  0.042   0.129   1136
  Planarity :  0.002   0.017   1332
  Dihedral  :  6.130  59.749   1039
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.70 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 22.56 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.27), residues: 936
  helix: -0.22 (0.86), residues: 42
  sheet: -0.47 (0.30), residues: 350
  loop : -1.52 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 138 
 TYR   0.014   0.001   TYR D  83 
 PHE   0.012   0.001   PHE J 141 
 TRP   0.024   0.002   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7864)
  covalent geometry    : angle       0.53948 (10568)
  hydrogen bonds       : bond        0.02435 (   90)
  hydrogen bonds       : angle       4.92379 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 109
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.7778 (tmm) cc_final: 0.7528 (tmm)
REVERT: A   82 ASP cc_start: 0.8330 (t0) cc_final: 0.8000 (t0)
REVERT: A  117 MET cc_start: 0.7742 (ppp) cc_final: 0.7332 (ppp)
REVERT: B   22 TRP cc_start: 0.8306 (OUTLIER) cc_final: 0.8016 (p-90)
REVERT: B   83 TYR cc_start: 0.8327 (m-80) cc_final: 0.7846 (m-80)
REVERT: B  135 LYS cc_start: 0.9070 (mttm) cc_final: 0.8571 (mttp)
REVERT: H  174 ASN cc_start: 0.7363 (t0) cc_final: 0.7017 (t0)
REVERT: F   45 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.5753 (tpp80)
REVERT: F  123 TYR cc_start: 0.8627 (m-80) cc_final: 0.8405 (m-80)
REVERT: I   35 MET cc_start: 0.8632 (ttp) cc_final: 0.8308 (ttt)
REVERT: I   50 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6537 (pm20)
REVERT: I   77 ASP cc_start: 0.7657 (p0) cc_final: 0.7294 (p0)
REVERT: I   82 ASP cc_start: 0.7695 (t0) cc_final: 0.7160 (t0)
REVERT: I   97 GLU cc_start: 0.7372 (tt0) cc_final: 0.6806 (tp30)
REVERT: I  112 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7580 (pm20)
REVERT: I  117 MET cc_start: 0.7082 (ttm) cc_final: 0.6525 (ttm)
REVERT: I  118 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7681 (tm-30)
REVERT: I  119 SER cc_start: 0.7629 (OUTLIER) cc_final: 0.6812 (t)
REVERT: I  138 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.7555 (mmm-85)
REVERT: J   82 ASP cc_start: 0.8205 (p0) cc_final: 0.6993 (p0)
REVERT: J  123 TYR cc_start: 0.7827 (m-80) cc_final: 0.7503 (m-80)
REVERT: J  126 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8472 (m)
REVERT: L   28 LYS cc_start: 0.5380 (OUTLIER) cc_final: 0.3629 (pmtt)
  outliers start: 54
  outliers final: 38
  residues processed: 152
  average time/residue: 0.0798
  time to fit residues: 16.2507
Evaluate side-chains
  150 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 104
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   22 TRP
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  112 GLU
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  175 THR
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   50 GLU
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   85 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  114 THR
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  137 ILE
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  175 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 92 optimal weight:    0.0060
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.117319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.091266 restraints weight = 14177.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 3.83
r_work: 0.3377 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7864  Z= 0.135
  Angle     :  0.564  10.525  10568  Z= 0.302
  Chirality :  0.042   0.129   1136
  Planarity :  0.003   0.084   1332
  Dihedral  :  5.760  53.620   1037
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.13 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 23.26 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.57 (0.27), residues: 936
  helix: -0.46 (0.84), residues: 42
  sheet: -0.49 (0.30), residues: 350
  loop : -1.48 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 138 
 TYR   0.013   0.001   TYR D  83 
 PHE   0.012   0.001   PHE D  43 
 TRP   0.023   0.002   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7864)
  covalent geometry    : angle       0.56401 (10568)
  hydrogen bonds       : bond        0.02488 (   90)
  hydrogen bonds       : angle       4.98512 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 108
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.7728 (tmm) cc_final: 0.7504 (tmm)
REVERT: A   82 ASP cc_start: 0.8228 (t0) cc_final: 0.7894 (t0)
REVERT: A   99 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7659 (mtt180)
REVERT: A  117 MET cc_start: 0.7754 (ppp) cc_final: 0.7340 (ppp)
REVERT: B   22 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.8025 (p-90)
REVERT: B   83 TYR cc_start: 0.8404 (m-80) cc_final: 0.7857 (m-10)
REVERT: B  135 LYS cc_start: 0.9082 (mttm) cc_final: 0.8457 (mmtm)
REVERT: H  174 ASN cc_start: 0.7380 (t0) cc_final: 0.7038 (t0)
REVERT: D  123 TYR cc_start: 0.8552 (m-80) cc_final: 0.8283 (m-80)
REVERT: F   45 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5661 (tpp80)
REVERT: F  123 TYR cc_start: 0.8616 (m-80) cc_final: 0.8396 (m-80)
REVERT: I   35 MET cc_start: 0.8629 (ttp) cc_final: 0.8310 (ttt)
REVERT: I   45 ARG cc_start: 0.8411 (tpt-90) cc_final: 0.8071 (tpt-90)
REVERT: I   46 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6915 (mm-30)
REVERT: I   50 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6454 (pm20)
REVERT: I   77 ASP cc_start: 0.7693 (p0) cc_final: 0.7307 (p0)
REVERT: I   82 ASP cc_start: 0.7851 (t0) cc_final: 0.7373 (t0)
REVERT: I   97 GLU cc_start: 0.7369 (tt0) cc_final: 0.6746 (tp30)
REVERT: I  112 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7547 (pm20)
REVERT: I  117 MET cc_start: 0.7078 (ttm) cc_final: 0.6557 (ttm)
REVERT: I  118 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7684 (tm-30)
REVERT: I  124 ARG cc_start: 0.8908 (ttt-90) cc_final: 0.7967 (ttt-90)
REVERT: I  138 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7633 (mmm-85)
REVERT: J   83 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7586 (m-80)
REVERT: J  123 TYR cc_start: 0.7810 (m-80) cc_final: 0.7515 (m-80)
REVERT: J  126 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8413 (m)
REVERT: L   28 LYS cc_start: 0.5450 (OUTLIER) cc_final: 0.3682 (pmtt)
  outliers start: 47
  outliers final: 36
  residues processed: 146
  average time/residue: 0.0829
  time to fit residues: 16.2135
Evaluate side-chains
  150 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 106
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   22 TRP
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  112 GLU
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  175 THR
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   50 GLU
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   83 TYR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   85 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  114 THR
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  175 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0010
   chunk 81 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 93 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0000
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.118028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.092364 restraints weight = 13965.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 3.80
r_work: 0.3402 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7864  Z= 0.117
  Angle     :  0.559   9.798  10568  Z= 0.301
  Chirality :  0.042   0.147   1136
  Planarity :  0.003   0.027   1332
  Dihedral  :  5.406  53.474   1035
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.17 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 23.60 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.27), residues: 936
  helix: -0.48 (0.82), residues: 42
  sheet: -0.45 (0.30), residues: 348
  loop : -1.38 (0.24), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 138 
 TYR   0.015   0.001   TYR D  83 
 PHE   0.021   0.001   PHE J 141 
 TRP   0.022   0.001   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7864)
  covalent geometry    : angle       0.55881 (10568)
  hydrogen bonds       : bond        0.02398 (   90)
  hydrogen bonds       : angle       4.87219 (  219)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 108
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 ASP cc_start: 0.8184 (t0) cc_final: 0.7829 (t0)
REVERT: A  117 MET cc_start: 0.7710 (ppp) cc_final: 0.7320 (ppp)
REVERT: B   22 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7907 (p-90)
REVERT: B   83 TYR cc_start: 0.8366 (m-80) cc_final: 0.7835 (m-10)
REVERT: B  135 LYS cc_start: 0.9066 (mttm) cc_final: 0.8475 (mmtm)
REVERT: H  174 ASN cc_start: 0.7349 (t0) cc_final: 0.7005 (t0)
REVERT: D  123 TYR cc_start: 0.8532 (m-80) cc_final: 0.8305 (m-80)
REVERT: D  124 ARG cc_start: 0.8338 (tmm-80) cc_final: 0.8011 (tmm-80)
REVERT: F   45 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.5633 (tpp80)
REVERT: F  123 TYR cc_start: 0.8595 (m-80) cc_final: 0.8388 (m-80)
REVERT: I   35 MET cc_start: 0.8603 (ttp) cc_final: 0.8294 (ttt)
REVERT: I   45 ARG cc_start: 0.8318 (tpt-90) cc_final: 0.8052 (tpt-90)
REVERT: I   46 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6826 (mm-30)
REVERT: I   50 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6281 (pm20)
REVERT: I   77 ASP cc_start: 0.7685 (p0) cc_final: 0.7251 (p0)
REVERT: I   97 GLU cc_start: 0.7272 (tt0) cc_final: 0.6726 (tp30)
REVERT: I  112 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7478 (pm20)
REVERT: I  117 MET cc_start: 0.7070 (ttm) cc_final: 0.6544 (ttm)
REVERT: I  118 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7762 (tm-30)
REVERT: J   84 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7277 (tm)
REVERT: J  123 TYR cc_start: 0.7754 (m-80) cc_final: 0.7513 (m-80)
REVERT: J  126 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8432 (m)
REVERT: L   28 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.3653 (pmtt)
  outliers start: 44
  outliers final: 35
  residues processed: 143
  average time/residue: 0.0860
  time to fit residues: 16.5134
Evaluate side-chains
  147 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 104
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   22 TRP
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain H residue  175 THR
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  112 GLU
Chi-restraints excluded: chain F residue   37 THR
Chi-restraints excluded: chain F residue   44 CYS
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  175 THR
Chi-restraints excluded: chain I residue   30 VAL
Chi-restraints excluded: chain I residue   50 GLU
Chi-restraints excluded: chain I residue   54 SER
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  156 THR
Chi-restraints excluded: chain J residue   48 MET
Chi-restraints excluded: chain J residue   54 SER
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   85 SER
Chi-restraints excluded: chain J residue   86 LEU
Chi-restraints excluded: chain J residue  114 THR
Chi-restraints excluded: chain J residue  126 VAL
Chi-restraints excluded: chain J residue  147 ASN
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   28 LYS
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  175 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0770
   chunk 65 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.118103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.092219 restraints weight = 14178.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 3.84
r_work: 0.3396 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3406
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7864  Z= 0.124
  Angle     :  0.580  12.091  10568  Z= 0.309
  Chirality :  0.042   0.165   1136
  Planarity :  0.003   0.027   1332
  Dihedral  :  5.408  53.750   1035
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.70 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 23.84 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.26), residues: 936
  helix: -0.32 (0.83), residues: 42
  sheet: -0.34 (0.31), residues: 322
  loop : -1.41 (0.23), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 138 
 TYR   0.015   0.001   TYR D  83 
 PHE   0.029   0.001   PHE I 141 
 TRP   0.022   0.001   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7864)
  covalent geometry    : angle       0.57953 (10568)
  hydrogen bonds       : bond        0.02393 (   90)
  hydrogen bonds       : angle       4.87450 (  219)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1790.38 seconds
wall clock time: 31 minutes 38.96 seconds (1898.96 seconds total)