Starting phenix.real_space_refine
on Fri Oct 23 08:21:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sdg_54785/10_2026/9sdg_54785.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sdg_54785/10_2026/9sdg_54785.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9sdg_54785/10_2026/9sdg_54785.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sdg_54785/10_2026/9sdg_54785.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sdg_54785/10_2026/9sdg_54785.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sdg_54785/10_2026/9sdg_54785.map"
  }
  resolution = 2.8
  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=   0.002
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    6318      2.51       5
     N    1267      2.21       5
     O    1554      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  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: 9167
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 1184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1184
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 3, 'TRANS': 152}
    Chain: "B"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1188
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "C"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1188
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "D"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1188
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "E"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1188
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
    Chain: "F"
      Number of atoms: 1176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1176
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 3, 'TRANS': 151}
    Chain: "G"
      Number of atoms: 1176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1176
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 3, 'TRANS': 151}
    Chain: "A"
      Number of atoms: 188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 188
          Unusual residues: {'C14': 3, 'D10': 2, 'D12': 3, 'OCT': 2, 'PEE': 2}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 28
    Chain: "B"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 88
          Unusual residues: {'C14': 2, 'D10': 2, 'D12': 2, 'OCT': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
    Chain: "C"
      Number of atoms: 156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 156
          Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 1, 'PEE': 2}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 28
    Chain: "D"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 88
          Unusual residues: {'C14': 2, 'D10': 2, 'D12': 2, 'OCT': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
    Chain: "E"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 117
          Unusual residues: {'C14': 2, 'D10': 2, 'D12': 2, 'OCT': 1, 'PEE': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "F"
      Number of atoms: 125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 125
          Unusual residues: {'C14': 2, 'D10': 2, 'D12': 2, 'OCT': 2, 'PEE': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "G"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 117
          Unusual residues: {'C14': 3, 'D10': 1, 'D12': 1, 'OCT': 2, 'PEE': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
  Time building chain proxies: 2.26, per 1000 atoms: 0.25
  Number of scatterers: 9167
  At special positions: 0
  Unit cell: (86.086, 85.14, 99.33, 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    1554      8.00
     N    1267      7.00
     C    6318      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: 1.02
  Conformation dependent library (CDL) restraints added in 357.2 milliseconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1998

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      65.0% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 41
      removed outlier: 4.057A  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
    Processing helix  chain 'A' and resid 93 through 109
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'B' and resid 9 through 41
    Processing helix  chain 'B' and resid 45 through 72
    Processing helix  chain 'B' and resid 75 through 91
    Processing helix  chain 'B' and resid 93 through 109
    Processing helix  chain 'B' and resid 149 through 153
    Processing helix  chain 'C' and resid 7 through 40
      removed outlier: 4.210A  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
    Processing helix  chain 'C' and resid 93 through 109
    Processing helix  chain 'C' and resid 149 through 153
    Processing helix  chain 'D' and resid 8 through 41
    Processing helix  chain 'D' and resid 45 through 72
    Processing helix  chain 'D' and resid 75 through 93
      removed outlier: 3.511A  pdb=" N   LEU D  93 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 109
    Processing helix  chain 'D' and resid 149 through 153
    Processing helix  chain 'E' and resid 8 through 41
    Processing helix  chain 'E' and resid 45 through 72
    Processing helix  chain 'E' and resid 75 through 93
      removed outlier: 4.096A  pdb=" N   LEU E  93 " --> pdb=" O   ILE E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 109
    Processing helix  chain 'E' and resid 149 through 153
    Processing helix  chain 'F' and resid 9 through 40
    Processing helix  chain 'F' and resid 45 through 72
    Processing helix  chain 'F' and resid 75 through 92
      removed outlier: 3.638A  pdb=" N   SER F  92 " --> pdb=" O   GLY F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 109
    Processing helix  chain 'F' and resid 149 through 153
    Processing helix  chain 'G' and resid 9 through 41
    Processing helix  chain 'G' and resid 45 through 72
    Processing helix  chain 'G' and resid 75 through 92
      removed outlier: 3.633A  pdb=" N   GLY G  88 " --> pdb=" O   GLY G  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 109
    Processing helix  chain 'G' and resid 149 through 153
    Processing sheet with id=AA1, first strand: chain 'B' and resid 129 through 130
      removed outlier: 3.688A  pdb=" N   ILE B 145 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LYS A 136 " --> pdb=" O   LYS A 128 " (cutoff:3.500A)
      removed outlier: 4.832A  pdb=" N   ILE A 130 " --> pdb=" O   TYR A 134 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   TYR A 134 " --> pdb=" O   ILE A 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 117 through 120
      removed outlier: 3.522A  pdb=" N   GLY B 125 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 159
    Processing sheet with id=AA4, first strand: chain 'C' and resid 117 through 119
    Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159
      removed outlier: 3.548A  pdb=" N   ILE D 145 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TYR D 134 " --> pdb=" O   ILE D 130 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   ILE D 130 " --> pdb=" O   TYR D 134 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LYS D 136 " --> pdb=" O   LYS D 128 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   TYR E 134 " --> pdb=" O   ILE E 130 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ILE E 130 " --> pdb=" O   TYR E 134 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LYS E 136 " --> pdb=" O   LYS E 128 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE F 145 " --> pdb=" O   LEU F 137 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   TYR F 134 " --> pdb=" O   ILE F 130 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   ILE F 130 " --> pdb=" O   TYR F 134 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LYS F 136 " --> pdb=" O   LYS F 128 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL F 118 " --> pdb=" O   GLY F 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 157 through 159
      removed outlier: 3.793A  pdb=" N   ILE G 145 " --> pdb=" O   LEU G 137 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   TYR G 134 " --> pdb=" O   ILE G 130 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ILE G 130 " --> pdb=" O   TYR G 134 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS G 136 " --> pdb=" O   LYS G 128 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY G 125 " --> pdb=" O   VAL G 118 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL G 118 " --> pdb=" O   GLY G 125 " (cutoff:3.500A)

    656 hydrogen bonds defined for protein.
    1917 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: 1.25

  Time building geometry restraints manager: 1.25 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: 1315
        1.32 -     1.44: 2133
        1.44 -     1.56: 5748
        1.56 -     1.69: 14
        1.69 -     1.81: 35
  Bond restraints: 9245
  Sorted by residual:
  bond pdb=" C38 PEE F 202 "
       pdb=" C39 PEE F 202 "
    ideal  model  delta    sigma   weight residual
    1.523  1.315  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C38 PEE A 201 "
       pdb=" C39 PEE A 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.316  0.207 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C38 PEE G 205 "
       pdb=" C39 PEE G 205 "
    ideal  model  delta    sigma   weight residual
    1.523  1.316  0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" C38 PEE E 201 "
       pdb=" C39 PEE E 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.316  0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" C38 PEE C 201 "
       pdb=" C39 PEE C 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.316  0.207 2.00e-02 2.50e+03 1.07e+02
  ... (remaining 9240 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 12137
        2.75 -     5.50: 74
        5.50 -     8.25: 8
        8.25 -    11.00: 7
       11.00 -    13.74: 14
  Bond angle restraints: 12240
  Sorted by residual:
  angle pdb=" C38 PEE A 206 "
        pdb=" C39 PEE A 206 "
        pdb=" C40 PEE A 206 "
      ideal   model   delta    sigma   weight residual
     112.47  126.21  -13.74 3.00e+00 1.11e-01 2.10e+01
  angle pdb=" C38 PEE C 206 "
        pdb=" C39 PEE C 206 "
        pdb=" C40 PEE C 206 "
      ideal   model   delta    sigma   weight residual
     112.47  126.09  -13.62 3.00e+00 1.11e-01 2.06e+01
  angle pdb=" C38 PEE G 205 "
        pdb=" C39 PEE G 205 "
        pdb=" C40 PEE G 205 "
      ideal   model   delta    sigma   weight residual
     112.47  125.93  -13.46 3.00e+00 1.11e-01 2.01e+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  125.76  -13.29 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C38 PEE C 201 "
        pdb=" C39 PEE C 201 "
        pdb=" C40 PEE C 201 "
      ideal   model   delta    sigma   weight residual
     112.47  125.73  -13.26 3.00e+00 1.11e-01 1.95e+01
  ... (remaining 12235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.74: 5441
       29.74 -    59.48: 128
       59.48 -    89.22: 24
       89.22 -   118.96: 10
      118.96 -   148.71: 5
  Dihedral angle restraints: 5608
    sinusoidal: 2481
      harmonic: 3127
  Sorted by residual:
  dihedral pdb=" C4  PEE C 206 "
           pdb=" O4P PEE C 206 "
           pdb=" P   PEE C 206 "
           pdb=" O2P PEE C 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
     284.22  135.51  148.71     1      3.00e+01 1.11e-03 1.98e+01
  dihedral pdb=" C4  PEE F 202 "
           pdb=" O4P PEE F 202 "
           pdb=" P   PEE F 202 "
           pdb=" O2P PEE F 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     284.22  137.09  147.13     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" N   PEE F 202 "
           pdb=" C4  PEE F 202 "
           pdb=" C5  PEE F 202 "
           pdb=" O4P PEE F 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.03  179.33  123.70     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 5605 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1223
       0.054 -    0.108: 193
       0.108 -    0.161: 45
       0.161 -    0.215: 0
       0.215 -    0.269: 7
  Chirality restraints: 1468
  Sorted by residual:
  chirality pdb=" C2  PEE C 201 "
            pdb=" C1  PEE C 201 "
            pdb=" C3  PEE C 201 "
            pdb=" O2  PEE C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.60    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" C2  PEE A 201 "
            pdb=" C1  PEE A 201 "
            pdb=" C3  PEE A 201 "
            pdb=" O2  PEE A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.59    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" C2  PEE A 206 "
            pdb=" C1  PEE A 206 "
            pdb=" C3  PEE A 206 "
            pdb=" O2  PEE A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.59    0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1465 not shown)

  Planarity restraints: 1372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  87 "    0.015 2.00e-02 2.50e+03   1.44e-02 3.64e+00
        pdb=" CG  PHE F  87 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  87 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  87 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  87 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  87 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  87 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 110 "    0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO C 111 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 111 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 111 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  87 "   -0.009 2.00e-02 2.50e+03   7.59e-03 1.01e+00
        pdb=" CG  PHE A  87 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  87 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  87 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  87 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  87 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  87 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1369 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1378
        2.76 -     3.29: 8392
        3.29 -     3.83: 14595
        3.83 -     4.36: 17742
        4.36 -     4.90: 31053
  Nonbonded interactions: 73160
  Sorted by model distance:
  nonbonded pdb=" OG  SER F 148 "
            pdb=" OD1 ASN F 150 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER B 148 "
            pdb=" OD1 ASN B 150 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   SER A 109 "
            pdb=" OG  SER A 109 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG  SER D 148 "
            pdb=" OD1 ASN D 150 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   SER B  90 "
            pdb=" OH  TYR B  97 "
     model   vdw
     2.314 3.040
  ... (remaining 73155 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 8 through 162)
  selection = (chain 'B' and resid 8 through 162)
  selection = (chain 'C' and resid 8 through 162)
  selection = (chain 'D' and resid 8 through 162)
  selection = (chain 'E' and resid 8 through 162)
  selection = (chain 'F' and resid 8 through 162)
  selection = (chain 'G' and resid 8 through 162)
}

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:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.280
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  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:5.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
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   0.208   9245  Z= 0.380
  Angle     :  0.732  13.745  12240  Z= 0.315
  Chirality :  0.044   0.269   1468
  Planarity :  0.002   0.030   1372
  Dihedral  : 15.217 148.706   3610
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  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:  2.91 (0.26), residues: 1080
  helix:  3.07 (0.18), residues: 728
  sheet: -0.81 (0.51), residues: 100
  loop : -0.43 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 159 
 TYR   0.015   0.001   TYR D  31 
 PHE   0.033   0.001   PHE F  87 
 TRP   0.001   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00770 /  0.38 ( 9245)
  covalent geometry    : angle       0.73234 /  0.31 (12240)
  hydrogen bonds       : bond        0.11470 /  8.07 (  656)
  hydrogen bonds       : angle       4.85301 /  3.64 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.394 
Fit side-chains
REVERT: B   45 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7894 (ttmm)
REVERT: B  113 GLU cc_start: 0.7883 (tt0) cc_final: 0.7669 (tt0)
REVERT: B  155 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8158 (mttp)
REVERT: C   41 LYS cc_start: 0.8457 (tptp) cc_final: 0.8253 (tptp)
REVERT: D  116 GLU cc_start: 0.8579 (pt0) cc_final: 0.8269 (pt0)
REVERT: E  128 LYS cc_start: 0.8274 (mtpt) cc_final: 0.8033 (mtpp)
REVERT: F  155 LYS cc_start: 0.8616 (mttt) cc_final: 0.8385 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.5589
  time to fit residues: 89.9630
Evaluate side-chains
  110 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   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 = 0.3604 r_free = 0.3604 target = 0.136298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.106625 restraints weight = 10441.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.18
r_work: 0.3080 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9245  Z= 0.139
  Angle     :  0.492   7.391  12240  Z= 0.249
  Chirality :  0.040   0.131   1468
  Planarity :  0.003   0.022   1372
  Dihedral  : 15.295 130.428   1815
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  7.37 %
    Favored  : 90.92 %
  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:  3.15 (0.26), residues: 1080
  helix:  3.31 (0.18), residues: 730
  sheet: -0.59 (0.50), residues: 105
  loop : -0.63 (0.42), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 159 
 TYR   0.018   0.001   TYR C  56 
 PHE   0.031   0.001   PHE F  87 
 TRP   0.001   0.000   TRP A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 9245)
  covalent geometry    : angle       0.49235 /  0.25 (12240)
  hydrogen bonds       : bond        0.04270 /  2.90 (  656)
  hydrogen bonds       : angle       3.77532 /  2.82 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.337 
Fit side-chains
REVERT: B  155 LYS cc_start: 0.8287 (mmtp) cc_final: 0.7950 (mttp)
REVERT: C   41 LYS cc_start: 0.8548 (tptp) cc_final: 0.7804 (tptp)
REVERT: D  116 GLU cc_start: 0.8437 (pt0) cc_final: 0.8044 (pt0)
REVERT: D  117 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8229 (mmmt)
REVERT: E   30 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7523 (mmmt)
REVERT: E  124 LYS cc_start: 0.8542 (mttm) cc_final: 0.8027 (mppt)
REVERT: E  128 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7650 (mtpp)
REVERT: E  132 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7724 (t80)
REVERT: F  113 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7648 (mm-30)
REVERT: F  116 GLU cc_start: 0.8630 (pt0) cc_final: 0.8385 (pt0)
REVERT: G  105 MET cc_start: 0.8297 (mtp) cc_final: 0.8090 (mtp)
  outliers start: 16
  outliers final: 8
  residues processed: 125
  average time/residue: 0.4729
  time to fit residues: 63.9693
Evaluate side-chains
  114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain F residue  110 LYS
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [25, 12, 92, 87, 6, 63, 11, 39, 64, 45, 91]
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 63 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0170
   chunk 39 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.4618

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.140960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.111472 restraints weight = 10269.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.18
r_work: 0.3143 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9245  Z= 0.094
  Angle     :  0.426   7.657  12240  Z= 0.217
  Chirality :  0.039   0.126   1468
  Planarity :  0.002   0.017   1372
  Dihedral  : 14.728 161.394   1815
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  8.44 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.51 (0.26), residues: 1080
  helix:  3.57 (0.17), residues: 729
  sheet: -0.23 (0.53), residues: 105
  loop : -0.61 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 159 
 TYR   0.022   0.001   TYR B  37 
 PHE   0.019   0.001   PHE F  87 
 TRP   0.002   0.000   TRP D  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00197 /  0.09 ( 9245)
  covalent geometry    : angle       0.42628 /  0.22 (12240)
  hydrogen bonds       : bond        0.03583 /  2.42 (  656)
  hydrogen bonds       : angle       3.38422 /  2.52 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B  105 MET cc_start: 0.8050 (mtp) cc_final: 0.7823 (mtp)
REVERT: B  113 GLU cc_start: 0.8186 (tt0) cc_final: 0.7779 (pt0)
REVERT: D  116 GLU cc_start: 0.8392 (pt0) cc_final: 0.8020 (pt0)
REVERT: D  117 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8226 (mmmt)
REVERT: D  134 TYR cc_start: 0.8857 (m-80) cc_final: 0.8633 (m-80)
REVERT: E  124 LYS cc_start: 0.8491 (mttm) cc_final: 0.8052 (mppt)
REVERT: E  132 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7724 (t80)
REVERT: F  113 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7655 (mm-30)
REVERT: F  116 GLU cc_start: 0.8525 (pt0) cc_final: 0.8318 (pt0)
REVERT: G  105 MET cc_start: 0.8333 (mtp) cc_final: 0.8098 (mtp)
  outliers start: 16
  outliers final: 9
  residues processed: 120
  average time/residue: 0.4687
  time to fit residues: 60.7557
Evaluate side-chains
  106 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [41, 104, 76, 98, 21, 91, 78, 27, 85, 101, 8]
   chunk 41 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   chunk 98 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.138427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.107783 restraints weight = 10428.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.28
r_work: 0.3076 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9245  Z= 0.118
  Angle     :  0.454   7.833  12240  Z= 0.229
  Chirality :  0.039   0.128   1468
  Planarity :  0.002   0.014   1372
  Dihedral  : 14.796 158.638   1815
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.94 %
    Favored  : 88.35 %
  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:  3.36 (0.26), residues: 1080
  helix:  3.48 (0.17), residues: 730
  sheet: -0.26 (0.51), residues: 105
  loop : -0.74 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 159 
 TYR   0.017   0.001   TYR D  37 
 PHE   0.018   0.001   PHE F  87 
 TRP   0.001   0.000   TRP A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 9245)
  covalent geometry    : angle       0.45419 /  0.23 (12240)
  hydrogen bonds       : bond        0.03903 /  2.64 (  656)
  hydrogen bonds       : angle       3.44303 /  2.57 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.325 
Fit side-chains
REVERT: B  105 MET cc_start: 0.8166 (mtp) cc_final: 0.7872 (mtp)
REVERT: B  113 GLU cc_start: 0.8232 (tt0) cc_final: 0.7804 (pt0)
REVERT: C  105 MET cc_start: 0.8205 (ttp) cc_final: 0.7983 (ttp)
REVERT: D  116 GLU cc_start: 0.8413 (pt0) cc_final: 0.8016 (pt0)
REVERT: D  117 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8286 (mmmm)
REVERT: E  124 LYS cc_start: 0.8595 (mttm) cc_final: 0.8206 (mppt)
REVERT: E  132 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7801 (t80)
REVERT: F  113 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7702 (mm-30)
REVERT: F  116 GLU cc_start: 0.8558 (pt0) cc_final: 0.8316 (pt0)
REVERT: G  105 MET cc_start: 0.8406 (mtp) cc_final: 0.8146 (mtp)
REVERT: G  117 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7686 (mttp)
  outliers start: 16
  outliers final: 11
  residues processed: 111
  average time/residue: 0.4336
  time to fit residues: 52.4426
Evaluate side-chains
  104 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   82 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [52, 74, 67, 90, 97, 51, 58, 64, 71, 5, 86]
   chunk 52 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.106779 restraints weight = 10458.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.28
r_work: 0.3068 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9245  Z= 0.129
  Angle     :  0.454   8.826  12240  Z= 0.228
  Chirality :  0.040   0.126   1468
  Planarity :  0.002   0.014   1372
  Dihedral  : 14.923 158.557   1815
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.47 %
    Favored  : 87.39 %
  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:  3.30 (0.26), residues: 1080
  helix:  3.44 (0.18), residues: 730
  sheet: -0.22 (0.49), residues: 105
  loop : -0.81 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 159 
 TYR   0.017   0.001   TYR B  37 
 PHE   0.015   0.001   PHE F  87 
 TRP   0.001   0.000   TRP C  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 9245)
  covalent geometry    : angle       0.45390 /  0.23 (12240)
  hydrogen bonds       : bond        0.03962 /  2.69 (  656)
  hydrogen bonds       : angle       3.46128 /  2.59 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.334 
Fit side-chains
REVERT: B  105 MET cc_start: 0.8110 (mtp) cc_final: 0.7803 (mtp)
REVERT: B  113 GLU cc_start: 0.8255 (tt0) cc_final: 0.7895 (pt0)
REVERT: B  116 GLU cc_start: 0.8627 (pt0) cc_final: 0.8242 (pt0)
REVERT: D  116 GLU cc_start: 0.8398 (pt0) cc_final: 0.8010 (pt0)
REVERT: D  117 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8274 (mmmm)
REVERT: E  124 LYS cc_start: 0.8656 (mttm) cc_final: 0.8271 (mppt)
REVERT: E  132 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7831 (t80)
REVERT: F  116 GLU cc_start: 0.8598 (pt0) cc_final: 0.8379 (pt0)
REVERT: G  105 MET cc_start: 0.8366 (mtp) cc_final: 0.8084 (mtp)
REVERT: G  117 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7705 (mttp)
  outliers start: 20
  outliers final: 12
  residues processed: 112
  average time/residue: 0.4644
  time to fit residues: 56.4046
Evaluate side-chains
  109 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  117 LYS
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  110 LYS
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   82 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [80, 91, 36, 49, 62, 11, 31, 45, 88, 78, 87]
   chunk 80 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0980
   chunk 31 optimal weight:    0.5980
   chunk 45 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.138608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.108391 restraints weight = 10442.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.26
r_work: 0.3090 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9245  Z= 0.107
  Angle     :  0.438   9.448  12240  Z= 0.222
  Chirality :  0.039   0.126   1468
  Planarity :  0.002   0.014   1372
  Dihedral  : 14.745 158.125   1815
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.11 %
    Favored  : 86.75 %
  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:  3.44 (0.26), residues: 1080
  helix:  3.54 (0.18), residues: 730
  sheet: -0.08 (0.50), residues: 105
  loop : -0.80 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 159 
 TYR   0.013   0.001   TYR D  56 
 PHE   0.012   0.001   PHE F  87 
 TRP   0.001   0.000   TRP E  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.11 ( 9245)
  covalent geometry    : angle       0.43803 /  0.22 (12240)
  hydrogen bonds       : bond        0.03713 /  2.51 (  656)
  hydrogen bonds       : angle       3.36689 /  2.52 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.339 
Fit side-chains
REVERT: B  105 MET cc_start: 0.8061 (mtp) cc_final: 0.7766 (mtp)
REVERT: B  113 GLU cc_start: 0.8238 (tt0) cc_final: 0.7830 (pt0)
REVERT: D  116 GLU cc_start: 0.8370 (pt0) cc_final: 0.8004 (pt0)
REVERT: D  117 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8260 (mmmm)
REVERT: E   96 SER cc_start: 0.7204 (OUTLIER) cc_final: 0.6988 (t)
REVERT: E  124 LYS cc_start: 0.8550 (mttm) cc_final: 0.8309 (mppt)
REVERT: E  132 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7973 (t80)
REVERT: F   37 TYR cc_start: 0.7669 (t80) cc_final: 0.7404 (t80)
REVERT: F  116 GLU cc_start: 0.8542 (pt0) cc_final: 0.8314 (pt0)
REVERT: G  105 MET cc_start: 0.8308 (mtp) cc_final: 0.8056 (mtp)
REVERT: G  117 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7689 (mttp)
  outliers start: 20
  outliers final: 11
  residues processed: 114
  average time/residue: 0.4284
  time to fit residues: 53.1997
Evaluate side-chains
  106 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue  117 LYS
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   82 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [67, 64, 47, 16, 21, 42, 32, 80, 35, 1, 19]
   chunk 67 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0170
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.139442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.109257 restraints weight = 10429.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.28
r_work: 0.3104 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9245  Z= 0.101
  Angle     :  0.434   8.865  12240  Z= 0.218
  Chirality :  0.039   0.126   1468
  Planarity :  0.002   0.013   1372
  Dihedral  : 14.651 159.691   1815
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.18 %
    Favored  : 86.32 %
  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:  3.52 (0.26), residues: 1080
  helix:  3.60 (0.18), residues: 729
  sheet:  0.03 (0.50), residues: 105
  loop : -0.79 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 159 
 TYR   0.015   0.001   TYR B  37 
 PHE   0.011   0.001   PHE F  87 
 TRP   0.001   0.000   TRP E  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 9245)
  covalent geometry    : angle       0.43419 /  0.22 (12240)
  hydrogen bonds       : bond        0.03597 /  2.43 (  656)
  hydrogen bonds       : angle       3.30902 /  2.47 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  119 ASP cc_start: 0.8035 (t70) cc_final: 0.7592 (t0)
REVERT: B  105 MET cc_start: 0.8001 (mtp) cc_final: 0.7700 (mtp)
REVERT: B  113 GLU cc_start: 0.8192 (tt0) cc_final: 0.7828 (pt0)
REVERT: D  116 GLU cc_start: 0.8346 (pt0) cc_final: 0.7982 (pt0)
REVERT: D  117 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8263 (mmmm)
REVERT: E  124 LYS cc_start: 0.8581 (mttm) cc_final: 0.8253 (mppt)
REVERT: E  132 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7998 (t80)
REVERT: F   37 TYR cc_start: 0.7651 (t80) cc_final: 0.7355 (t80)
REVERT: F  116 GLU cc_start: 0.8539 (pt0) cc_final: 0.8301 (pt0)
REVERT: G  105 MET cc_start: 0.8311 (mtp) cc_final: 0.8091 (mtp)
REVERT: G  117 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7636 (mttp)
  outliers start: 14
  outliers final: 11
  residues processed: 113
  average time/residue: 0.4215
  time to fit residues: 51.8889
Evaluate side-chains
  108 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue  117 LYS
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [35, 11, 81, 82, 84, 9, 77, 2, 53, 18, 58]
   chunk 35 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.139469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109139 restraints weight = 10446.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.30
r_work: 0.3098 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9245  Z= 0.102
  Angle     :  0.442   9.153  12240  Z= 0.220
  Chirality :  0.039   0.125   1468
  Planarity :  0.002   0.020   1372
  Dihedral  : 14.610 162.059   1815
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.29 %
    Favored  : 86.11 %
  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:  3.51 (0.26), residues: 1080
  helix:  3.59 (0.18), residues: 729
  sheet:  0.06 (0.50), residues: 105
  loop : -0.79 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 159 
 TYR   0.013   0.001   TYR A  56 
 PHE   0.011   0.001   PHE F  87 
 TRP   0.001   0.000   TRP E  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 ( 9245)
  covalent geometry    : angle       0.44172 /  0.22 (12240)
  hydrogen bonds       : bond        0.03598 /  2.43 (  656)
  hydrogen bonds       : angle       3.30034 /  2.46 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.280 
Fit side-chains
REVERT: B  105 MET cc_start: 0.8170 (mtp) cc_final: 0.7845 (mtp)
REVERT: B  113 GLU cc_start: 0.8201 (tt0) cc_final: 0.7906 (pt0)
REVERT: D  116 GLU cc_start: 0.8387 (pt0) cc_final: 0.8053 (pt0)
REVERT: D  117 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8443 (mmmt)
REVERT: E  132 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8062 (t80)
REVERT: F   37 TYR cc_start: 0.7685 (t80) cc_final: 0.7358 (t80)
REVERT: G  105 MET cc_start: 0.8455 (mtp) cc_final: 0.8251 (mtp)
REVERT: G  117 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7727 (mttp)
REVERT: G  155 LYS cc_start: 0.8374 (mttm) cc_final: 0.8064 (ptpt)
  outliers start: 15
  outliers final: 11
  residues processed: 106
  average time/residue: 0.4148
  time to fit residues: 48.0384
Evaluate side-chains
  109 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   48 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue  117 LYS
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [12, 15, 18, 87, 55, 6, 27, 7, 95, 97, 81]
   chunk 12 optimal weight:    0.0370
   chunk 15 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.140702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.110499 restraints weight = 10399.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.28
r_work: 0.3118 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9245  Z= 0.096
  Angle     :  0.443   9.314  12240  Z= 0.221
  Chirality :  0.039   0.125   1468
  Planarity :  0.002   0.013   1372
  Dihedral  : 14.495 164.626   1815
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.82 %
    Favored  : 85.79 %
  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:  3.60 (0.26), residues: 1080
  helix:  3.65 (0.18), residues: 729
  sheet:  0.13 (0.50), residues: 105
  loop : -0.78 (0.41), residues: 246

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00209 /  0.10 ( 9245)
  covalent geometry    : angle       0.44274 /  0.22 (12240)
  hydrogen bonds       : bond        0.03461 /  2.34 (  656)
  hydrogen bonds       : angle       3.23976 /  2.42 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.327 
Fit side-chains
REVERT: B  105 MET cc_start: 0.8142 (mtp) cc_final: 0.7833 (mtp)
REVERT: B  113 GLU cc_start: 0.8195 (tt0) cc_final: 0.7932 (pt0)
REVERT: D  116 GLU cc_start: 0.8380 (pt0) cc_final: 0.8047 (pt0)
REVERT: D  117 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8357 (mmmm)
REVERT: D  134 TYR cc_start: 0.8904 (m-80) cc_final: 0.8271 (m-80)
REVERT: E  132 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8058 (t80)
REVERT: F   37 TYR cc_start: 0.7649 (t80) cc_final: 0.7381 (t80)
REVERT: G  117 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7733 (mttp)
REVERT: G  155 LYS cc_start: 0.8357 (mttm) cc_final: 0.8074 (ptpt)
  outliers start: 13
  outliers final: 11
  residues processed: 109
  average time/residue: 0.4155
  time to fit residues: 49.4889
Evaluate side-chains
  108 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   48 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   82 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [49, 76, 22, 91, 80, 13, 2, 93, 102, 57, 61]
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 93 optimal weight:    0.2980
   chunk 102 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.139228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.109550 restraints weight = 10432.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.24
r_work: 0.3114 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9245  Z= 0.103
  Angle     :  0.452   9.432  12240  Z= 0.225
  Chirality :  0.039   0.126   1468
  Planarity :  0.002   0.023   1372
  Dihedral  : 14.477 165.409   1815
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.82 %
    Favored  : 85.68 %
  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:  3.54 (0.26), residues: 1080
  helix:  3.60 (0.18), residues: 729
  sheet:  0.16 (0.50), residues: 105
  loop : -0.82 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 159 
 TYR   0.018   0.001   TYR E  43 
 PHE   0.011   0.001   PHE F  87 
 TRP   0.001   0.000   TRP E  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.10 ( 9245)
  covalent geometry    : angle       0.45183 /  0.22 (12240)
  hydrogen bonds       : bond        0.03563 /  2.41 (  656)
  hydrogen bonds       : angle       3.26715 /  2.44 ( 1917)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.322 
Fit side-chains
REVERT: B  105 MET cc_start: 0.8082 (mtp) cc_final: 0.7835 (mtp)
REVERT: B  113 GLU cc_start: 0.8184 (tt0) cc_final: 0.7888 (pt0)
REVERT: D  116 GLU cc_start: 0.8354 (pt0) cc_final: 0.8011 (pt0)
REVERT: D  117 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8393 (mmmt)
REVERT: D  134 TYR cc_start: 0.8901 (m-80) cc_final: 0.8235 (m-80)
REVERT: E  132 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7837 (t80)
REVERT: F   37 TYR cc_start: 0.7613 (t80) cc_final: 0.7307 (t80)
REVERT: G  117 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7660 (mttp)
REVERT: G  155 LYS cc_start: 0.8311 (mttm) cc_final: 0.7882 (ptpt)
  outliers start: 14
  outliers final: 10
  residues processed: 108
  average time/residue: 0.4268
  time to fit residues: 50.3492
Evaluate side-chains
  108 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   48 SER
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  117 LYS
Chi-restraints excluded: chain E residue  132 PHE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue  126 THR
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   82 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks: [13, 33, 3, 56, 79, 53, 91, 89, 17, 82, 19]
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 3 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.139771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110383 restraints weight = 10236.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.19
r_work: 0.3127 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9245  Z= 0.099
  Angle     :  0.450   9.453  12240  Z= 0.225
  Chirality :  0.039   0.125   1468
  Planarity :  0.002   0.013   1372
  Dihedral  : 14.398 166.840   1815
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.57 %
    Favored  : 85.15 %
  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:  3.58 (0.26), residues: 1080
  helix:  3.63 (0.18), residues: 729
  sheet:  0.22 (0.50), residues: 105
  loop : -0.81 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 159 
 TYR   0.014   0.001   TYR B  37 
 PHE   0.010   0.001   PHE F  87 
 TRP   0.001   0.000   TRP E  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.10 ( 9245)
  covalent geometry    : angle       0.45022 /  0.22 (12240)
  hydrogen bonds       : bond        0.03497 /  2.36 (  656)
  hydrogen bonds       : angle       3.24342 /  2.42 ( 1917)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2238.58 seconds
wall clock time: 39 minutes 5.51 seconds (2345.51 seconds total)