Starting phenix.real_space_refine
on Fri Jun 13 16:47:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zgl_11210/06_2025/6zgl_11210.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zgl_11210/06_2025/6zgl_11210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zgl_11210/06_2025/6zgl_11210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zgl_11210/06_2025/6zgl_11210.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zgl_11210/06_2025/6zgl_11210.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zgl_11210/06_2025/6zgl_11210.cif"
  }
  resolution = 1.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    9324      2.51       5
     N    2568      2.21       5
     O    3832      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15760
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 1233
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 154, 1221
          Classifications: {'peptide': 154}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 151}
      Conformer: "B"
        Number of residues, atoms: 154, 1221
          Classifications: {'peptide': 154}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 151}
          bond proxies already assigned to first conformer: 1225
    Chain: "A"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "B"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "C"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "D"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "E"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 81
          Classifications: {'water': 81}
          Link IDs: {None: 80}
    Chain: "F"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 81
          Classifications: {'water': 81}
          Link IDs: {None: 80}
    Chain: "G"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "H"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "I"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 80
          Classifications: {'water': 80}
          Link IDs: {None: 79}
    Chain: "J"
      Number of atoms: 82
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 82
          Classifications: {'water': 82}
          Link IDs: {None: 81}
    Chain: "K"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 79
          Classifications: {'water': 79}
          Link IDs: {None: 78}
    Chain: "L"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 81
          Classifications: {'water': 81}
          Link IDs: {None: 80}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 6.10, per 1000 atoms: 0.39
  Number of scatterers: 15760
  At special positions: 0
  Unit cell: (105.298, 101.422, 94.962, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    3832      8.00
     N    2568      7.00
     C    9324      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: 4.04
  Conformation dependent library (CDL) restraints added in 3.3 seconds
  

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3600

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      80.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 54
    Processing helix  chain 'A' and resid 58 through 87
      removed outlier: 3.575A  pdb=" N   VAL A  62 " --> pdb=" O   ASN A  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP A  67 " --> pdb=" O   HIS A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 102
    Processing helix  chain 'A' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 165
    Processing helix  chain 'B' and resid 22 through 54
    Processing helix  chain 'B' and resid 58 through 87
      removed outlier: 3.575A  pdb=" N   VAL B  62 " --> pdb=" O   ASN B  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP B  67 " --> pdb=" O   HIS B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 102
    Processing helix  chain 'B' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY B 137 " --> pdb=" O   ARG B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 165
    Processing helix  chain 'C' and resid 22 through 54
    Processing helix  chain 'C' and resid 58 through 87
      removed outlier: 3.574A  pdb=" N   VAL C  62 " --> pdb=" O   ASN C  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP C  67 " --> pdb=" O   HIS C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 102
    Processing helix  chain 'C' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY C 137 " --> pdb=" O   ARG C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 165
    Processing helix  chain 'D' and resid 22 through 54
    Processing helix  chain 'D' and resid 58 through 87
      removed outlier: 3.575A  pdb=" N   VAL D  62 " --> pdb=" O   ASN D  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP D  67 " --> pdb=" O   HIS D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 102
    Processing helix  chain 'D' and resid 113 through 139
      removed outlier: 4.272A  pdb=" N   GLY D 137 " --> pdb=" O   ARG D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 165
    Processing helix  chain 'E' and resid 22 through 54
    Processing helix  chain 'E' and resid 58 through 87
      removed outlier: 3.574A  pdb=" N   VAL E  62 " --> pdb=" O   ASN E  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP E  67 " --> pdb=" O   HIS E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 94 through 102
    Processing helix  chain 'E' and resid 113 through 139
      removed outlier: 4.272A  pdb=" N   GLY E 137 " --> pdb=" O   ARG E 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 141 through 165
    Processing helix  chain 'F' and resid 22 through 54
    Processing helix  chain 'F' and resid 58 through 87
      removed outlier: 3.574A  pdb=" N   VAL F  62 " --> pdb=" O   ASN F  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP F  67 " --> pdb=" O   HIS F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 94 through 102
    Processing helix  chain 'F' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY F 137 " --> pdb=" O   ARG F 133 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 141 through 165
    Processing helix  chain 'G' and resid 22 through 54
    Processing helix  chain 'G' and resid 58 through 87
      removed outlier: 3.575A  pdb=" N   VAL G  62 " --> pdb=" O   ASN G  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP G  67 " --> pdb=" O   HIS G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 94 through 102
    Processing helix  chain 'G' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY G 137 " --> pdb=" O   ARG G 133 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 141 through 165
    Processing helix  chain 'H' and resid 22 through 54
    Processing helix  chain 'H' and resid 58 through 87
      removed outlier: 3.574A  pdb=" N   VAL H  62 " --> pdb=" O   ASN H  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP H  67 " --> pdb=" O   HIS H  63 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 94 through 102
    Processing helix  chain 'H' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY H 137 " --> pdb=" O   ARG H 133 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 141 through 165
    Processing helix  chain 'I' and resid 22 through 54
    Processing helix  chain 'I' and resid 58 through 87
      removed outlier: 3.574A  pdb=" N   VAL I  62 " --> pdb=" O   ASN I  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP I  67 " --> pdb=" O   HIS I  63 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 94 through 102
    Processing helix  chain 'I' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY I 137 " --> pdb=" O   ARG I 133 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 141 through 165
    Processing helix  chain 'J' and resid 22 through 54
    Processing helix  chain 'J' and resid 58 through 87
      removed outlier: 3.574A  pdb=" N   VAL J  62 " --> pdb=" O   ASN J  58 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASP J  67 " --> pdb=" O   HIS J  63 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 94 through 102
    Processing helix  chain 'J' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY J 137 " --> pdb=" O   ARG J 133 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 141 through 165
    Processing helix  chain 'K' and resid 22 through 54
    Processing helix  chain 'K' and resid 58 through 87
      removed outlier: 3.575A  pdb=" N   VAL K  62 " --> pdb=" O   ASN K  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP K  67 " --> pdb=" O   HIS K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 94 through 102
    Processing helix  chain 'K' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY K 137 " --> pdb=" O   ARG K 133 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 141 through 165
    Processing helix  chain 'L' and resid 22 through 54
    Processing helix  chain 'L' and resid 58 through 87
      removed outlier: 3.574A  pdb=" N   VAL L  62 " --> pdb=" O   ASN L  58 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP L  67 " --> pdb=" O   HIS L  63 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 94 through 102
    Processing helix  chain 'L' and resid 113 through 139
      removed outlier: 4.273A  pdb=" N   GLY L 137 " --> pdb=" O   ARG L 133 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 141 through 165

    1212 hydrogen bonds defined for protein.
    3612 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: 4.85

  Time building geometry restraints manager: 4.73 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 3925
        1.33 -     1.46: 3738
        1.46 -     1.59: 7301
        1.59 -     1.72: 0
        1.72 -     1.85: 72
  Bond restraints: 15036
  Sorted by residual:
  bond pdb=" C   GLU G  31 "
       pdb=" CA BGLU G  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.457  0.067 1.27e-02 6.20e+03 2.76e+01
  bond pdb=" C   GLU E  31 "
       pdb=" CA BGLU E  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.457  0.067 1.27e-02 6.20e+03 2.75e+01
  bond pdb=" C   GLU J  31 "
       pdb=" CA BGLU J  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.457  0.067 1.27e-02 6.20e+03 2.75e+01
  bond pdb=" C   GLU I  31 "
       pdb=" CA BGLU I  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.457  0.067 1.27e-02 6.20e+03 2.74e+01
  bond pdb=" C   GLU F  31 "
       pdb=" CA BGLU F  31 "
    ideal  model  delta    sigma   weight residual
    1.524  1.457  0.067 1.27e-02 6.20e+03 2.74e+01
  ... (remaining 15031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 15613
        1.68 -     3.35: 3938
        3.35 -     5.03: 669
        5.03 -     6.70: 156
        6.70 -     8.38: 24
  Bond angle restraints: 20400
  Sorted by residual:
  angle pdb=" CA  SER D 100 "
        pdb=" C   SER D 100 "
        pdb=" O   SER D 100 "
      ideal   model   delta    sigma   weight residual
     119.79  128.17   -8.38 1.18e+00 7.18e-01 5.04e+01
  angle pdb=" CA  SER E 100 "
        pdb=" C   SER E 100 "
        pdb=" O   SER E 100 "
      ideal   model   delta    sigma   weight residual
     119.79  128.14   -8.35 1.18e+00 7.18e-01 5.01e+01
  angle pdb=" CA  SER J 100 "
        pdb=" C   SER J 100 "
        pdb=" O   SER J 100 "
      ideal   model   delta    sigma   weight residual
     119.79  128.13   -8.34 1.18e+00 7.18e-01 4.99e+01
  angle pdb=" CA  SER H 100 "
        pdb=" C   SER H 100 "
        pdb=" O   SER H 100 "
      ideal   model   delta    sigma   weight residual
     119.79  128.13   -8.34 1.18e+00 7.18e-01 4.99e+01
  angle pdb=" CA  SER F 100 "
        pdb=" C   SER F 100 "
        pdb=" O   SER F 100 "
      ideal   model   delta    sigma   weight residual
     119.79  128.13   -8.34 1.18e+00 7.18e-01 4.99e+01
  ... (remaining 20395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 7995
       17.43 -    34.87: 981
       34.87 -    52.30: 144
       52.30 -    69.74: 60
       69.74 -    87.17: 12
  Dihedral angle restraints: 9192
    sinusoidal: 3672
      harmonic: 5520
  Sorted by residual:
  dihedral pdb=" C   THR B  29 "
           pdb=" N   THR B  29 "
           pdb=" CA  THR B  29 "
           pdb=" CB  THR B  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.91    9.91     0      2.50e+00 1.60e-01 1.57e+01
  dihedral pdb=" C   THR E  29 "
           pdb=" N   THR E  29 "
           pdb=" CA  THR E  29 "
           pdb=" CB  THR E  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.90    9.90     0      2.50e+00 1.60e-01 1.57e+01
  dihedral pdb=" C   THR D  29 "
           pdb=" N   THR D  29 "
           pdb=" CA  THR D  29 "
           pdb=" CB  THR D  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.90    9.90     0      2.50e+00 1.60e-01 1.57e+01
  ... (remaining 9189 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1762
       0.107 -    0.213: 519
       0.213 -    0.319: 71
       0.319 -    0.426: 28
       0.426 -    0.532: 20
  Chirality restraints: 2400
  Sorted by residual:
  chirality pdb=" CG  LEU D  66 "
            pdb=" CB  LEU D  66 "
            pdb=" CD1 LEU D  66 "
            pdb=" CD2 LEU D  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.09e+00
  chirality pdb=" CG  LEU B  66 "
            pdb=" CB  LEU B  66 "
            pdb=" CD1 LEU B  66 "
            pdb=" CD2 LEU B  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.09e+00
  chirality pdb=" CG  LEU K  66 "
            pdb=" CB  LEU K  66 "
            pdb=" CD1 LEU K  66 "
            pdb=" CD2 LEU K  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.08e+00
  ... (remaining 2397 not shown)

  Planarity restraints: 2640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  59 "    0.018 2.00e-02 2.50e+03   4.43e-02 3.43e+01
        pdb=" CG  PHE F  59 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  59 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  59 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  59 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  59 "    0.081 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  59 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K  59 "    0.018 2.00e-02 2.50e+03   4.42e-02 3.42e+01
        pdb=" CG  PHE K  59 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE K  59 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE K  59 "   -0.048 2.00e-02 2.50e+03
        pdb=" CE1 PHE K  59 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 PHE K  59 "    0.081 2.00e-02 2.50e+03
        pdb=" CZ  PHE K  59 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  59 "   -0.018 2.00e-02 2.50e+03   4.42e-02 3.42e+01
        pdb=" CG  PHE B  59 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  59 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  59 "    0.047 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  59 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  59 "   -0.081 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  59 "    0.056 2.00e-02 2.50e+03
  ... (remaining 2637 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1998
        2.74 -     3.28: 18358
        3.28 -     3.82: 31261
        3.82 -     4.36: 38557
        4.36 -     4.90: 62168
  Nonbonded interactions: 152342
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E  75 "
            pdb=" O   HOH E 201 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD1 ASP I  75 "
            pdb=" O   HOH I 201 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASP H  75 "
            pdb=" O   HOH H 201 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OD1 ASP J  75 "
            pdb=" O   HOH J 201 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OD1 ASP L  75 "
            pdb=" O   HOH L 201 "
     model   vdw
     2.204 3.040
  ... (remaining 152337 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.010
  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:             0.020
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     34.960
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  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:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
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      :  0.013   0.067  15036  Z= 0.801
  Angle     :  1.549   8.379  20400  Z= 1.068
  Chirality :  0.115   0.532   2400
  Planarity :  0.010   0.044   2640
  Dihedral  : 15.524  87.169   5592
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  :  8.21 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.17), residues: 1848
  helix:  0.45 (0.12), residues: 1404
  sheet:  None (None), residues: 0
  loop : -0.77 (0.24), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.013   TRP I 160 
 HIS   0.010   0.003   HIS G  51 
 PHE   0.081   0.012   PHE F  59 
 TYR   0.036   0.014   TYR J  16 
 ARG   0.031   0.005   ARG L 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21630 ( 1212)
  hydrogen bonds       : angle       6.13417 ( 3612)
  covalent geometry    : bond        0.01294 (15036)
  covalent geometry    : angle       1.54903 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 275
  time to evaluate  : 1.868 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.6760 (tt0) cc_final: 0.6329 (tp30)
REVERT: A  134 LYS cc_start: 0.7747 (mttp) cc_final: 0.7534 (mttt)
REVERT: B   25 GLU cc_start: 0.6780 (tt0) cc_final: 0.6328 (tp30)
REVERT: B  142 ASP cc_start: 0.7973 (m-30) cc_final: 0.7734 (m-30)
REVERT: C   25 GLU cc_start: 0.6764 (tt0) cc_final: 0.6331 (tp30)
REVERT: C  101 LYS cc_start: 0.7221 (mttt) cc_final: 0.6932 (mttm)
REVERT: D  101 LYS cc_start: 0.7262 (mttt) cc_final: 0.7023 (mttm)
REVERT: D  134 LYS cc_start: 0.7748 (mttp) cc_final: 0.7537 (mttp)
REVERT: D  138 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7024 (mm-30)
REVERT: E   22 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (p)
REVERT: E   25 GLU cc_start: 0.6758 (tt0) cc_final: 0.6317 (tp30)
REVERT: E  134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7486 (mttp)
REVERT: F   25 GLU cc_start: 0.6737 (tt0) cc_final: 0.6352 (tp30)
REVERT: F   70 ARG cc_start: 0.8416 (ttt180) cc_final: 0.7465 (ttp80)
REVERT: F   75 ASP cc_start: 0.8570 (m-30) cc_final: 0.8297 (t70)
REVERT: F  101 LYS cc_start: 0.7181 (mttt) cc_final: 0.6896 (mttm)
REVERT: F  134 LYS cc_start: 0.7664 (mttp) cc_final: 0.7463 (mttt)
REVERT: G   25 GLU cc_start: 0.6671 (tt0) cc_final: 0.6261 (tp30)
REVERT: G   35 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7730 (mtm110)
REVERT: G  134 LYS cc_start: 0.7695 (mttp) cc_final: 0.7478 (mttm)
REVERT: H   24 SER cc_start: 0.7174 (OUTLIER) cc_final: 0.6967 (p)
REVERT: H   25 GLU cc_start: 0.6767 (tt0) cc_final: 0.6349 (tp30)
REVERT: H   70 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8116 (ttt180)
REVERT: H   75 ASP cc_start: 0.8558 (m-30) cc_final: 0.8269 (t70)
REVERT: H  120 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8180 (mm-30)
REVERT: H  138 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6937 (mm-30)
REVERT: H  142 ASP cc_start: 0.7942 (m-30) cc_final: 0.7644 (m-30)
REVERT: I   25 GLU cc_start: 0.6744 (tt0) cc_final: 0.6359 (tp30)
REVERT: I  101 LYS cc_start: 0.7180 (mttt) cc_final: 0.6910 (mttm)
REVERT: J   35 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7695 (mtm110)
REVERT: J  101 LYS cc_start: 0.7248 (mttt) cc_final: 0.7033 (mttm)
REVERT: J  134 LYS cc_start: 0.7731 (mttp) cc_final: 0.7489 (mttp)
REVERT: J  142 ASP cc_start: 0.8001 (m-30) cc_final: 0.7790 (m-30)
REVERT: K   25 GLU cc_start: 0.6860 (tt0) cc_final: 0.6367 (tp30)
REVERT: K  134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7154 (mtpt)
REVERT: K  142 ASP cc_start: 0.8026 (m-30) cc_final: 0.7781 (m-30)
REVERT: L   25 GLU cc_start: 0.6769 (tt0) cc_final: 0.6321 (tp30)
REVERT: L  101 LYS cc_start: 0.7307 (mttt) cc_final: 0.7052 (mttm)
REVERT: L  142 ASP cc_start: 0.7957 (m-30) cc_final: 0.7726 (m-30)
  outliers start: 48
  outliers final: 9
  residues processed: 287
  average time/residue: 1.8551
  time to fit residues: 571.1066
Evaluate side-chains
  288 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 273
  time to evaluate  : 1.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain C residue   22 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain F residue   22 SER
Chi-restraints excluded: chain G residue   22 SER
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain H residue   22 SER
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue  138 GLU
Chi-restraints excluded: chain I residue   22 SER
Chi-restraints excluded: chain J residue   22 SER
Chi-restraints excluded: chain J residue   35 ARG
Chi-restraints excluded: chain L residue   22 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 151 optimal weight:    5.9990
   chunk 136 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 141 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 163 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 113 ASN
D 113 ASN
E 113 ASN
F 113 ASN
G 113 ASN
I 113 ASN
K 113 ASN
L 113 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.174771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.160973 restraints weight = 44077.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 1.04
r_work: 0.3610 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018  15036  Z= 0.168
  Angle     :  0.575   6.885  20400  Z= 0.326
  Chirality :  0.041   0.129   2400
  Planarity :  0.004   0.019   2640
  Dihedral  :  4.657  29.564   2053
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.64 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.18 (0.18), residues: 1848
  helix:  2.55 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop :  0.35 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP J 160 
 HIS   0.006   0.002   HIS K  63 
 PHE   0.010   0.002   PHE L  69 
 TYR   0.008   0.001   TYR C  16 
 ARG   0.003   0.001   ARG K  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08138 ( 1212)
  hydrogen bonds       : angle       4.05950 ( 3612)
  covalent geometry    : bond        0.00289 (15036)
  covalent geometry    : angle       0.57490 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 1.713 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7741 (ttp80)
REVERT: A  134 LYS cc_start: 0.7815 (mttp) cc_final: 0.7605 (mttp)
REVERT: F   70 ARG cc_start: 0.8303 (ttt180) cc_final: 0.7503 (ttp80)
REVERT: F  134 LYS cc_start: 0.7838 (mttp) cc_final: 0.7488 (mtpt)
REVERT: G  134 LYS cc_start: 0.7882 (mttp) cc_final: 0.7656 (mttp)
REVERT: H   35 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7754 (ttp80)
REVERT: J  101 LYS cc_start: 0.7530 (mttt) cc_final: 0.7249 (mttm)
REVERT: J  134 LYS cc_start: 0.7829 (mttp) cc_final: 0.7624 (mttp)
REVERT: L   35 ARG cc_start: 0.8011 (mtp-110) cc_final: 0.7715 (ttp80)
REVERT: L   65 MET cc_start: 0.8684 (ttp) cc_final: 0.8470 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 1.9885
  time to fit residues: 614.0922
Evaluate side-chains
  268 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 1.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 129 optimal weight:    0.7980
   chunk 154 optimal weight:    7.9990
   chunk 144 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 133 optimal weight:    6.9990
   chunk 164 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 116 optimal weight:    6.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
B 113 ASN
C 113 ASN
D  39 GLN
D 113 ASN
E  39 GLN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I 113 ASN
J  39 GLN
L 113 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.171990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.157907 restraints weight = 45018.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 1.09
r_work: 0.3585 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  15036  Z= 0.181
  Angle     :  0.585   7.870  20400  Z= 0.334
  Chirality :  0.041   0.146   2400
  Planarity :  0.004   0.030   2640
  Dihedral  :  4.147  18.696   2028
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.63 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.23 (0.17), residues: 1848
  helix:  2.53 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.74 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K  52 
 HIS   0.007   0.002   HIS B  63 
 PHE   0.011   0.002   PHE C  59 
 TYR   0.009   0.001   TYR C  16 
 ARG   0.003   0.001   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08533 ( 1212)
  hydrogen bonds       : angle       4.08918 ( 3612)
  covalent geometry    : bond        0.00322 (15036)
  covalent geometry    : angle       0.58480 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 286
  time to evaluate  : 1.859 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.7839 (mttp) cc_final: 0.7623 (mttt)
REVERT: F  134 LYS cc_start: 0.7877 (mttp) cc_final: 0.7515 (mtpt)
REVERT: G  134 LYS cc_start: 0.7897 (mttp) cc_final: 0.7677 (mttp)
REVERT: H  140 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6760 (mtmm)
REVERT: J   55 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7492 (ptm160)
REVERT: J  134 LYS cc_start: 0.7845 (mttp) cc_final: 0.7641 (mttp)
  outliers start: 5
  outliers final: 2
  residues processed: 286
  average time/residue: 1.9993
  time to fit residues: 611.3095
Evaluate side-chains
  283 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 280
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain J residue   55 ARG
Chi-restraints excluded: chain K residue   17 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 122 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 177 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 164 optimal weight:    0.5980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A 113 ASN
B 113 ASN
C 113 ASN
D  39 GLN
D 113 ASN
E  39 GLN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I 113 ASN
J  39 GLN
K 113 ASN
L 113 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.172389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.158304 restraints weight = 45790.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.13
r_work: 0.3586 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3498 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  15036  Z= 0.176
  Angle     :  0.572   7.697  20400  Z= 0.325
  Chirality :  0.040   0.137   2400
  Planarity :  0.003   0.028   2640
  Dihedral  :  4.171  18.896   2028
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.13 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.30 (0.17), residues: 1848
  helix:  2.56 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.80 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K  52 
 HIS   0.007   0.002   HIS K  63 
 PHE   0.010   0.002   PHE C  59 
 TYR   0.009   0.001   TYR C  16 
 ARG   0.003   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08319 ( 1212)
  hydrogen bonds       : angle       4.03286 ( 3612)
  covalent geometry    : bond        0.00312 (15036)
  covalent geometry    : angle       0.57175 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 290
  time to evaluate  : 1.860 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7750 (ttp80)
REVERT: A  134 LYS cc_start: 0.7850 (mttp) cc_final: 0.7623 (mttt)
REVERT: B   35 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7610 (ttp80)
REVERT: F  134 LYS cc_start: 0.7860 (mttp) cc_final: 0.7495 (mtpt)
REVERT: H   35 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7718 (ttp80)
REVERT: H  120 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8212 (mm-30)
REVERT: J   55 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7505 (ptm160)
REVERT: L  138 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6590 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 290
  average time/residue: 1.9716
  time to fit residues: 611.2974
Evaluate side-chains
  286 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 281
  time to evaluate  : 1.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain J residue   17 THR
Chi-restraints excluded: chain J residue   55 ARG
Chi-restraints excluded: chain K residue   17 THR
Chi-restraints excluded: chain L residue  138 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 136 optimal weight:    6.9990
   chunk 157 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 134 optimal weight:    8.9990
   chunk 129 optimal weight:    0.0070
   chunk 15 optimal weight:   10.0000
   chunk 161 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 144 optimal weight:    0.1980
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.4404

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
B 113 ASN
C  39 GLN
C 113 ASN
D  39 GLN
D 113 ASN
E  39 GLN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I 113 ASN
J  39 GLN
L 113 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.173362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.159376 restraints weight = 46903.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 1.08
r_work: 0.3602 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  15036  Z= 0.169
  Angle     :  0.563   9.375  20400  Z= 0.316
  Chirality :  0.040   0.135   2400
  Planarity :  0.003   0.025   2640
  Dihedral  :  4.144  18.954   2028
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.32 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.43 (0.18), residues: 1848
  helix:  2.65 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.88 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K  52 
 HIS   0.006   0.002   HIS K  63 
 PHE   0.009   0.002   PHE C  59 
 TYR   0.008   0.001   TYR C  16 
 ARG   0.004   0.000   ARG E  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08100 ( 1212)
  hydrogen bonds       : angle       3.97925 ( 3612)
  covalent geometry    : bond        0.00295 (15036)
  covalent geometry    : angle       0.56299 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 287
  time to evaluate  : 1.655 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7770 (ttp80)
REVERT: A   55 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7362 (ptm160)
REVERT: B   35 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7667 (ttp80)
REVERT: F  134 LYS cc_start: 0.7858 (mttp) cc_final: 0.7497 (mtpt)
REVERT: H   35 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7686 (ttp80)
REVERT: H  120 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8246 (mm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 287
  average time/residue: 1.9529
  time to fit residues: 599.1735
Evaluate side-chains
  284 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 279
  time to evaluate  : 1.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain I residue  138 GLU
Chi-restraints excluded: chain J residue   17 THR
Chi-restraints excluded: chain K residue   17 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 179 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 146 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
B 113 ASN
C  39 GLN
C 113 ASN
D  39 GLN
D 113 ASN
E  39 GLN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I 113 ASN
J  39 GLN
K 113 ASN
L 113 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.172185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.158398 restraints weight = 43200.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.02
r_work: 0.3592 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  15036  Z= 0.179
  Angle     :  0.582   8.064  20400  Z= 0.328
  Chirality :  0.041   0.144   2400
  Planarity :  0.004   0.043   2640
  Dihedral  :  4.195  19.176   2028
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.57 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.33 (0.17), residues: 1848
  helix:  2.56 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.89 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K  52 
 HIS   0.007   0.002   HIS A  63 
 PHE   0.010   0.002   PHE C  59 
 TYR   0.009   0.001   TYR C  16 
 ARG   0.007   0.001   ARG G  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08398 ( 1212)
  hydrogen bonds       : angle       4.03509 ( 3612)
  covalent geometry    : bond        0.00320 (15036)
  covalent geometry    : angle       0.58234 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 284
  time to evaluate  : 1.934 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7973 (mtp-110) cc_final: 0.7742 (ttp80)
REVERT: A   55 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7341 (ptm160)
REVERT: A  138 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6505 (mp0)
REVERT: B   35 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7644 (ttp80)
REVERT: F  134 LYS cc_start: 0.7846 (mttp) cc_final: 0.7471 (mtpt)
REVERT: G   55 ARG cc_start: 0.8041 (ptp90) cc_final: 0.7829 (ptm160)
REVERT: J   55 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7511 (ptm160)
REVERT: J  101 LYS cc_start: 0.7515 (mttp) cc_final: 0.7264 (mttm)
  outliers start: 12
  outliers final: 3
  residues processed: 284
  average time/residue: 2.1281
  time to fit residues: 646.4751
Evaluate side-chains
  287 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 281
  time to evaluate  : 1.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain J residue   17 THR
Chi-restraints excluded: chain J residue   55 ARG
Chi-restraints excluded: chain K residue   17 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 137 optimal weight:    4.9990
   chunk 145 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 140 optimal weight:    0.9980
   chunk 135 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A 113 ASN
C  39 GLN
C 113 ASN
D  39 GLN
D 113 ASN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I 113 ASN
J  39 GLN
L 113 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.170996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.156710 restraints weight = 46400.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.10
r_work: 0.3566 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  15036  Z= 0.194
  Angle     :  0.609   8.142  20400  Z= 0.344
  Chirality :  0.042   0.155   2400
  Planarity :  0.004   0.041   2640
  Dihedral  :  4.265  19.364   2028
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.70 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.15 (0.17), residues: 1848
  helix:  2.44 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.84 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 160 
 HIS   0.008   0.002   HIS B  63 
 PHE   0.011   0.002   PHE C  59 
 TYR   0.010   0.002   TYR C  16 
 ARG   0.009   0.001   ARG G  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08755 ( 1212)
  hydrogen bonds       : angle       4.11460 ( 3612)
  covalent geometry    : bond        0.00358 (15036)
  covalent geometry    : angle       0.60892 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 283
  time to evaluate  : 1.809 
Fit side-chains
REVERT: A   55 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7411 (ptm160)
REVERT: B   35 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7664 (ttp80)
REVERT: F  134 LYS cc_start: 0.7879 (mttp) cc_final: 0.7500 (mtpt)
REVERT: G   55 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7913 (ptm160)
REVERT: J   55 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7537 (ptm160)
REVERT: J  101 LYS cc_start: 0.7539 (mttp) cc_final: 0.7290 (mttm)
  outliers start: 10
  outliers final: 3
  residues processed: 283
  average time/residue: 2.0857
  time to fit residues: 632.6704
Evaluate side-chains
  285 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 280
  time to evaluate  : 3.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain J residue   17 THR
Chi-restraints excluded: chain J residue   55 ARG
Chi-restraints excluded: chain K residue   17 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 134 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 142 optimal weight:    7.9990
   chunk 153 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 163 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 179 optimal weight:    7.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
C  39 GLN
C 113 ASN
D  39 GLN
D 113 ASN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I 113 ASN
J  39 GLN
K 113 ASN
L 113 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.177647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.164283 restraints weight = 40064.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 0.98
r_work: 0.3657 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  15036  Z= 0.149
  Angle     :  0.517   7.509  20400  Z= 0.289
  Chirality :  0.038   0.110   2400
  Planarity :  0.003   0.035   2640
  Dihedral  :  4.048  18.364   2028
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.07 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.66 (0.18), residues: 1848
  helix:  2.82 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop :  0.83 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP I  52 
 HIS   0.005   0.001   HIS K  63 
 PHE   0.006   0.001   PHE L  69 
 TYR   0.006   0.001   TYR C  16 
 ARG   0.005   0.000   ARG G  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07236 ( 1212)
  hydrogen bonds       : angle       3.82018 ( 3612)
  covalent geometry    : bond        0.00249 (15036)
  covalent geometry    : angle       0.51680 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 301
  time to evaluate  : 1.713 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.7691 (ttp80)
REVERT: A   55 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7294 (ptm160)
REVERT: B   70 ARG cc_start: 0.8382 (tpt170) cc_final: 0.8021 (ttt-90)
REVERT: B  138 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6341 (mp0)
REVERT: C  142 ASP cc_start: 0.7681 (m-30) cc_final: 0.7480 (m-30)
REVERT: F  134 LYS cc_start: 0.7778 (mttp) cc_final: 0.7373 (mtpt)
REVERT: G   35 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7587 (ttp80)
REVERT: H   35 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7650 (ttp80)
REVERT: H  120 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8225 (mm-30)
REVERT: J   35 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7747 (ttp80)
REVERT: J   55 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7440 (ptm160)
REVERT: J  101 LYS cc_start: 0.7474 (mttp) cc_final: 0.7224 (mttm)
REVERT: K  138 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6378 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 301
  average time/residue: 1.9640
  time to fit residues: 633.4100
Evaluate side-chains
  291 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 287
  time to evaluate  : 1.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain J residue   55 ARG
Chi-restraints excluded: chain K residue   17 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 147 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 73 optimal weight:    8.9990
   chunk 163 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 174 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 113 ASN
C  39 GLN
C 113 ASN
D  39 GLN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I  39 GLN
I 113 ASN
J  39 GLN
L 113 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.170901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.157199 restraints weight = 40563.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 0.94
r_work: 0.3587 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3499 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  15036  Z= 0.199
  Angle     :  0.609   8.252  20400  Z= 0.347
  Chirality :  0.042   0.161   2400
  Planarity :  0.004   0.035   2640
  Dihedral  :  4.257  19.384   2028
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.38 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.20 (0.17), residues: 1848
  helix:  2.48 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.85 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 160 
 HIS   0.008   0.002   HIS A  63 
 PHE   0.012   0.002   PHE C  59 
 TYR   0.010   0.002   TYR C  16 
 ARG   0.006   0.001   ARG G 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08809 ( 1212)
  hydrogen bonds       : angle       4.12079 ( 3612)
  covalent geometry    : bond        0.00372 (15036)
  covalent geometry    : angle       0.60866 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 288
  time to evaluate  : 1.915 
Fit side-chains
REVERT: A   55 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7369 (ptm160)
REVERT: C   70 ARG cc_start: 0.8308 (ttt180) cc_final: 0.7641 (ttp80)
REVERT: F  134 LYS cc_start: 0.7860 (mttp) cc_final: 0.7505 (mtpt)
REVERT: J   55 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7464 (ptm160)
REVERT: J  101 LYS cc_start: 0.7510 (mttp) cc_final: 0.7262 (mttm)
  outliers start: 7
  outliers final: 2
  residues processed: 288
  average time/residue: 1.9290
  time to fit residues: 594.7953
Evaluate side-chains
  285 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 281
  time to evaluate  : 1.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain J residue   55 ARG
Chi-restraints excluded: chain K residue   17 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 166 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 118 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 164 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 177 optimal weight:    8.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 113 ASN
C  39 GLN
C 113 ASN
D  39 GLN
D 113 ASN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I  39 GLN
I 113 ASN
J  39 GLN
K 113 ASN
L 113 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.171956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.157805 restraints weight = 45496.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.14
r_work: 0.3574 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3466
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15036  Z= 0.185
  Angle     :  0.589   8.136  20400  Z= 0.334
  Chirality :  0.041   0.149   2400
  Planarity :  0.004   0.032   2640
  Dihedral  :  4.249  19.228   2028
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.38 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.23 (0.17), residues: 1848
  helix:  2.50 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.84 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K  52 
 HIS   0.007   0.002   HIS A  63 
 PHE   0.010   0.002   PHE C  59 
 TYR   0.009   0.001   TYR C  16 
 ARG   0.005   0.001   ARG I  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08493 ( 1212)
  hydrogen bonds       : angle       4.06526 ( 3612)
  covalent geometry    : bond        0.00334 (15036)
  covalent geometry    : angle       0.58851 (20400)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 286
  time to evaluate  : 1.745 
Fit side-chains
REVERT: A   55 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7372 (ptm160)
REVERT: C   70 ARG cc_start: 0.8354 (ttt180) cc_final: 0.7687 (ttp80)
REVERT: F  134 LYS cc_start: 0.7875 (mttp) cc_final: 0.7501 (mtpt)
REVERT: J   55 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7516 (ptm160)
REVERT: J  101 LYS cc_start: 0.7531 (mttp) cc_final: 0.7274 (mttm)
  outliers start: 5
  outliers final: 2
  residues processed: 286
  average time/residue: 2.1777
  time to fit residues: 673.5588
Evaluate side-chains
  287 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 283
  time to evaluate  : 1.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain J residue   55 ARG
Chi-restraints excluded: chain K residue   17 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 166 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 133 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 165 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 162 optimal weight:    6.9990
   chunk 34 optimal weight:    0.2980
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
C  39 GLN
C 113 ASN
D  39 GLN
D 113 ASN
E 113 ASN
F 113 ASN
G 113 ASN
H 113 ASN
I  39 GLN
I 113 ASN
J  39 GLN
K 113 ASN
L 113 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.171666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.157677 restraints weight = 42322.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 0.97
r_work: 0.3575 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  15036  Z= 0.186
  Angle     :  0.592   8.084  20400  Z= 0.336
  Chirality :  0.041   0.153   2400
  Planarity :  0.004   0.035   2640
  Dihedral  :  4.260  19.311   2028
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.26 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.21 (0.17), residues: 1848
  helix:  2.49 (0.12), residues: 1452
  sheet:  None (None), residues: 0
  loop :  0.82 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K  52 
 HIS   0.007   0.002   HIS B  63 
 PHE   0.010   0.002   PHE C  59 
 TYR   0.010   0.001   TYR C  16 
 ARG   0.005   0.001   ARG I  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08548 ( 1212)
  hydrogen bonds       : angle       4.07306 ( 3612)
  covalent geometry    : bond        0.00338 (15036)
  covalent geometry    : angle       0.59198 (20400)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 18014.24 seconds
wall clock time: 312 minutes 55.30 seconds (18775.30 seconds total)