Starting phenix.real_space_refine
on Mon Feb 10 21:45:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tdo_41172/02_2025/8tdo_41172.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tdo_41172/02_2025/8tdo_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_41172/02_2025/8tdo_41172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tdo_41172/02_2025/8tdo_41172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tdo_41172/02_2025/8tdo_41172.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tdo_41172/02_2025/8tdo_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-5592/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: 1.93, per 1000 atoms: 0.67
  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: 0.67
  Conformation dependent library (CDL) restraints added in 352.2 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: 0.36
  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: 0.68

  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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             0.680
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.410
  Find NCS groups from input model:        0.060
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.250
-------------------------------------------------------------------------------
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  : 0.304 
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: 0.2030
  time to fit residues: 15.8525
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  : 0.287 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.153074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.120432 restraints weight = 3485.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.4017 rms_B_bonded: 3.24
r_work: 0.3873 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
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  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: B   21 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7225 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8534 (mtm180) cc_final: 0.8136 (mtm-85)
REVERT: C   13 MET cc_start: 0.7450 (tpt) cc_final: 0.6949 (tmm)
REVERT: C   21 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.6897 (ttm-80)
REVERT: C   23 SER cc_start: 0.8863 (p) cc_final: 0.8365 (m)
REVERT: C   69 TYR cc_start: 0.9063 (m-80) cc_final: 0.8244 (m-80)
REVERT: E   18 ASP cc_start: 0.8448 (t0) cc_final: 0.8030 (m-30)
REVERT: E   21 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7529 (ttm-80)
REVERT: E   23 SER cc_start: 0.8679 (p) cc_final: 0.8274 (t)
REVERT: E   72 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8229 (mt-10)
REVERT: E   84 SER cc_start: 0.8169 (t) cc_final: 0.7677 (m)
REVERT: E  103 ARG cc_start: 0.8777 (mtm180) cc_final: 0.8560 (mtm-85)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 0.2279
  time to fit residues: 17.2829
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  : 0.303 
-------------------------------------------------------------------------------
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 14 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0170
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.9420

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.152719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.119709 restraints weight = 3473.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.4004 rms_B_bonded: 3.21
r_work: 0.3861 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2960  Z= 0.258
  Angle     :  0.489   3.472   4032  Z= 0.268
  Chirality :  0.047   0.117    472
  Planarity :  0.005   0.031    504
  Dihedral  :  4.851  20.173    400
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.71 %
    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   0.002   0.001   TRP C  79 
 HIS   0.003   0.001   HIS E  90 
 PHE   0.011   0.001   PHE A  87 
 TYR   0.023   0.002   TYR A 114 
 ARG   0.003   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: 8
    poor density    : 60
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 MET cc_start: 0.7626 (tpt) cc_final: 0.7328 (tpp)
REVERT: B   21 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7275 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8519 (mtm180) cc_final: 0.8054 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8381 (m-80) cc_final: 0.7962 (m-80)
REVERT: C   13 MET cc_start: 0.7420 (tpt) cc_final: 0.6878 (tmm)
REVERT: C   21 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.6937 (ttm-80)
REVERT: C   23 SER cc_start: 0.8848 (p) cc_final: 0.8359 (m)
REVERT: C   69 TYR cc_start: 0.9076 (m-80) cc_final: 0.8246 (m-80)
REVERT: E   18 ASP cc_start: 0.8440 (t0) cc_final: 0.8020 (m-30)
REVERT: E   21 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7530 (ttm-80)
REVERT: E   23 SER cc_start: 0.8701 (p) cc_final: 0.8128 (t)
REVERT: E   72 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8195 (mt-10)
REVERT: E   84 SER cc_start: 0.8183 (t) cc_final: 0.7698 (m)
REVERT: E  103 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8396 (mtm-85)
  outliers start: 8
  outliers final: 6
  residues processed: 64
  average time/residue: 0.2360
  time to fit residues: 17.1578
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  : 0.349 
-------------------------------------------------------------------------------
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 4 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0170
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.9020

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.152538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.119888 restraints weight = 3511.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 3.17
r_work: 0.3868 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2960  Z= 0.244
  Angle     :  0.476   3.496   4032  Z= 0.259
  Chirality :  0.047   0.114    472
  Planarity :  0.004   0.032    504
  Dihedral  :  4.742  20.101    400
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 11.71 %
    Favored  : 85.44 %
  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: -3.58 (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 C  90 
 PHE   0.007   0.001   PHE E  87 
 TYR   0.021   0.002   TYR A 114 
 ARG   0.004   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
  69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7528 (tpt) cc_final: 0.7193 (tpp)
REVERT: A   69 TYR cc_start: 0.9150 (m-80) cc_final: 0.8588 (m-80)
REVERT: B   13 MET cc_start: 0.7562 (tpt) cc_final: 0.7315 (tpp)
REVERT: B   21 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7263 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8489 (mtm180) cc_final: 0.8121 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8386 (m-80) cc_final: 0.7913 (m-80)
REVERT: C   13 MET cc_start: 0.7445 (tpt) cc_final: 0.6891 (tmm)
REVERT: C   21 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.6892 (ttm-80)
REVERT: C   23 SER cc_start: 0.8866 (p) cc_final: 0.8313 (m)
REVERT: C   89 GLU cc_start: 0.8031 (tp30) cc_final: 0.7828 (tp30)
REVERT: E   18 ASP cc_start: 0.8435 (t0) cc_final: 0.8019 (m-30)
REVERT: E   21 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7505 (ttm-80)
REVERT: E   23 SER cc_start: 0.8718 (p) cc_final: 0.8112 (t)
REVERT: E   72 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8107 (mt-10)
REVERT: E   84 SER cc_start: 0.8239 (t) cc_final: 0.7748 (m)
REVERT: E   89 GLU cc_start: 0.7864 (tp30) cc_final: 0.7649 (tp30)
REVERT: E  103 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8409 (mtm-85)
  outliers start: 9
  outliers final: 8
  residues processed: 64
  average time/residue: 0.2473
  time to fit residues: 17.8655
Evaluate side-chains
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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 24 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.147648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.114629 restraints weight = 3580.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 3.24
r_work: 0.3786 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.025   2960  Z= 0.403
  Angle     :  0.527   3.588   4032  Z= 0.286
  Chirality :  0.048   0.122    472
  Planarity :  0.005   0.044    504
  Dihedral  :  4.951  21.416    400
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.66 %
    Favored  : 84.18 %
  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: -3.53 (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 E  79 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.011   0.002   PHE A  87 
 TYR   0.020   0.002   TYR A 114 
 ARG   0.005   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: 10
    poor density    : 61
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7630 (tpt) cc_final: 0.7250 (tpp)
REVERT: A   69 TYR cc_start: 0.9190 (m-80) cc_final: 0.8630 (m-80)
REVERT: B   13 MET cc_start: 0.7630 (tpt) cc_final: 0.7410 (tpp)
REVERT: B   21 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7332 (ttm-80)
REVERT: B   89 GLU cc_start: 0.7834 (tp30) cc_final: 0.7304 (pm20)
REVERT: B  103 ARG cc_start: 0.8482 (mtm180) cc_final: 0.8117 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8527 (m-80) cc_final: 0.8193 (m-80)
REVERT: C   13 MET cc_start: 0.7494 (tpt) cc_final: 0.7016 (tmm)
REVERT: C   21 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.6979 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8469 (t0) cc_final: 0.8063 (m-30)
REVERT: E   21 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7516 (ttm-80)
REVERT: E   23 SER cc_start: 0.8804 (p) cc_final: 0.8170 (t)
REVERT: E   72 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8258 (mt-10)
REVERT: E   89 GLU cc_start: 0.7917 (tp30) cc_final: 0.7692 (tp30)
  outliers start: 10
  outliers final: 7
  residues processed: 69
  average time/residue: 0.2326
  time to fit residues: 18.1984
Evaluate side-chains
  65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
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   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 12 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0170
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7218

-------------------------------------------------------------------------------
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**
B  90 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.151281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.119073 restraints weight = 3602.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 3.21
r_work: 0.3846 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2960  Z= 0.211
  Angle     :  0.468   3.488   4032  Z= 0.256
  Chirality :  0.047   0.115    472
  Planarity :  0.005   0.044    504
  Dihedral  :  4.710  19.617    400
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.61 %
    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: -3.56 (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 A  79 
 HIS   0.002   0.001   HIS A  90 
 PHE   0.008   0.001   PHE A  87 
 TYR   0.016   0.002   TYR A 114 
 ARG   0.006   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
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7542 (tpt) cc_final: 0.7133 (tpp)
REVERT: B   13 MET cc_start: 0.7548 (tpt) cc_final: 0.7346 (tpp)
REVERT: B  103 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8053 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8416 (m-80) cc_final: 0.7999 (m-80)
REVERT: C   13 MET cc_start: 0.7476 (tpt) cc_final: 0.6995 (tmm)
REVERT: C   21 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.6962 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8447 (t0) cc_final: 0.8050 (m-30)
REVERT: E   21 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7520 (ttm-80)
REVERT: E   23 SER cc_start: 0.8769 (p) cc_final: 0.8129 (t)
REVERT: E   72 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8230 (mt-10)
REVERT: E   89 GLU cc_start: 0.7946 (tp30) cc_final: 0.7739 (tp30)
  outliers start: 8
  outliers final: 7
  residues processed: 64
  average time/residue: 0.2258
  time to fit residues: 16.4482
Evaluate side-chains
  65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  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   82 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0870
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.7764

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.152218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.120214 restraints weight = 3600.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 3.18
r_work: 0.3863 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1840

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= 0.225
  Angle     :  0.477   3.603   4032  Z= 0.259
  Chirality :  0.047   0.119    472
  Planarity :  0.005   0.045    504
  Dihedral  :  4.640  19.725    400
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.61 %
    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: -3.52 (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 B  79 
 HIS   0.002   0.000   HIS C  90 
 PHE   0.012   0.001   PHE A  87 
 TYR   0.015   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
  69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7511 (tpt) cc_final: 0.7290 (tpp)
REVERT: B  103 ARG cc_start: 0.8520 (mtm180) cc_final: 0.8096 (mtm-85)
REVERT: C   13 MET cc_start: 0.7489 (tpt) cc_final: 0.7017 (tmm)
REVERT: C   21 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.6618 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8483 (t0) cc_final: 0.8089 (m-30)
REVERT: E   21 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7411 (ttm-80)
REVERT: E   23 SER cc_start: 0.8786 (p) cc_final: 0.8151 (t)
REVERT: E   72 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8228 (mt-10)
REVERT: E   89 GLU cc_start: 0.7985 (tp30) cc_final: 0.7776 (tp30)
  outliers start: 10
  outliers final: 9
  residues processed: 65
  average time/residue: 0.2301
  time to fit residues: 16.9658
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
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   96 THR
Chi-restraints excluded: chain E residue   82 LEU
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 11 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   chunk 26 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0570
   overall best weight:    0.5496

-------------------------------------------------------------------------------
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 = 0.4412 r_free = 0.4412 target = 0.154429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.121968 restraints weight = 3488.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 3.27
r_work: 0.3879 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2960  Z= 0.181
  Angle     :  0.455   3.627   4032  Z= 0.248
  Chirality :  0.047   0.115    472
  Planarity :  0.005   0.049    504
  Dihedral  :  4.496  18.452    400
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  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: -3.52 (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   0.001   0.000   HIS A  90 
 PHE   0.012   0.001   PHE A  87 
 TYR   0.013   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
  72 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7503 (tpt) cc_final: 0.7102 (tpp)
REVERT: B  103 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8174 (mtm-85)
REVERT: C   13 MET cc_start: 0.7561 (tpt) cc_final: 0.7010 (tmm)
REVERT: C   21 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.6584 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8499 (t0) cc_final: 0.8111 (m-30)
REVERT: E   21 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7486 (ttm-80)
REVERT: E   23 SER cc_start: 0.8802 (p) cc_final: 0.8168 (t)
REVERT: E   72 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8253 (mt-10)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.2208
  time to fit residues: 17.1529
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  : 0.291 
-------------------------------------------------------------------------------
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   96 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   90 HIS
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4404 r_free = 0.4404 target = 0.153671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.121336 restraints weight = 3543.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 3.24
r_work: 0.3866 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2960  Z= 0.216
  Angle     :  0.497   8.078   4032  Z= 0.263
  Chirality :  0.047   0.150    472
  Planarity :  0.005   0.046    504
  Dihedral  :  4.504  19.143    400
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  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: -3.49 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.65 (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 E  90 
 PHE   0.015   0.001   PHE A  87 
 TYR   0.014   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
  70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  103 ARG cc_start: 0.8587 (mtm180) cc_final: 0.8184 (mtm-85)
REVERT: C   13 MET cc_start: 0.7595 (tpt) cc_final: 0.7029 (tmm)
REVERT: C   21 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7339 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8522 (t0) cc_final: 0.8136 (m-30)
REVERT: E   23 SER cc_start: 0.8857 (p) cc_final: 0.8227 (t)
REVERT: E   72 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8277 (mt-10)
REVERT: E   89 GLU cc_start: 0.7899 (tp30) cc_final: 0.7690 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 67
  average time/residue: 0.2279
  time to fit residues: 17.3781
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  : 0.384 
-------------------------------------------------------------------------------
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   82 LEU
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0270
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.4437 r_free = 0.4437 target = 0.156316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.124045 restraints weight = 3520.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.20
r_work: 0.3918 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2960  Z= 0.174
  Angle     :  0.487   7.790   4032  Z= 0.257
  Chirality :  0.047   0.151    472
  Planarity :  0.005   0.047    504
  Dihedral  :  4.382  18.325    400
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  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: -3.50 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (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   0.010   0.001   PHE B  64 
 TYR   0.012   0.002   TYR A 114 
 ARG   0.009   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
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7506 (tpt) cc_final: 0.7069 (tpp)
REVERT: B  103 ARG cc_start: 0.8555 (mtm180) cc_final: 0.8183 (mtm-85)
REVERT: C   13 MET cc_start: 0.7532 (tpt) cc_final: 0.7012 (tmm)
REVERT: C   21 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.6523 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8504 (t0) cc_final: 0.8104 (m-30)
REVERT: E   21 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7511 (ttm-80)
REVERT: E   23 SER cc_start: 0.8817 (p) cc_final: 0.8162 (t)
REVERT: E   72 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8284 (mt-10)
REVERT: E   89 GLU cc_start: 0.7851 (tp30) cc_final: 0.7630 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2252
  time to fit residues: 16.6810
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  : 0.359 
-------------------------------------------------------------------------------
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  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 5 optimal weight:    0.1980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4377 r_free = 0.4377 target = 0.150697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.117836 restraints weight = 3495.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 3.20
r_work: 0.3831 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   2960  Z= 0.333
  Angle     :  0.534   7.349   4032  Z= 0.283
  Chirality :  0.047   0.144    472
  Planarity :  0.005   0.048    504
  Dihedral  :  4.668  20.385    400
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.87 %
    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: -3.43 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  79 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.011   0.002   PHE A  87 
 TYR   0.016   0.002   TYR A 114 
 ARG   0.007   0.001   ARG E  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1783.15 seconds
wall clock time: 32 minutes 21.47 seconds (1941.47 seconds total)