Starting phenix.real_space_refine
on Fri Oct 23 08:15:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sed_54807/10_2026/9sed_54807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sed_54807/10_2026/9sed_54807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sed_54807/10_2026/9sed_54807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sed_54807/10_2026/9sed_54807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9sed_54807/10_2026/9sed_54807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sed_54807/10_2026/9sed_54807.cif"
  }
  resolution = 2.77
  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=   0.002 sd=   0.370
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      21      5.16       5
     C    6125      2.51       5
     N    1267      2.21       5
     O    1561      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8981
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1184
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "B"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1184
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "C"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1184
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "D"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1184
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "E"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1184
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "F"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1184
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "G"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1184
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "A"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 99
          Unusual residues: {'C14': 3, 'D12': 1, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "B"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 99
          Unusual residues: {'C14': 3, 'D12': 1, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "C"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 99
          Unusual residues: {'C14': 3, 'D12': 1, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "D"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 99
          Unusual residues: {'C14': 3, 'D12': 1, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "E"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 99
          Unusual residues: {'C14': 3, 'D12': 1, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "F"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 99
          Unusual residues: {'C14': 3, 'D12': 1, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "G"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 99
          Unusual residues: {'C14': 3, 'D12': 1, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
  Time building chain proxies: 2.01, per 1000 atoms: 0.22
  Number of scatterers: 8981
  At special positions: 0
  Unit cell: (85.08, 86.1435, 96.7785, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P       7     15.00
     O    1561      8.00
     N    1267      7.00
     C    6125      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: 0.92
  Conformation dependent library (CDL) restraints added in 339.0 milliseconds
  

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2002

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      65.6% alpha, 8.7% 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 7 through 41
      removed outlier: 4.354A  pdb=" N   PHE A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 72
    Processing helix  chain 'A' and resid 75 through 92
      removed outlier: 3.526A  pdb=" N   SER A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 109
      removed outlier: 4.081A  pdb=" N   TYR A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'B' and resid 7 through 41
      removed outlier: 4.354A  pdb=" N   PHE B  11 " --> pdb=" O   ASN B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 72
    Processing helix  chain 'B' and resid 75 through 92
      removed outlier: 3.526A  pdb=" N   SER B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 109
      removed outlier: 4.079A  pdb=" N   TYR B  97 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 153
    Processing helix  chain 'C' and resid 7 through 41
      removed outlier: 4.355A  pdb=" N   PHE C  11 " --> pdb=" O   ASN C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 72
    Processing helix  chain 'C' and resid 75 through 92
      removed outlier: 3.527A  pdb=" N   SER C  92 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 109
      removed outlier: 4.079A  pdb=" N   TYR C  97 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 153
    Processing helix  chain 'D' and resid 7 through 41
      removed outlier: 4.354A  pdb=" N   PHE D  11 " --> pdb=" O   ASN D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 72
    Processing helix  chain 'D' and resid 75 through 92
      removed outlier: 3.525A  pdb=" N   SER D  92 " --> pdb=" O   GLY D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 109
      removed outlier: 4.080A  pdb=" N   TYR D  97 " --> pdb=" O   LEU D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 153
    Processing helix  chain 'E' and resid 7 through 41
      removed outlier: 4.353A  pdb=" N   PHE E  11 " --> pdb=" O   ASN E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 72
    Processing helix  chain 'E' and resid 75 through 92
      removed outlier: 3.526A  pdb=" N   SER E  92 " --> pdb=" O   GLY E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 109
      removed outlier: 4.080A  pdb=" N   TYR E  97 " --> pdb=" O   LEU E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 153
    Processing helix  chain 'F' and resid 7 through 41
      removed outlier: 4.354A  pdb=" N   PHE F  11 " --> pdb=" O   ASN F   7 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 72
    Processing helix  chain 'F' and resid 75 through 92
      removed outlier: 3.526A  pdb=" N   SER F  92 " --> pdb=" O   GLY F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 109
      removed outlier: 4.079A  pdb=" N   TYR F  97 " --> pdb=" O   LEU F  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 149 through 153
    Processing helix  chain 'G' and resid 7 through 41
      removed outlier: 4.354A  pdb=" N   PHE G  11 " --> pdb=" O   ASN G   7 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 72
    Processing helix  chain 'G' and resid 75 through 92
      removed outlier: 3.526A  pdb=" N   SER G  92 " --> pdb=" O   GLY G  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 109
      removed outlier: 4.080A  pdb=" N   TYR G  97 " --> pdb=" O   LEU G  93 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 149 through 153
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120
      removed outlier: 3.718A  pdb=" N   SER B 129 " --> pdb=" O   LYS B 136 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130
      removed outlier: 3.718A  pdb=" N   SER A 129 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 120
      removed outlier: 3.719A  pdb=" N   SER C 129 " --> pdb=" O   LYS C 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 120
      removed outlier: 3.718A  pdb=" N   SER D 129 " --> pdb=" O   LYS D 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 118 through 120
      removed outlier: 3.718A  pdb=" N   SER E 129 " --> pdb=" O   LYS E 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 120
      removed outlier: 3.718A  pdb=" N   SER F 129 " --> pdb=" O   LYS F 136 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 118 through 120
      removed outlier: 3.718A  pdb=" N   SER G 129 " --> pdb=" O   LYS G 136 " (cutoff:3.500A)

    637 hydrogen bonds defined for protein.
    1884 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: 1.42

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1323
        1.32 -     1.44: 2133
        1.44 -     1.56: 5574
        1.56 -     1.69: 14
        1.69 -     1.81: 35
  Bond restraints: 9079
  Sorted by residual:
  bond pdb=" C38 PEE B 201 "
       pdb=" C39 PEE B 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.313  0.210 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" C38 PEE G 203 "
       pdb=" C39 PEE G 203 "
    ideal  model  delta    sigma   weight residual
    1.523  1.313  0.210 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" C38 PEE E 201 "
       pdb=" C39 PEE E 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.314  0.209 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" C38 PEE C 201 "
       pdb=" C39 PEE C 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.314  0.209 2.00e-02 2.50e+03 1.09e+02
  bond pdb=" C38 PEE A 201 "
       pdb=" C39 PEE A 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.314  0.209 2.00e-02 2.50e+03 1.09e+02
  ... (remaining 9074 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 12002
        2.97 -     5.95: 73
        5.95 -     8.92: 7
        8.92 -    11.90: 7
       11.90 -    14.87: 14
  Bond angle restraints: 12103
  Sorted by residual:
  angle pdb=" C38 PEE C 201 "
        pdb=" C39 PEE C 201 "
        pdb=" C40 PEE C 201 "
      ideal   model   delta    sigma   weight residual
     112.47  127.34  -14.87 3.00e+00 1.11e-01 2.46e+01
  angle pdb=" C38 PEE B 201 "
        pdb=" C39 PEE B 201 "
        pdb=" C40 PEE B 201 "
      ideal   model   delta    sigma   weight residual
     112.47  127.33  -14.86 3.00e+00 1.11e-01 2.45e+01
  angle pdb=" C38 PEE D 201 "
        pdb=" C39 PEE D 201 "
        pdb=" C40 PEE D 201 "
      ideal   model   delta    sigma   weight residual
     112.47  127.31  -14.84 3.00e+00 1.11e-01 2.45e+01
  angle pdb=" C38 PEE E 201 "
        pdb=" C39 PEE E 201 "
        pdb=" C40 PEE E 201 "
      ideal   model   delta    sigma   weight residual
     112.47  127.31  -14.84 3.00e+00 1.11e-01 2.45e+01
  angle pdb=" C38 PEE A 201 "
        pdb=" C39 PEE A 201 "
        pdb=" C40 PEE A 201 "
      ideal   model   delta    sigma   weight residual
     112.47  127.30  -14.83 3.00e+00 1.11e-01 2.44e+01
  ... (remaining 12098 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.37: 5327
       29.37 -    58.73: 98
       58.73 -    88.10: 28
       88.10 -   117.46: 0
      117.46 -   146.83: 14
  Dihedral angle restraints: 5467
    sinusoidal: 2331
      harmonic: 3136
  Sorted by residual:
  dihedral pdb=" C4  PEE E 201 "
           pdb=" O4P PEE E 201 "
           pdb=" P   PEE E 201 "
           pdb=" O3P PEE E 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.78  -41.39 -146.83     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" C4  PEE B 201 "
           pdb=" O4P PEE B 201 "
           pdb=" P   PEE B 201 "
           pdb=" O3P PEE B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.78  -41.42 -146.80     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" C4  PEE C 201 "
           pdb=" O4P PEE C 201 "
           pdb=" P   PEE C 201 "
           pdb=" O3P PEE C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.78  -41.43 -146.79     1      3.00e+01 1.11e-03 1.96e+01
  ... (remaining 5464 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1148
       0.047 -    0.094: 240
       0.094 -    0.141: 75
       0.141 -    0.188: 0
       0.188 -    0.234: 7
  Chirality restraints: 1470
  Sorted by residual:
  chirality pdb=" C2  PEE D 201 "
            pdb=" C1  PEE D 201 "
            pdb=" C3  PEE D 201 "
            pdb=" O2  PEE D 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.56    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C2  PEE F 202 "
            pdb=" C1  PEE F 202 "
            pdb=" C3  PEE F 202 "
            pdb=" O2  PEE F 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.56    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C2  PEE E 201 "
            pdb=" C1  PEE E 201 "
            pdb=" C3  PEE E 201 "
            pdb=" O2  PEE E 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.56    0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1467 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  56 "    0.007 2.00e-02 2.50e+03   4.78e-03 4.58e-01
        pdb=" CG  TYR E  56 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  56 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  56 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  56 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E  56 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  56 "    0.007 2.00e-02 2.50e+03   4.75e-03 4.52e-01
        pdb=" CG  TYR C  56 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  56 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  56 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C  56 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  56 "    0.007 2.00e-02 2.50e+03   4.75e-03 4.52e-01
        pdb=" CG  TYR A  56 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  56 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  56 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2450
        2.81 -     3.34: 8729
        3.34 -     3.86: 14543
        3.86 -     4.38: 16796
        4.38 -     4.90: 30051
  Nonbonded interactions: 72569
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D  98 "
            pdb=" OG1 THR E  95 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OD1 ASN B  98 "
            pdb=" OG1 THR C  95 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" OD1 ASN E  98 "
            pdb=" OG1 THR F  95 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   MET E 105 "
            pdb=" OG  SER E 109 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" O   MET B 105 "
            pdb=" OG  SER B 109 "
     model   vdw
     2.377 3.040
  ... (remaining 72564 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 162 or resid 205))
  selection = (chain 'B' and (resid 6 through 162 or resid 205))
  selection = (chain 'C' and (resid 6 through 162 or resid 205))
  selection = (chain 'D' and (resid 6 through 162 or resid 205))
  selection = (chain 'E' and (resid 6 through 162 or resid 205))
  selection = (chain 'F' and (resid 6 through 162 or resid 205))
  selection = (chain 'G' and (resid 6 through 162 or resid 205))
}

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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.630
  Find NCS groups from input model:        0.270
  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:6.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
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      :  0.008   0.210   9079  Z= 0.383
  Angle     :  0.757  14.870  12103  Z= 0.326
  Chirality :  0.043   0.234   1470
  Planarity :  0.002   0.015   1379
  Dihedral  : 15.357 146.826   3465
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  3.02 (0.26), residues: 1085
  helix:  3.37 (0.18), residues: 714
  sheet: -0.66 (0.53), residues: 70
  loop : -0.90 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG F 159 
 TYR   0.011   0.001   TYR E  56 
 PHE   0.006   0.001   PHE C  11 
 TRP   0.001   0.000   TRP D  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00778 /  0.38 ( 9079)
  covalent geometry    : angle       0.75690 /  0.33 (12103)
  hydrogen bonds       : bond        0.09164 /  6.12 (  637)
  hydrogen bonds       : angle       4.67350 /  3.50 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  134 TYR cc_start: 0.8669 (m-80) cc_final: 0.8412 (m-80)
REVERT: B  134 TYR cc_start: 0.8658 (m-80) cc_final: 0.7738 (m-80)
REVERT: D  134 TYR cc_start: 0.8796 (m-80) cc_final: 0.7782 (m-80)
REVERT: E  105 MET cc_start: 0.7453 (mtm) cc_final: 0.7228 (mtp)
REVERT: E  134 TYR cc_start: 0.8643 (m-80) cc_final: 0.7862 (m-80)
REVERT: F  134 TYR cc_start: 0.8710 (m-80) cc_final: 0.7778 (m-80)
REVERT: G  134 TYR cc_start: 0.8684 (m-80) cc_final: 0.8330 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.5831
  time to fit residues: 32.3562
Evaluate side-chains
  51 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61]
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    0.0270
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4036

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.177195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.146493 restraints weight = 8328.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.79
r_work: 0.3536 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9079  Z= 0.097
  Angle     :  0.445   6.170  12103  Z= 0.222
  Chirality :  0.040   0.132   1470
  Planarity :  0.002   0.012   1379
  Dihedral  : 16.421 150.357   1694
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  4.19 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  3.19 (0.26), residues: 1085
  helix:  3.29 (0.18), residues: 714
  sheet:  0.95 (0.63), residues: 70
  loop : -0.68 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 159 
 TYR   0.013   0.001   TYR F  56 
 PHE   0.011   0.001   PHE D 120 
 TRP   0.002   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00193 /  0.10 ( 9079)
  covalent geometry    : angle       0.44509 /  0.22 (12103)
  hydrogen bonds       : bond        0.03669 /  2.53 (  637)
  hydrogen bonds       : angle       3.50975 /  2.59 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  134 TYR cc_start: 0.8695 (m-80) cc_final: 0.8398 (m-80)
REVERT: B  134 TYR cc_start: 0.8648 (m-80) cc_final: 0.7718 (m-80)
REVERT: D  134 TYR cc_start: 0.8751 (m-80) cc_final: 0.7478 (m-80)
REVERT: E  134 TYR cc_start: 0.8699 (m-80) cc_final: 0.7835 (m-80)
REVERT: F  105 MET cc_start: 0.7273 (mtm) cc_final: 0.7005 (mtp)
REVERT: F  134 TYR cc_start: 0.8718 (m-80) cc_final: 0.7816 (m-80)
REVERT: G  134 TYR cc_start: 0.8695 (m-80) cc_final: 0.8104 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 52
  average time/residue: 0.5980
  time to fit residues: 33.3136
Evaluate side-chains
  46 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [89, 80, 42, 22, 84, 1, 74, 37, 20, 3, 56]
   chunk 89 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.7782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.166187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.136150 restraints weight = 8535.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.79
r_work: 0.3288 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   9079  Z= 0.116
  Angle     :  0.461   5.717  12103  Z= 0.228
  Chirality :  0.040   0.126   1470
  Planarity :  0.002   0.012   1379
  Dihedral  : 16.236 163.747   1694
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  7.20 %
    Favored  : 92.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.91 (0.26), residues: 1085
  helix:  3.08 (0.18), residues: 714
  sheet:  1.45 (0.65), residues: 70
  loop : -0.97 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 159 
 TYR   0.012   0.001   TYR F  56 
 PHE   0.010   0.001   PHE D  87 
 TRP   0.002   0.000   TRP F  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 ( 9079)
  covalent geometry    : angle       0.46090 /  0.23 (12103)
  hydrogen bonds       : bond        0.03875 /  2.69 (  637)
  hydrogen bonds       : angle       3.35069 /  2.47 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.7626 (tp) cc_final: 0.7404 (tp)
REVERT: A   91 MET cc_start: 0.5239 (OUTLIER) cc_final: 0.4969 (ttm)
REVERT: A  134 TYR cc_start: 0.8690 (m-80) cc_final: 0.8439 (m-80)
REVERT: A  144 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7735 (tt0)
REVERT: B  134 TYR cc_start: 0.8653 (m-80) cc_final: 0.7858 (m-80)
REVERT: C   91 MET cc_start: 0.5209 (tmm) cc_final: 0.4993 (tmm)
REVERT: D   91 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5668 (ptm)
REVERT: E  128 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7297 (pttp)
REVERT: E  134 TYR cc_start: 0.8665 (m-80) cc_final: 0.8130 (m-80)
REVERT: G  134 TYR cc_start: 0.8651 (m-80) cc_final: 0.8248 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 66
  average time/residue: 0.5743
  time to fit residues: 40.7280
Evaluate side-chains
  64 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain D residue   91 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [38, 51, 21, 94, 102, 25, 26, 53, 42, 92, 99]
   chunk 38 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0980
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.6984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.165557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.135226 restraints weight = 8702.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.79
r_work: 0.3415 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   9079  Z= 0.106
  Angle     :  0.443   5.562  12103  Z= 0.218
  Chirality :  0.040   0.123   1470
  Planarity :  0.002   0.015   1379
  Dihedral  : 16.277 166.312   1694
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  8.27 %
    Favored  : 91.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  2.92 (0.26), residues: 1085
  helix:  3.06 (0.18), residues: 714
  sheet:  1.73 (0.67), residues: 70
  loop : -0.97 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 159 
 TYR   0.011   0.001   TYR D  56 
 PHE   0.009   0.001   PHE D  87 
 TRP   0.001   0.000   TRP B  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.11 ( 9079)
  covalent geometry    : angle       0.44345 /  0.22 (12103)
  hydrogen bonds       : bond        0.03621 /  2.51 (  637)
  hydrogen bonds       : angle       3.26191 /  2.40 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   91 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5251 (ttm)
REVERT: A  134 TYR cc_start: 0.8647 (m-80) cc_final: 0.8417 (m-80)
REVERT: A  144 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7703 (tm-30)
REVERT: B  134 TYR cc_start: 0.8632 (m-80) cc_final: 0.7814 (m-80)
REVERT: E  128 LYS cc_start: 0.7823 (ptpt) cc_final: 0.7272 (pttp)
REVERT: E  134 TYR cc_start: 0.8672 (m-80) cc_final: 0.8171 (m-80)
REVERT: F   91 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.4999 (ttm)
REVERT: G  134 TYR cc_start: 0.8638 (m-80) cc_final: 0.8276 (m-80)
  outliers start: 5
  outliers final: 1
  residues processed: 66
  average time/residue: 0.5631
  time to fit residues: 39.9130
Evaluate side-chains
  69 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain E residue  129 SER
Chi-restraints excluded: chain F residue   91 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [1, 4, 104, 61, 11, 36, 29, 50, 58, 47, 9]
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.8182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.163492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.133306 restraints weight = 8693.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.80
r_work: 0.3252 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   9079  Z= 0.115
  Angle     :  0.485  11.070  12103  Z= 0.230
  Chirality :  0.040   0.124   1470
  Planarity :  0.002   0.018   1379
  Dihedral  : 16.305 165.264   1694
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.99 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  2.60 (0.27), residues: 1085
  helix:  2.98 (0.18), residues: 714
  sheet: -0.60 (0.55), residues: 105
  loop : -0.93 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 159 
 TYR   0.011   0.001   TYR D  56 
 PHE   0.010   0.001   PHE D  87 
 TRP   0.001   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 ( 9079)
  covalent geometry    : angle       0.48525 /  0.23 (12103)
  hydrogen bonds       : bond        0.03776 /  2.62 (  637)
  hydrogen bonds       : angle       3.28058 /  2.41 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   91 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5540 (ttm)
REVERT: A  134 TYR cc_start: 0.8708 (m-80) cc_final: 0.8473 (m-80)
REVERT: B  134 TYR cc_start: 0.8658 (m-80) cc_final: 0.7871 (m-80)
REVERT: E   30 LYS cc_start: 0.7393 (mmtp) cc_final: 0.6997 (mmmm)
REVERT: E  128 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7326 (pttp)
REVERT: E  134 TYR cc_start: 0.8714 (m-80) cc_final: 0.8223 (m-80)
REVERT: F   12 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5982 (tp)
REVERT: G  134 TYR cc_start: 0.8632 (m-80) cc_final: 0.8308 (m-80)
  outliers start: 9
  outliers final: 2
  residues processed: 79
  average time/residue: 0.4850
  time to fit residues: 41.6040
Evaluate side-chains
  73 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain E residue  129 SER
Chi-restraints excluded: chain F residue   12 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [51, 11, 58, 12, 82, 31, 21, 44, 41, 10, 39]
   chunk 51 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0770
   chunk 58 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7138

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.163319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.133108 restraints weight = 8737.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.80
r_work: 0.3343 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   9079  Z= 0.108
  Angle     :  0.503  11.536  12103  Z= 0.232
  Chirality :  0.040   0.125   1470
  Planarity :  0.002   0.018   1379
  Dihedral  : 16.246 165.305   1694
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.63 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  2.66 (0.27), residues: 1085
  helix:  3.03 (0.18), residues: 714
  sheet: -0.50 (0.55), residues: 105
  loop : -0.94 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 159 
 TYR   0.011   0.001   TYR D  56 
 PHE   0.009   0.001   PHE D  87 
 TRP   0.001   0.000   TRP A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 9079)
  covalent geometry    : angle       0.50314 /  0.23 (12103)
  hydrogen bonds       : bond        0.03599 /  2.50 (  637)
  hydrogen bonds       : angle       3.21426 /  2.36 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  134 TYR cc_start: 0.8690 (m-80) cc_final: 0.8449 (m-80)
REVERT: B  134 TYR cc_start: 0.8595 (m-80) cc_final: 0.7781 (m-80)
REVERT: C   30 LYS cc_start: 0.7106 (mmtp) cc_final: 0.6888 (mmtp)
REVERT: E   30 LYS cc_start: 0.7494 (mmtp) cc_final: 0.7121 (mmmm)
REVERT: E  128 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7269 (pttp)
REVERT: E  134 TYR cc_start: 0.8683 (m-80) cc_final: 0.7944 (m-80)
REVERT: F   91 MET cc_start: 0.5658 (OUTLIER) cc_final: 0.5070 (ttm)
REVERT: G  134 TYR cc_start: 0.8563 (m-80) cc_final: 0.8251 (m-80)
  outliers start: 10
  outliers final: 2
  residues processed: 71
  average time/residue: 0.5341
  time to fit residues: 40.8354
Evaluate side-chains
  67 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain E residue  129 SER
Chi-restraints excluded: chain F residue   91 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [85, 43, 69, 73, 14, 28, 41, 11, 92, 17, 74]
   chunk 85 optimal weight:    0.0980
   chunk 43 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.7584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.162830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.132474 restraints weight = 8836.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.81
r_work: 0.3247 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   9079  Z= 0.112
  Angle     :  0.502   9.692  12103  Z= 0.233
  Chirality :  0.040   0.124   1470
  Planarity :  0.002   0.018   1379
  Dihedral  : 16.261 164.905   1694
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.92 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  2.65 (0.26), residues: 1085
  helix:  3.00 (0.18), residues: 714
  sheet: -0.52 (0.54), residues: 105
  loop : -0.91 (0.42), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 159 
 TYR   0.010   0.001   TYR D  56 
 PHE   0.011   0.001   PHE A  87 
 TRP   0.001   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 ( 9079)
  covalent geometry    : angle       0.50209 /  0.23 (12103)
  hydrogen bonds       : bond        0.03673 /  2.55 (  637)
  hydrogen bonds       : angle       3.19869 /  2.35 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  134 TYR cc_start: 0.8729 (m-80) cc_final: 0.8485 (m-80)
REVERT: B  134 TYR cc_start: 0.8633 (m-80) cc_final: 0.7841 (m-80)
REVERT: C  155 LYS cc_start: 0.8014 (mttt) cc_final: 0.7638 (ptpt)
REVERT: E   30 LYS cc_start: 0.7481 (mmtp) cc_final: 0.7119 (mmmm)
REVERT: E  128 LYS cc_start: 0.7855 (ptpt) cc_final: 0.7307 (pttp)
REVERT: E  134 TYR cc_start: 0.8705 (m-80) cc_final: 0.7994 (m-80)
REVERT: F   91 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4907 (ttm)
REVERT: G  134 TYR cc_start: 0.8603 (m-80) cc_final: 0.8350 (m-80)
  outliers start: 11
  outliers final: 4
  residues processed: 72
  average time/residue: 0.5202
  time to fit residues: 40.4455
Evaluate side-chains
  72 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue  129 SER
Chi-restraints excluded: chain F residue   91 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [73, 60, 80, 103, 78, 20, 39, 91, 100, 77, 81]
   chunk 73 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 78 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 81 optimal weight:    0.4980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.162190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.131868 restraints weight = 8738.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.80
r_work: 0.3251 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9079  Z= 0.112
  Angle     :  0.514  11.532  12103  Z= 0.237
  Chirality :  0.040   0.125   1470
  Planarity :  0.002   0.020   1379
  Dihedral  : 16.146 165.592   1694
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 12.57 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.26), residues: 1085
  helix:  2.99 (0.18), residues: 714
  sheet: -0.50 (0.54), residues: 105
  loop : -0.87 (0.42), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 159 
 TYR   0.010   0.001   TYR D  56 
 PHE   0.010   0.001   PHE D  87 
 TRP   0.002   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.11 ( 9079)
  covalent geometry    : angle       0.51445 /  0.24 (12103)
  hydrogen bonds       : bond        0.03650 /  2.52 (  637)
  hydrogen bonds       : angle       3.18956 /  2.34 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  134 TYR cc_start: 0.8724 (m-80) cc_final: 0.8485 (m-80)
REVERT: B  134 TYR cc_start: 0.8634 (m-80) cc_final: 0.7857 (m-80)
REVERT: C  155 LYS cc_start: 0.8008 (mttt) cc_final: 0.7634 (ptpt)
REVERT: E   30 LYS cc_start: 0.7465 (mmtp) cc_final: 0.7089 (mmmm)
REVERT: E  128 LYS cc_start: 0.7848 (ptpt) cc_final: 0.7313 (pttp)
REVERT: E  134 TYR cc_start: 0.8723 (m-80) cc_final: 0.8020 (m-80)
REVERT: F   91 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4941 (ttm)
REVERT: G   30 LYS cc_start: 0.7124 (mmtp) cc_final: 0.6766 (mmmm)
REVERT: G  134 TYR cc_start: 0.8607 (m-80) cc_final: 0.8274 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 71
  average time/residue: 0.5113
  time to fit residues: 39.1681
Evaluate side-chains
  74 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue  129 SER
Chi-restraints excluded: chain F residue   91 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [64, 98, 13, 104, 0, 58, 94, 57, 80, 99, 10]
   chunk 64 optimal weight:    6.9990
   chunk 98 optimal weight:    0.0970
   chunk 13 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0980
   overall best weight:    1.4384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.160024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.129842 restraints weight = 8887.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.81
r_work: 0.3210 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9079  Z= 0.167
  Angle     :  0.596  11.937  12103  Z= 0.275
  Chirality :  0.042   0.129   1470
  Planarity :  0.003   0.024   1379
  Dihedral  : 17.007 164.634   1694
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.78 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  2.17 (0.26), residues: 1085
  helix:  2.63 (0.18), residues: 721
  sheet: -0.68 (0.53), residues: 105
  loop : -1.19 (0.42), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 159 
 TYR   0.011   0.001   TYR D  56 
 PHE   0.014   0.002   PHE A  87 
 TRP   0.004   0.001   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.17 ( 9079)
  covalent geometry    : angle       0.59599 /  0.27 (12103)
  hydrogen bonds       : bond        0.04266 /  2.95 (  637)
  hydrogen bonds       : angle       3.37937 /  2.48 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.282 
Fit side-chains
REVERT: B  134 TYR cc_start: 0.8652 (m-80) cc_final: 0.7781 (m-80)
REVERT: C   91 MET cc_start: 0.5802 (tmm) cc_final: 0.5286 (ttm)
REVERT: E  128 LYS cc_start: 0.7902 (ptpt) cc_final: 0.7337 (pttp)
REVERT: E  134 TYR cc_start: 0.8761 (m-80) cc_final: 0.8506 (m-80)
REVERT: F   91 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.4954 (ttm)
REVERT: G  134 TYR cc_start: 0.8621 (m-80) cc_final: 0.8378 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 84
  average time/residue: 0.4776
  time to fit residues: 43.3803
Evaluate side-chains
  82 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue  129 SER
Chi-restraints excluded: chain F residue   91 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [73, 47, 36, 90, 91, 71, 58, 85, 50, 20, 18]
   chunk 73 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 90 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0270
   chunk 50 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6638

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.162477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.128382 restraints weight = 8576.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.09
r_work: 0.3336 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9079  Z= 0.108
  Angle     :  0.529  12.366  12103  Z= 0.241
  Chirality :  0.040   0.126   1470
  Planarity :  0.002   0.022   1379
  Dihedral  : 16.403 165.500   1694
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 13.96 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  2.48 (0.26), residues: 1085
  helix:  2.89 (0.18), residues: 714
  sheet: -0.59 (0.53), residues: 105
  loop : -0.99 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 159 
 TYR   0.010   0.001   TYR D  56 
 PHE   0.013   0.001   PHE A  87 
 TRP   0.001   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 ( 9079)
  covalent geometry    : angle       0.52886 /  0.24 (12103)
  hydrogen bonds       : bond        0.03658 /  2.53 (  637)
  hydrogen bonds       : angle       3.21658 /  2.35 ( 1884)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  134 TYR cc_start: 0.8595 (m-80) cc_final: 0.8299 (m-80)
REVERT: B  134 TYR cc_start: 0.8628 (m-80) cc_final: 0.7889 (m-80)
REVERT: C   91 MET cc_start: 0.5710 (tmm) cc_final: 0.5162 (ttm)
REVERT: C  155 LYS cc_start: 0.8113 (mttt) cc_final: 0.7787 (ptpt)
REVERT: E   30 LYS cc_start: 0.7801 (mmtp) cc_final: 0.7410 (mmmm)
REVERT: E  128 LYS cc_start: 0.7898 (ptpt) cc_final: 0.7386 (pttp)
REVERT: E  134 TYR cc_start: 0.8707 (m-80) cc_final: 0.8059 (m-80)
REVERT: F   91 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.5114 (ttm)
REVERT: G   30 LYS cc_start: 0.7461 (mmtp) cc_final: 0.7064 (mmmm)
REVERT: G  134 TYR cc_start: 0.8596 (m-80) cc_final: 0.8293 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 74
  average time/residue: 0.5463
  time to fit residues: 43.3438
Evaluate side-chains
  76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue  129 SER
Chi-restraints excluded: chain F residue   91 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [91, 11, 82, 59, 96, 0, 57, 75, 102, 18, 12]
   chunk 91 optimal weight:    2.9990
   chunk 11 optimal weight:    0.2980
   chunk 82 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 57 optimal weight:    0.6980
   chunk 75 optimal weight:    8.9990
   chunk 102 optimal weight:    0.6980
   chunk 18 optimal weight:    0.2980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.162784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.132766 restraints weight = 8704.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.79
r_work: 0.3255 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9079  Z= 0.099
  Angle     :  0.508  11.235  12103  Z= 0.233
  Chirality :  0.040   0.126   1470
  Planarity :  0.002   0.022   1379
  Dihedral  : 15.905 164.170   1694
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 14.29 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole:  2.62 (0.26), residues: 1085
  helix:  2.98 (0.18), residues: 714
  sheet: -0.47 (0.54), residues: 105
  loop : -0.95 (0.41), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 159 
 TYR   0.010   0.001   TYR G  56 
 PHE   0.012   0.001   PHE A  87 
 TRP   0.001   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.10 ( 9079)
  covalent geometry    : angle       0.50827 /  0.23 (12103)
  hydrogen bonds       : bond        0.03520 /  2.43 (  637)
  hydrogen bonds       : angle       3.14955 /  2.31 ( 1884)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2489.28 seconds
wall clock time: 43 minutes 18.56 seconds (2598.56 seconds total)