Starting phenix.real_space_refine
on Fri Aug 22 13:01:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tdo_41172/08_2025/8tdo_41172.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tdo_41172/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tdo_41172/08_2025/8tdo_41172.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tdo_41172/08_2025/8tdo_41172.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tdo_41172/08_2025/8tdo_41172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tdo_41172/08_2025/8tdo_41172.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C, E
  Time building chain proxies: 0.76, per 1000 atoms: 0.26
  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: 0.23
  Conformation dependent library (CDL) restraints added in 130.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.10
  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: 0.37

  Time building geometry restraints manager: 0.29 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: 0.01
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.600
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.810
-------------------------------------------------------------------------------
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= 0.237
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.001   ARG E  21 
 TYR   0.014   0.003   TYR C 114 
 PHE   0.011   0.003   PHE B  87 
 TRP   0.002   0.001   TRP B  79 
 HIS   0.001   0.000   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 2960)
  covalent geometry    : angle       0.55554 ( 4032)
  hydrogen bonds       : bond        0.12924 (   68)
  hydrogen bonds       : angle       7.69555 (  204)

*********************** 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  : 0.116 
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: 0.0883
  time to fit residues: 6.8712
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  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0370
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.4058

-------------------------------------------------------------------------------
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 = 0.4408 r_free = 0.4408 target = 0.156307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.124196 restraints weight = 3454.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 3.22
r_work: 0.3929 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1074

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= 0.116
  Angle     :  0.487   3.578   4032  Z= 0.269
  Chirality :  0.048   0.115    472
  Planarity :  0.005   0.045    504
  Dihedral  :  4.796  18.789    400
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.03 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.64 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 104 
 TYR   0.014   0.002   TYR C 114 
 PHE   0.010   0.001   PHE A  87 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.002   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 2960)
  covalent geometry    : angle       0.48669 ( 4032)
  hydrogen bonds       : bond        0.02071 (   68)
  hydrogen bonds       : angle       5.40084 (  204)

*********************** 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: 6
    poor density    : 64
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: B   21 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7140 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8482 (mtm180) cc_final: 0.8141 (mtm-85)
REVERT: C   13 MET cc_start: 0.7361 (tpt) cc_final: 0.6791 (tmm)
REVERT: C   21 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6840 (ttm-80)
REVERT: C   23 SER cc_start: 0.8799 (p) cc_final: 0.8273 (m)
REVERT: C   69 TYR cc_start: 0.9002 (m-80) cc_final: 0.8211 (m-80)
REVERT: E   18 ASP cc_start: 0.8401 (t0) cc_final: 0.7977 (m-30)
REVERT: E   21 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7512 (ttm-80)
REVERT: E   23 SER cc_start: 0.8623 (p) cc_final: 0.8166 (t)
REVERT: E   72 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8146 (mt-10)
REVERT: E   84 SER cc_start: 0.8124 (t) cc_final: 0.7642 (m)
REVERT: E  103 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8463 (mtm-85)
  outliers start: 6
  outliers final: 4
  residues processed: 67
  average time/residue: 0.1007
  time to fit residues: 7.6017
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    1.8388

-------------------------------------------------------------------------------
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 = 0.4307 r_free = 0.4307 target = 0.147009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.113776 restraints weight = 3605.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 3.26
r_work: 0.3773 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.028   2960  Z= 0.288
  Angle     :  0.564   3.581   4032  Z= 0.308
  Chirality :  0.048   0.127    472
  Planarity :  0.005   0.035    504
  Dihedral  :  5.196  22.367    400
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG C 104 
 TYR   0.027   0.003   TYR A 114 
 PHE   0.017   0.003   PHE C  87 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.002   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 ( 2960)
  covalent geometry    : angle       0.56444 ( 4032)
  hydrogen bonds       : bond        0.02666 (   68)
  hydrogen bonds       : angle       5.17263 (  204)

*********************** 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: 6
    poor density    : 62
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.9167 (m-80) cc_final: 0.8628 (m-80)
REVERT: B   13 MET cc_start: 0.7651 (tpt) cc_final: 0.7344 (tpp)
REVERT: B   21 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7192 (ttm-80)
REVERT: B  103 ARG cc_start: 0.8438 (mtm180) cc_final: 0.8115 (mtm-85)
REVERT: C   13 MET cc_start: 0.7428 (tpt) cc_final: 0.6930 (tmm)
REVERT: C   23 SER cc_start: 0.8911 (p) cc_final: 0.8417 (m)
REVERT: C   69 TYR cc_start: 0.9105 (m-80) cc_final: 0.8250 (m-80)
REVERT: E   18 ASP cc_start: 0.8420 (t0) cc_final: 0.7999 (m-30)
REVERT: E   23 SER cc_start: 0.8746 (p) cc_final: 0.8156 (t)
REVERT: E   72 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8124 (mt-10)
REVERT: E   84 SER cc_start: 0.8127 (t) cc_final: 0.7627 (m)
  outliers start: 6
  outliers final: 4
  residues processed: 65
  average time/residue: 0.1199
  time to fit residues: 8.6982
Evaluate side-chains
  64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4339 r_free = 0.4339 target = 0.149268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.116026 restraints weight = 3552.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 3.25
r_work: 0.3805 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2960  Z= 0.209
  Angle     :  0.509   3.550   4032  Z= 0.278
  Chirality :  0.047   0.113    472
  Planarity :  0.005   0.036    504
  Dihedral  :  4.992  20.919    400
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 11.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.001   ARG E  21 
 TYR   0.020   0.002   TYR A 114 
 PHE   0.009   0.002   PHE C  87 
 TRP   0.002   0.001   TRP B  79 
 HIS   0.001   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 2960)
  covalent geometry    : angle       0.50926 ( 4032)
  hydrogen bonds       : bond        0.01958 (   68)
  hydrogen bonds       : angle       4.91225 (  204)

*********************** 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
  71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7546 (tpt) cc_final: 0.7197 (tpp)
REVERT: A   21 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6876 (ttm-80)
REVERT: A   69 TYR cc_start: 0.9198 (m-80) cc_final: 0.8695 (m-80)
REVERT: B   13 MET cc_start: 0.7616 (tpt) cc_final: 0.7345 (tpp)
REVERT: B  103 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8164 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8448 (m-80) cc_final: 0.8031 (m-80)
REVERT: C   13 MET cc_start: 0.7455 (tpt) cc_final: 0.6954 (tmm)
REVERT: C   21 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7262 (ttm-80)
REVERT: C   23 SER cc_start: 0.8870 (p) cc_final: 0.8363 (m)
REVERT: C   69 TYR cc_start: 0.9130 (m-80) cc_final: 0.8352 (m-80)
REVERT: E   18 ASP cc_start: 0.8458 (t0) cc_final: 0.8049 (m-30)
REVERT: E   21 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8096 (ttm-80)
REVERT: E   23 SER cc_start: 0.8745 (p) cc_final: 0.8154 (t)
REVERT: E   72 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8265 (mt-10)
REVERT: E   84 SER cc_start: 0.8119 (t) cc_final: 0.7614 (m)
  outliers start: 10
  outliers final: 7
  residues processed: 67
  average time/residue: 0.1050
  time to fit residues: 7.9387
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0670
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.6720

-------------------------------------------------------------------------------
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 = 0.4376 r_free = 0.4376 target = 0.152738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.120362 restraints weight = 3505.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 3.17
r_work: 0.3879 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1721

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= 0.131
  Angle     :  0.471   3.930   4032  Z= 0.256
  Chirality :  0.047   0.116    472
  Planarity :  0.004   0.040    504
  Dihedral  :  4.747  19.456    400
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.001   ARG C 104 
 TYR   0.016   0.002   TYR A 114 
 PHE   0.019   0.001   PHE C  87 
 TRP   0.002   0.001   TRP C  79 
 HIS   0.001   0.000   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 2960)
  covalent geometry    : angle       0.47085 ( 4032)
  hydrogen bonds       : bond        0.01660 (   68)
  hydrogen bonds       : angle       4.74376 (  204)

*********************** 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
  66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7501 (tpt) cc_final: 0.7119 (tpp)
REVERT: A   69 TYR cc_start: 0.9180 (m-80) cc_final: 0.8658 (m-80)
REVERT: B   13 MET cc_start: 0.7565 (tpt) cc_final: 0.7338 (tpp)
REVERT: B  103 ARG cc_start: 0.8494 (mtm180) cc_final: 0.8099 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8317 (m-80) cc_final: 0.8056 (m-80)
REVERT: C   13 MET cc_start: 0.7389 (tpt) cc_final: 0.6880 (tmm)
REVERT: C   21 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.6757 (ttm-80)
REVERT: E   18 ASP cc_start: 0.8432 (t0) cc_final: 0.8022 (m-30)
REVERT: E   21 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7380 (ttm-80)
REVERT: E   23 SER cc_start: 0.8762 (p) cc_final: 0.8134 (t)
REVERT: E   72 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8202 (mt-10)
REVERT: E   84 SER cc_start: 0.8200 (t) cc_final: 0.7721 (m)
REVERT: E   89 GLU cc_start: 0.7817 (tp30) cc_final: 0.7599 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0912
  time to fit residues: 6.4881
Evaluate side-chains
  63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
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   96 THR
Chi-restraints excluded: chain E residue  112 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.4284 r_free = 0.4284 target = 0.143435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.110501 restraints weight = 3648.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 3.22
r_work: 0.3719 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.045   2960  Z= 0.418
  Angle     :  0.630   4.286   4032  Z= 0.343
  Chirality :  0.050   0.129    472
  Planarity :  0.005   0.054    504
  Dihedral  :  5.329  22.166    400
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.29 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.53 (0.36), 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
 ARG   0.008   0.001   ARG E  34 
 TYR   0.021   0.003   TYR A 114 
 PHE   0.019   0.003   PHE A  87 
 TRP   0.004   0.001   TRP E  79 
 HIS   0.002   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00981 ( 2960)
  covalent geometry    : angle       0.62986 ( 4032)
  hydrogen bonds       : bond        0.02568 (   68)
  hydrogen bonds       : angle       5.04847 (  204)

*********************** 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
  71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.9280 (m-80) cc_final: 0.9040 (m-80)
REVERT: B   89 GLU cc_start: 0.7926 (tp30) cc_final: 0.7423 (pm20)
REVERT: B  103 ARG cc_start: 0.8578 (mtm180) cc_final: 0.8184 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8673 (m-80) cc_final: 0.8267 (m-80)
REVERT: C   13 MET cc_start: 0.7571 (tpt) cc_final: 0.7145 (tmm)
REVERT: C   69 TYR cc_start: 0.9185 (m-80) cc_final: 0.8981 (m-80)
REVERT: E   18 ASP cc_start: 0.8496 (t0) cc_final: 0.8093 (m-30)
REVERT: E   21 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.7560 (ttm-80)
REVERT: E   23 SER cc_start: 0.8926 (p) cc_final: 0.8319 (t)
REVERT: E   72 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8271 (mt-10)
  outliers start: 10
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0960
  time to fit residues: 7.4737
Evaluate side-chains
  65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
B  90 HIS
C  27 ASN
E  27 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.149572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.117331 restraints weight = 3598.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 3.21
r_work: 0.3832 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2960  Z= 0.137
  Angle     :  0.493   3.685   4032  Z= 0.270
  Chirality :  0.048   0.116    472
  Planarity :  0.005   0.050    504
  Dihedral  :  4.915  19.826    400
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG E  34 
 TYR   0.016   0.002   TYR A 114 
 PHE   0.025   0.002   PHE C  87 
 TRP   0.003   0.001   TRP A  79 
 HIS   0.002   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 2960)
  covalent geometry    : angle       0.49259 ( 4032)
  hydrogen bonds       : bond        0.01791 (   68)
  hydrogen bonds       : angle       4.76155 (  204)

*********************** 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
  68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.9217 (m-80) cc_final: 0.8746 (m-80)
REVERT: B  103 ARG cc_start: 0.8435 (mtm180) cc_final: 0.7990 (mtm-85)
REVERT: C   13 MET cc_start: 0.7451 (tpt) cc_final: 0.6809 (tmm)
REVERT: C   21 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.6935 (ttm-80)
REVERT: C   35 LYS cc_start: 0.8351 (ttmm) cc_final: 0.8096 (tttm)
REVERT: E   18 ASP cc_start: 0.8444 (t0) cc_final: 0.8029 (m-30)
REVERT: E   21 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.7446 (ttm-80)
REVERT: E   23 SER cc_start: 0.8818 (p) cc_final: 0.8184 (t)
REVERT: E   72 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8192 (mt-10)
REVERT: E   89 GLU cc_start: 0.7814 (tp30) cc_final: 0.7614 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 66
  average time/residue: 0.1223
  time to fit residues: 9.0164
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  : 0.120 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.4361 r_free = 0.4361 target = 0.149481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.116274 restraints weight = 3544.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 3.19
r_work: 0.3827 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2049

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= 0.203
  Angle     :  0.514   3.864   4032  Z= 0.278
  Chirality :  0.048   0.122    472
  Planarity :  0.005   0.050    504
  Dihedral  :  4.914  20.463    400
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.82 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.53 (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
 ARG   0.007   0.001   ARG E  34 
 TYR   0.016   0.002   TYR A 114 
 PHE   0.024   0.002   PHE C  87 
 TRP   0.002   0.001   TRP B  79 
 HIS   0.001   0.000   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 2960)
  covalent geometry    : angle       0.51364 ( 4032)
  hydrogen bonds       : bond        0.01990 (   68)
  hydrogen bonds       : angle       4.76693 (  204)

*********************** 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
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TYR cc_start: 0.9191 (m-80) cc_final: 0.8763 (m-80)
REVERT: B  103 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8092 (mtm-85)
REVERT: B  116 TYR cc_start: 0.8345 (m-80) cc_final: 0.8142 (m-80)
REVERT: C   13 MET cc_start: 0.7454 (tpt) cc_final: 0.6838 (tmm)
REVERT: C   21 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7266 (ttm-80)
REVERT: C   35 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8131 (tttt)
REVERT: E   18 ASP cc_start: 0.8457 (t0) cc_final: 0.8037 (m-30)
REVERT: E   21 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7989 (ttm-80)
REVERT: E   23 SER cc_start: 0.8805 (p) cc_final: 0.8141 (t)
REVERT: E   72 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8250 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1260
  time to fit residues: 9.0213
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  : 0.112 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0170
   chunk 9 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
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 = 0.4381 r_free = 0.4381 target = 0.151876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.119104 restraints weight = 3547.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 3.24
r_work: 0.3859 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2960  Z= 0.145
  Angle     :  0.487   4.062   4032  Z= 0.265
  Chirality :  0.047   0.116    472
  Planarity :  0.005   0.050    504
  Dihedral  :  4.766  19.356    400
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG E  34 
 TYR   0.015   0.002   TYR A 114 
 PHE   0.021   0.002   PHE C  87 
 TRP   0.002   0.001   TRP C  79 
 HIS   0.002   0.000   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 2960)
  covalent geometry    : angle       0.48690 ( 4032)
  hydrogen bonds       : bond        0.01758 (   68)
  hydrogen bonds       : angle       4.62778 (  204)

*********************** 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
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9179 (m-80) cc_final: 0.8790 (m-80)
REVERT: B   13 MET cc_start: 0.7644 (tpp) cc_final: 0.7393 (tpp)
REVERT: B  103 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8049 (mtm-85)
REVERT: C   13 MET cc_start: 0.7462 (tpt) cc_final: 0.6851 (tmm)
REVERT: C   21 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.6864 (ttm-80)
REVERT: C   35 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8155 (tttm)
REVERT: E   18 ASP cc_start: 0.8451 (t0) cc_final: 0.8024 (m-30)
REVERT: E   21 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7444 (ttm-80)
REVERT: E   23 SER cc_start: 0.8808 (p) cc_final: 0.8152 (t)
REVERT: E   72 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8251 (mt-10)
REVERT: E   90 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7844 (m170)
  outliers start: 6
  outliers final: 5
  residues processed: 64
  average time/residue: 0.1096
  time to fit residues: 7.8855
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  : 0.071 
-------------------------------------------------------------------------------
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 21 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0570
   chunk 23 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.4416 r_free = 0.4416 target = 0.154284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.121950 restraints weight = 3529.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 3.19
r_work: 0.3902 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2180

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= 0.124
  Angle     :  0.486   4.340   4032  Z= 0.263
  Chirality :  0.048   0.155    472
  Planarity :  0.005   0.048    504
  Dihedral  :  4.627  18.907    400
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.52 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  34 
 TYR   0.014   0.002   TYR A 114 
 PHE   0.020   0.002   PHE C  87 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.002   0.000   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 2960)
  covalent geometry    : angle       0.48614 ( 4032)
  hydrogen bonds       : bond        0.01706 (   68)
  hydrogen bonds       : angle       4.56047 (  204)

********************** 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  : 0.109 
Fit side-chains
REVERT: A   69 TYR cc_start: 0.9182 (m-80) cc_final: 0.8792 (m-80)
REVERT: B   13 MET cc_start: 0.7646 (tpp) cc_final: 0.7382 (tpp)
REVERT: B  103 ARG cc_start: 0.8529 (mtm180) cc_final: 0.8110 (mtm-85)
REVERT: C   13 MET cc_start: 0.7469 (tpt) cc_final: 0.6864 (tmm)
REVERT: C   80 LYS cc_start: 0.7243 (tttt) cc_final: 0.6928 (tttm)
REVERT: E   18 ASP cc_start: 0.8452 (t0) cc_final: 0.8017 (m-30)
REVERT: E   21 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.8074 (ttm-80)
REVERT: E   23 SER cc_start: 0.8775 (p) cc_final: 0.8069 (t)
REVERT: E   72 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8268 (mt-10)
REVERT: E   90 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7793 (m170)
  outliers start: 6
  outliers final: 5
  residues processed: 64
  average time/residue: 0.1088
  time to fit residues: 7.8326
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  : 0.071 
-------------------------------------------------------------------------------
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 25 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4407 r_free = 0.4407 target = 0.153184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.120355 restraints weight = 3471.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 3.17
r_work: 0.3875 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2164

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= 0.157
  Angle     :  0.495   3.975   4032  Z= 0.268
  Chirality :  0.048   0.149    472
  Planarity :  0.005   0.049    504
  Dihedral  :  4.666  19.665    400
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.45 (0.37), residues: 356
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  34 
 TYR   0.014   0.002   TYR A 114 
 PHE   0.022   0.002   PHE C  87 
 TRP   0.002   0.001   TRP C  79 
 HIS   0.001   0.000   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2960)
  covalent geometry    : angle       0.49477 ( 4032)
  hydrogen bonds       : bond        0.01820 (   68)
  hydrogen bonds       : angle       4.55039 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 918.83 seconds
wall clock time: 16 minutes 21.59 seconds (981.59 seconds total)