Starting phenix.real_space_refine
on Fri Dec 27 05:40:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tdo_41172/12_2024/8tdo_41172.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tdo_41172/12_2024/8tdo_41172.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tdo_41172/12_2024/8tdo_41172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tdo_41172/12_2024/8tdo_41172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tdo_41172/12_2024/8tdo_41172.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tdo_41172/12_2024/8tdo_41172.cif"
  }
  resolution = 3.1
  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=   1.000
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       8      5.16       5
     C    1856      2.51       5
     N     480      2.21       5
     O     548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 2892
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 723
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 5, 'TRANS': 87}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E
  Time building chain proxies: 2.02, per 1000 atoms: 0.70
  Number of scatterers: 2892
  At special positions: 0
  Unit cell: (78.02, 83.83, 36.52, 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       8     16.00
     O     548      8.00
     N     480      7.00
     C    1856      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 333.3 milliseconds
  

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  712

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 60.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 16
      removed outlier: 6.399A  pdb=" N   LEU A  12 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   LYS B  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL A  14 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 22
      removed outlier: 6.253A  pdb=" N   VAL A  20 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 35
      removed outlier: 6.419A  pdb=" N   ALA A  25 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL C  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ASN A  27 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   VAL C  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ALA A  29 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   VAL C  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   HIS A  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   ARG C  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   PHE A  33 " --> pdb=" O   ARG C  34 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ALA C  25 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   VAL E  28 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN C  27 " --> pdb=" O   VAL E  28 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   VAL E  30 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA C  29 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   VAL E  32 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   HIS C  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   ARG E  34 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   PHE C  33 " --> pdb=" O   ARG E  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 80
      removed outlier: 6.839A  pdb=" N   LYS B  70 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   VAL A  71 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   GLU B  72 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ILE A  73 " --> pdb=" O   GLU B  72 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   TRP A  79 " --> pdb=" O   TYR B  78 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   LYS B  80 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   GLU A  61 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   GLU C  62 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   GLU A  63 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   PHE C  64 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   VAL A  65 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   GLU C  66 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   GLY A  67 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ILE C  68 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TYR A  69 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ASP C  74 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   THR A  75 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LYS C  76 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   SER A  77 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   TYR C  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR C  60 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   GLU E  63 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLU C  62 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   VAL E  65 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   PHE C  64 " --> pdb=" O   VAL E  65 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   GLY E  67 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   GLU C  66 " --> pdb=" O   GLY E  67 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   TYR E  69 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 8.479A  pdb=" N   ILE C  68 " --> pdb=" O   TYR E  69 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   VAL E  71 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   LYS C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 9.983A  pdb=" N   ILE E  73 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   GLU C  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   THR E  75 " --> pdb=" O   GLU C  72 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ASP C  74 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   SER E  77 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   LYS C  76 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   TRP E  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   TYR C  78 " --> pdb=" O   TRP E  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 99
      removed outlier: 6.661A  pdb=" N   VAL A  93 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   THR C  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE A  95 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   ASN C  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ALA A  97 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL C  93 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   THR E  96 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   PHE C  95 " --> pdb=" O   THR E  96 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASN E  98 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ALA C  97 " --> pdb=" O   ASN E  98 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 110
      removed outlier: 6.632A  pdb=" N   ARG A 104 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   ILE B 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   THR A 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ALA B 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   ALA A 108 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   LEU C 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU E 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 118 through 123
      removed outlier: 5.728A  pdb=" N   THR A 118 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   VAL C 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ALA A 120 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   THR C 123 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL A 122 " --> pdb=" O   THR C 123 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   THR C 118 " --> pdb=" O   THR E 119 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   VAL E 121 " --> pdb=" O   THR C 118 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ALA C 120 " --> pdb=" O   VAL E 121 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   THR E 123 " --> pdb=" O   ALA C 120 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   VAL C 122 " --> pdb=" O   THR E 123 " (cutoff:3.500A)

    68 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.74

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 912
        1.34 -     1.45: 406
        1.45 -     1.57: 1630
        1.57 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 2960
  Sorted by residual:
  bond pdb=" CA  LYS E  35 "
       pdb=" C   LYS E  35 "
    ideal  model  delta    sigma   weight residual
    1.522  1.505  0.017 1.22e-02 6.72e+03 1.97e+00
  bond pdb=" CA  LYS B  35 "
       pdb=" C   LYS B  35 "
    ideal  model  delta    sigma   weight residual
    1.522  1.505  0.017 1.22e-02 6.72e+03 1.83e+00
  bond pdb=" C   LYS C  35 "
       pdb=" O   LYS C  35 "
    ideal  model  delta    sigma   weight residual
    1.235  1.218  0.017 1.28e-02 6.10e+03 1.77e+00
  bond pdb=" CA  LYS A  35 "
       pdb=" C   LYS A  35 "
    ideal  model  delta    sigma   weight residual
    1.522  1.506  0.016 1.22e-02 6.72e+03 1.76e+00
  bond pdb=" C   LYS A  35 "
       pdb=" O   LYS A  35 "
    ideal  model  delta    sigma   weight residual
    1.235  1.218  0.017 1.28e-02 6.10e+03 1.75e+00
  ... (remaining 2955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.73: 3493
        0.73 -     1.46: 430
        1.46 -     2.19: 65
        2.19 -     2.92: 31
        2.92 -     3.65: 13
  Bond angle restraints: 4032
  Sorted by residual:
  angle pdb=" C   TYR E 116 "
        pdb=" N   SER E 117 "
        pdb=" CA  SER E 117 "
      ideal   model   delta    sigma   weight residual
     122.53  119.82    2.71 1.61e+00 3.86e-01 2.84e+00
  angle pdb=" C   ARG A  34 "
        pdb=" N   LYS A  35 "
        pdb=" CA  LYS A  35 "
      ideal   model   delta    sigma   weight residual
     122.94  120.44    2.50 1.50e+00 4.44e-01 2.78e+00
  angle pdb=" C   TYR C 116 "
        pdb=" N   SER C 117 "
        pdb=" CA  SER C 117 "
      ideal   model   delta    sigma   weight residual
     122.53  119.86    2.67 1.61e+00 3.86e-01 2.75e+00
  angle pdb=" C   TYR B 116 "
        pdb=" N   SER B 117 "
        pdb=" CA  SER B 117 "
      ideal   model   delta    sigma   weight residual
     122.53  119.86    2.67 1.61e+00 3.86e-01 2.74e+00
  angle pdb=" C   TYR A 116 "
        pdb=" N   SER A 117 "
        pdb=" CA  SER A 117 "
      ideal   model   delta    sigma   weight residual
     122.53  119.87    2.66 1.61e+00 3.86e-01 2.73e+00
  ... (remaining 4027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.48: 1404
        9.48 -    18.96: 196
       18.96 -    28.43: 80
       28.43 -    37.91: 52
       37.91 -    47.39: 20
  Dihedral angle restraints: 1752
    sinusoidal: 656
      harmonic: 1096
  Sorted by residual:
  dihedral pdb=" CA  ILE B  26 "
           pdb=" C   ILE B  26 "
           pdb=" N   ASN B  27 "
           pdb=" CA  ASN B  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.50   18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ILE E  26 "
           pdb=" C   ILE E  26 "
           pdb=" N   ASN E  27 "
           pdb=" CA  ASN E  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.51   18.49     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ILE A  26 "
           pdb=" C   ILE A  26 "
           pdb=" N   ASN A  27 "
           pdb=" CA  ASN A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.52   18.48     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 1749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 167
       0.024 -    0.048: 182
       0.048 -    0.071: 56
       0.071 -    0.095: 23
       0.095 -    0.119: 44
  Chirality restraints: 472
  Sorted by residual:
  chirality pdb=" CA  VAL E 121 "
            pdb=" N   VAL E 121 "
            pdb=" C   VAL E 121 "
            pdb=" CB  VAL E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.53e-01
  chirality pdb=" CA  ILE B 107 "
            pdb=" N   ILE B 107 "
            pdb=" C   ILE B 107 "
            pdb=" CB  ILE B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.45e-01
  chirality pdb=" CA  ILE E 107 "
            pdb=" N   ILE E 107 "
            pdb=" C   ILE E 107 "
            pdb=" CB  ILE E 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 469 not shown)

  Planarity restraints: 504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 101 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO B 102 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 102 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 102 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 101 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO E 102 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO E 102 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO E 102 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 101 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 102 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 501 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 105
        2.72 -     3.26: 2646
        3.26 -     3.81: 4631
        3.81 -     4.35: 5577
        4.35 -     4.90: 10452
  Nonbonded interactions: 23411
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C  35 "
            pdb=" OE2 GLU E  62 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" OE2 GLU A  62 "
            pdb=" NZ  LYS B  35 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS A  35 "
            pdb=" OE2 GLU C  62 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   SER C  85 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.305 3.040
  ... (remaining 23406 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.180
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
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      :  0.005   0.024   2960  Z= 0.345
  Angle     :  0.556   3.654   4032  Z= 0.311
  Chirality :  0.048   0.119    472
  Planarity :  0.006   0.063    504
  Dihedral  : 13.248  47.389   1040
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.39 %
    Favored  : 88.61 %
  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: -3.41 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  79 
 HIS   0.001   0.000   HIS E  31 
 PHE   0.011   0.003   PHE B  87 
 TYR   0.014   0.003   TYR C 114 
 ARG   0.005   0.001   ARG E  21 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.6864 (ttm-80)
REVERT: B   89 GLU cc_start: 0.7445 (tp30) cc_final: 0.7180 (pm20)
REVERT: B  103 ARG cc_start: 0.8559 (mtm180) cc_final: 0.8117 (mtm-85)
REVERT: C   21 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6987 (ttm-80)
REVERT: C   23 SER cc_start: 0.8760 (p) cc_final: 0.8343 (m)
REVERT: C   69 TYR cc_start: 0.9063 (m-80) cc_final: 0.8265 (m-80)
REVERT: E   18 ASP cc_start: 0.8298 (t0) cc_final: 0.7880 (m-30)
REVERT: E   23 SER cc_start: 0.8577 (p) cc_final: 0.8258 (t)
REVERT: E   72 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8220 (mt-10)
REVERT: E   84 SER cc_start: 0.8072 (t) cc_final: 0.7610 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.2057
  time to fit residues: 16.1022
Evaluate side-chains
  61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0270
   chunk 28 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.9042

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2960  Z= 0.259
  Angle     :  0.507   3.751   4032  Z= 0.279
  Chirality :  0.048   0.113    472
  Planarity :  0.005   0.044    504
  Dihedral  :  4.949  19.896    400
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.03 %
    Favored  : 85.76 %
  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: -3.58 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  79 
 HIS   0.003   0.001   HIS E  88 
 PHE   0.010   0.002   PHE A  87 
 TYR   0.015   0.002   TYR C 114 
 ARG   0.003   0.000   ARG C 104 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: B   21 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7102 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8128 (mtm-85)
REVERT: C   13 MET cc_start: 0.7476 (tpt) cc_final: 0.6928 (tmm)
REVERT: C   21 ARG cc_start: 0.7233 (ttm-80) cc_final: 0.6591 (ttm-80)
REVERT: C   23 SER cc_start: 0.8883 (p) cc_final: 0.8338 (m)
REVERT: C   69 TYR cc_start: 0.9077 (m-80) cc_final: 0.8258 (m-80)
REVERT: E   18 ASP cc_start: 0.8483 (t0) cc_final: 0.8060 (m-30)
REVERT: E   21 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7315 (ttm-80)
REVERT: E   23 SER cc_start: 0.8656 (p) cc_final: 0.8209 (t)
REVERT: E   72 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8247 (mt-10)
REVERT: E   84 SER cc_start: 0.8117 (t) cc_final: 0.7655 (m)
REVERT: E  103 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8632 (mtm-85)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 0.2407
  time to fit residues: 18.3641
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.024   2960  Z= 0.373
  Angle     :  0.527   3.571   4032  Z= 0.288
  Chirality :  0.048   0.122    472
  Planarity :  0.005   0.032    504
  Dihedral  :  5.036  21.172    400
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.66 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  79 
 HIS   0.002   0.001   HIS E  90 
 PHE   0.012   0.002   PHE A  87 
 TYR   0.026   0.003   TYR A 114 
 ARG   0.004   0.000   ARG C 104 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.9154 (m-80) cc_final: 0.8591 (m-80)
REVERT: B   13 MET cc_start: 0.7666 (tpt) cc_final: 0.7363 (tpp)
REVERT: B   21 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7140 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8519 (mtm180) cc_final: 0.8319 (mtm180)
REVERT: B  116 TYR cc_start: 0.8406 (m-80) cc_final: 0.8107 (m-80)
REVERT: C   13 MET cc_start: 0.7477 (tpt) cc_final: 0.6919 (tmm)
REVERT: C   21 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6618 (ttm-80)
REVERT: C   23 SER cc_start: 0.8889 (p) cc_final: 0.8356 (m)
REVERT: C   69 TYR cc_start: 0.9125 (m-80) cc_final: 0.8228 (m-80)
REVERT: C   89 GLU cc_start: 0.8034 (tp30) cc_final: 0.7819 (tp30)
REVERT: E   18 ASP cc_start: 0.8485 (t0) cc_final: 0.8059 (m-30)
REVERT: E   21 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7275 (ttm-80)
REVERT: E   23 SER cc_start: 0.8720 (p) cc_final: 0.8107 (t)
REVERT: E   72 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8215 (mt-10)
REVERT: E   84 SER cc_start: 0.8122 (t) cc_final: 0.7649 (m)
  outliers start: 7
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2439
  time to fit residues: 17.9011
Evaluate side-chains
  66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2960  Z= 0.240
  Angle     :  0.479   3.482   4032  Z= 0.261
  Chirality :  0.047   0.114    472
  Planarity :  0.004   0.031    504
  Dihedral  :  4.814  20.175    400
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 11.08 %
    Favored  : 85.76 %
  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: -3.59 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  79 
 HIS   0.002   0.001   HIS E  90 
 PHE   0.009   0.001   PHE A  87 
 TYR   0.018   0.002   TYR A 114 
 ARG   0.003   0.000   ARG C 104 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.9160 (m-80) cc_final: 0.8617 (m-80)
REVERT: B   13 MET cc_start: 0.7637 (tpt) cc_final: 0.7404 (tpp)
REVERT: B   21 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7159 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8208 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8367 (m-80) cc_final: 0.7947 (m-80)
REVERT: C   13 MET cc_start: 0.7492 (tpt) cc_final: 0.6903 (tmm)
REVERT: C   21 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6626 (ttm-80)
REVERT: C   23 SER cc_start: 0.8863 (p) cc_final: 0.8301 (m)
REVERT: E   18 ASP cc_start: 0.8493 (t0) cc_final: 0.8082 (m-30)
REVERT: E   21 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7270 (ttm-80)
REVERT: E   23 SER cc_start: 0.8716 (p) cc_final: 0.8079 (t)
REVERT: E   72 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8183 (mt-10)
REVERT: E   84 SER cc_start: 0.8139 (t) cc_final: 0.7669 (m)
REVERT: E   89 GLU cc_start: 0.7828 (tp30) cc_final: 0.7594 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.2304
  time to fit residues: 17.2174
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   2960  Z= 0.309
  Angle     :  0.499   4.411   4032  Z= 0.270
  Chirality :  0.048   0.120    472
  Planarity :  0.004   0.038    504
  Dihedral  :  4.828  20.602    400
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.34 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  79 
 HIS   0.002   0.001   HIS A  88 
 PHE   0.007   0.001   PHE E  33 
 TYR   0.018   0.002   TYR A 114 
 ARG   0.004   0.000   ARG C 104 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7573 (tpt) cc_final: 0.7211 (tpp)
REVERT: B   13 MET cc_start: 0.7603 (tpt) cc_final: 0.7383 (tpp)
REVERT: B   21 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7180 (ttm-80)
REVERT: B   89 GLU cc_start: 0.7806 (tp30) cc_final: 0.7270 (pm20)
REVERT: B  103 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8156 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8402 (m-80) cc_final: 0.7984 (m-80)
REVERT: C   13 MET cc_start: 0.7491 (tpt) cc_final: 0.6903 (tmm)
REVERT: C   21 ARG cc_start: 0.7317 (ttm-80) cc_final: 0.6600 (ttm-80)
REVERT: C   23 SER cc_start: 0.8891 (p) cc_final: 0.8317 (m)
REVERT: C   89 GLU cc_start: 0.7993 (tp30) cc_final: 0.7773 (tp30)
REVERT: E   18 ASP cc_start: 0.8496 (t0) cc_final: 0.8090 (m-30)
REVERT: E   21 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7268 (ttm-80)
REVERT: E   23 SER cc_start: 0.8774 (p) cc_final: 0.8117 (t)
REVERT: E   72 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8244 (mt-10)
REVERT: E   84 SER cc_start: 0.8100 (t) cc_final: 0.7624 (m)
REVERT: E   89 GLU cc_start: 0.7800 (tp30) cc_final: 0.7587 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.2557
  time to fit residues: 19.5639
Evaluate side-chains
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 28 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
C  27 ASN
E  27 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2960  Z= 0.345
  Angle     :  0.510   4.232   4032  Z= 0.277
  Chirality :  0.048   0.116    472
  Planarity :  0.005   0.045    504
  Dihedral  :  4.888  20.808    400
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.66 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.55 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  79 
 HIS   0.001   0.001   HIS B  88 
 PHE   0.012   0.001   PHE A  87 
 TYR   0.018   0.002   TYR A 114 
 ARG   0.007   0.001   ARG E  34 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7568 (tpt) cc_final: 0.7168 (tpp)
REVERT: B   13 MET cc_start: 0.7581 (tpt) cc_final: 0.7374 (tpp)
REVERT: B   89 GLU cc_start: 0.7862 (tp30) cc_final: 0.7346 (pm20)
REVERT: B  103 ARG cc_start: 0.8506 (mtm180) cc_final: 0.8137 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8425 (m-80) cc_final: 0.8017 (m-80)
REVERT: C   13 MET cc_start: 0.7475 (tpt) cc_final: 0.6921 (tmm)
REVERT: C   21 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.6261 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8508 (t0) cc_final: 0.8096 (m-30)
REVERT: E   21 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7172 (ttm-80)
REVERT: E   23 SER cc_start: 0.8790 (p) cc_final: 0.8125 (t)
REVERT: E   72 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8228 (mt-10)
REVERT: E   89 GLU cc_start: 0.7906 (tp30) cc_final: 0.7656 (tp30)
  outliers start: 9
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2360
  time to fit residues: 17.5434
Evaluate side-chains
  66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   90 HIS
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0970
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2960  Z= 0.265
  Angle     :  0.489   3.815   4032  Z= 0.266
  Chirality :  0.047   0.114    472
  Planarity :  0.005   0.048    504
  Dihedral  :  4.780  19.943    400
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.97 %
    Favored  : 83.86 %
  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: -3.57 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  79 
 HIS   0.001   0.000   HIS B  88 
 PHE   0.016   0.001   PHE A  87 
 TYR   0.016   0.002   TYR A 114 
 ARG   0.009   0.001   ARG E  34 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7550 (tpt) cc_final: 0.7149 (tpp)
REVERT: B   13 MET cc_start: 0.7510 (tpt) cc_final: 0.7303 (tpp)
REVERT: B  103 ARG cc_start: 0.8511 (mtm180) cc_final: 0.8158 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8395 (m-80) cc_final: 0.7956 (m-80)
REVERT: C   13 MET cc_start: 0.7473 (tpt) cc_final: 0.6935 (tmm)
REVERT: C   21 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6587 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8499 (t0) cc_final: 0.8093 (m-30)
REVERT: E   21 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7270 (ttm-80)
REVERT: E   23 SER cc_start: 0.8755 (p) cc_final: 0.8085 (t)
REVERT: E   72 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8227 (mt-10)
REVERT: E   89 GLU cc_start: 0.7896 (tp30) cc_final: 0.7678 (tp30)
  outliers start: 10
  outliers final: 9
  residues processed: 66
  average time/residue: 0.2432
  time to fit residues: 18.1956
Evaluate side-chains
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   90 HIS
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0040
   overall best weight:    1.3398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2960  Z= 0.343
  Angle     :  0.515   4.048   4032  Z= 0.279
  Chirality :  0.047   0.119    472
  Planarity :  0.005   0.051    504
  Dihedral  :  4.852  20.491    400
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.24 %
    Favored  : 82.91 %
  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: -3.56 (0.36), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  79 
 HIS   0.001   0.001   HIS A  90 
 PHE   0.016   0.002   PHE A  87 
 TYR   0.017   0.002   TYR A 114 
 ARG   0.008   0.001   ARG E  34 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7553 (tpt) cc_final: 0.7352 (tpp)
REVERT: B   89 GLU cc_start: 0.7862 (tp30) cc_final: 0.7270 (pm20)
REVERT: B  103 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8132 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8459 (m-80) cc_final: 0.8102 (m-80)
REVERT: C   13 MET cc_start: 0.7459 (tpt) cc_final: 0.6943 (tmm)
REVERT: C   21 ARG cc_start: 0.7404 (ttm-80) cc_final: 0.6584 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8500 (t0) cc_final: 0.8088 (m-30)
REVERT: E   21 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7273 (ttm-80)
REVERT: E   23 SER cc_start: 0.8776 (p) cc_final: 0.8094 (t)
REVERT: E   72 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8205 (mt-10)
REVERT: E   89 GLU cc_start: 0.7879 (tp30) cc_final: 0.7667 (tp30)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.2275
  time to fit residues: 17.7275
Evaluate side-chains
  70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   90 HIS
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0030
   chunk 35 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.7190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2960  Z= 0.216
  Angle     :  0.481   4.365   4032  Z= 0.261
  Chirality :  0.047   0.115    472
  Planarity :  0.005   0.049    504
  Dihedral  :  4.690  19.407    400
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.19 %
    Favored  : 82.59 %
  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: -3.57 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  79 
 HIS   0.001   0.000   HIS B  88 
 PHE   0.022   0.001   PHE C  87 
 TYR   0.015   0.002   TYR A 114 
 ARG   0.009   0.001   ARG E  34 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: B   89 GLU cc_start: 0.7850 (tp30) cc_final: 0.7249 (pm20)
REVERT: B  103 ARG cc_start: 0.8501 (mtm180) cc_final: 0.8051 (mtm-85)
REVERT: C   13 MET cc_start: 0.7527 (tpt) cc_final: 0.6913 (tmm)
REVERT: C   21 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6579 (ttm-80)
REVERT: C   35 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7952 (tttt)
REVERT: E   18 ASP cc_start: 0.8493 (t0) cc_final: 0.8077 (m-30)
REVERT: E   21 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7344 (ttm-80)
REVERT: E   23 SER cc_start: 0.8729 (p) cc_final: 0.8009 (t)
REVERT: E   72 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8211 (mt-10)
REVERT: E   89 GLU cc_start: 0.7900 (tp30) cc_final: 0.7692 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 66
  average time/residue: 0.2350
  time to fit residues: 17.5878
Evaluate side-chains
  66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   90 HIS
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2960  Z= 0.239
  Angle     :  0.485   4.104   4032  Z= 0.264
  Chirality :  0.047   0.118    472
  Planarity :  0.005   0.049    504
  Dihedral  :  4.658  19.612    400
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.19 %
    Favored  : 82.91 %
  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: -3.52 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  79 
 HIS   0.002   0.000   HIS A  88 
 PHE   0.016   0.001   PHE C  87 
 TYR   0.015   0.002   TYR A 114 
 ARG   0.008   0.001   ARG E  34 

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

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

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  712 Ramachandran restraints generated.
    356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7547 (tpt) cc_final: 0.7124 (tpp)
REVERT: B   89 GLU cc_start: 0.7834 (tp30) cc_final: 0.7203 (pm20)
REVERT: B  103 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8151 (mtm-85)
REVERT: C   13 MET cc_start: 0.7536 (tpt) cc_final: 0.6941 (tmm)
REVERT: C   21 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.6525 (ttm-80)
REVERT: C   35 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7943 (tttt)
REVERT: E   18 ASP cc_start: 0.8508 (t0) cc_final: 0.8095 (m-30)
REVERT: E   21 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7366 (ttm-80)
REVERT: E   23 SER cc_start: 0.8770 (p) cc_final: 0.8075 (t)
REVERT: E   72 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8279 (mt-10)
REVERT: E   89 GLU cc_start: 0.7908 (tp30) cc_final: 0.7703 (tp30)
  outliers start: 6
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2317
  time to fit residues: 17.1830
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   90 HIS
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 20 optimal weight:    6.9990
   chunk 32 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.152634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.120358 restraints weight = 3518.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 3.25
r_work: 0.3861 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2960  Z= 0.217
  Angle     :  0.479   4.144   4032  Z= 0.260
  Chirality :  0.047   0.139    472
  Planarity :  0.005   0.049    504
  Dihedral  :  4.583  19.301    400
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.87 %
    Favored  : 83.23 %
  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: -3.54 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  79 
 HIS   0.002   0.000   HIS A  90 
 PHE   0.008   0.001   PHE A  87 
 TYR   0.014   0.002   TYR A 114 
 ARG   0.008   0.001   ARG E  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1288.78 seconds
wall clock time: 24 minutes 1.78 seconds (1441.78 seconds total)