Starting phenix.real_space_refine
on Tue Feb  3 14:24:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xbo_66707/02_2026/9xbo_66707.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xbo_66707/02_2026/9xbo_66707.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/9xbo_66707/02_2026/9xbo_66707.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xbo_66707/02_2026/9xbo_66707.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xbo_66707/02_2026/9xbo_66707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xbo_66707/02_2026/9xbo_66707.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
-------------------------------------------------------------------------------
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       5      5.16       5
     C    2290      2.51       5
     N     700      2.21       5
     O     775      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3770
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 754
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.57, per 1000 atoms: 0.15
  Number of scatterers: 3770
  At special positions: 0
  Unit cell: (84.084, 73.304, 49.588, 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       5     16.00
     O     775      8.00
     N     700      7.00
     C    2290      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: 0.28
  Conformation dependent library (CDL) restraints added in 133.7 milliseconds
  

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  790

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 41.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 10 through 17
      removed outlier: 6.689A  pdb=" N   GLN B  10 " --> pdb=" O   GLN D  11 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   TYR D  13 " --> pdb=" O   GLN B  10 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   ASN B  12 " --> pdb=" O   TYR D  13 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   GLN D  15 " --> pdb=" O   ASN B  12 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   GLN B  14 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   SER D  17 " --> pdb=" O   GLN B  14 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   TYR B  16 " --> pdb=" O   SER D  17 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN A  10 " --> pdb=" O   GLN B  11 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   TYR B  13 " --> pdb=" O   GLN A  10 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ASN A  12 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   GLN B  15 " --> pdb=" O   ASN A  12 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   GLN A  14 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   SER B  17 " --> pdb=" O   GLN A  14 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   TYR A  16 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 22 through 23
      removed outlier: 6.553A  pdb=" N   GLN A  22 " --> pdb=" O   GLN C  23 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   GLN C  22 " --> pdb=" O   GLN E  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 34
      removed outlier: 6.356A  pdb=" N   TYR B  29 " --> pdb=" O   GLN D  30 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   TYR D  32 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLY B  31 " --> pdb=" O   TYR D  32 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   ALA D  34 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   GLN B  33 " --> pdb=" O   ALA D  34 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   TYR A  29 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   TYR B  32 " --> pdb=" O   TYR A  29 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLY A  31 " --> pdb=" O   TYR B  32 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   ALA B  34 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   GLN A  33 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 48 through 51
      removed outlier: 5.902A  pdb=" N   TYR A  49 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   TYR C  49 " --> pdb=" O   GLN E  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 55 through 57
      removed outlier: 6.665A  pdb=" N   GLN B  56 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   GLN A  56 " --> pdb=" O   GLN B  57 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 61 through 63
      removed outlier: 6.282A  pdb=" N   GLN A  62 " --> pdb=" O   TYR C  63 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   GLN C  62 " --> pdb=" O   TYR E  63 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.201A  pdb=" N   ASN B 103 " --> pdb=" O   PHE D 104 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   TYR D 106 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ASN B 105 " --> pdb=" O   TYR D 106 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   ASN D 108 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN B 107 " --> pdb=" O   ASN D 108 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LEU D 110 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASN B 109 " --> pdb=" O   LEU D 110 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ASN A 103 " --> pdb=" O   PHE B 104 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   TYR B 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASN A 105 " --> pdb=" O   TYR B 106 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   ASN B 108 " --> pdb=" O   ASN A 105 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN A 107 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LEU B 110 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASN A 109 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 117
      removed outlier: 6.957A  pdb=" N   PHE D 117 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   PHE B 117 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   TYR A 113 " --> pdb=" O   GLN C 114 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   GLY C 116 " --> pdb=" O   TYR A 113 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   ALA A 115 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   TYR C 113 " --> pdb=" O   GLN E 114 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   GLY E 116 " --> pdb=" O   TYR C 113 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   ALA C 115 " --> pdb=" O   GLY E 116 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 122 through 128
      removed outlier: 6.259A  pdb=" N   GLN B 122 " --> pdb=" O   GLY D 123 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   SER D 125 " --> pdb=" O   GLN B 122 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   MET B 124 " --> pdb=" O   SER D 125 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   ASN D 127 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LEU B 126 " --> pdb=" O   ASN D 127 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   GLN A 122 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   SER B 125 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   MET A 124 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   ASN B 127 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LEU A 126 " --> pdb=" O   ASN B 127 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    222 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: 0.51

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1365
        1.34 -     1.46: 931
        1.46 -     1.58: 1554
        1.58 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 3860
  Sorted by residual:
  bond pdb=" N   PHE B 104 "
       pdb=" CA  PHE B 104 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.53e+00
  bond pdb=" N   PHE A 104 "
       pdb=" CA  PHE A 104 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.47e+00
  bond pdb=" N   PHE E 104 "
       pdb=" CA  PHE E 104 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.35e+00
  bond pdb=" N   TYR E  16 "
       pdb=" CA  TYR E  16 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.24e-02 6.50e+03 6.33e+00
  bond pdb=" N   PHE D 104 "
       pdb=" CA  PHE D 104 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.32e+00
  ... (remaining 3855 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 4953
        1.31 -     2.62: 202
        2.62 -     3.93: 10
        3.93 -     5.24: 15
        5.24 -     6.55: 20
  Bond angle restraints: 5200
  Sorted by residual:
  angle pdb=" N   ASN E 105 "
        pdb=" CA  ASN E 105 "
        pdb=" CB  ASN E 105 "
      ideal   model   delta    sigma   weight residual
     110.77  104.79    5.98 1.57e+00 4.06e-01 1.45e+01
  angle pdb=" N   ASN B 105 "
        pdb=" CA  ASN B 105 "
        pdb=" CB  ASN B 105 "
      ideal   model   delta    sigma   weight residual
     110.77  104.83    5.94 1.57e+00 4.06e-01 1.43e+01
  angle pdb=" N   ASN A 105 "
        pdb=" CA  ASN A 105 "
        pdb=" CB  ASN A 105 "
      ideal   model   delta    sigma   weight residual
     110.77  104.83    5.94 1.57e+00 4.06e-01 1.43e+01
  angle pdb=" N   ASN C 105 "
        pdb=" CA  ASN C 105 "
        pdb=" CB  ASN C 105 "
      ideal   model   delta    sigma   weight residual
     110.77  104.84    5.93 1.57e+00 4.06e-01 1.43e+01
  angle pdb=" N   ASN D 105 "
        pdb=" CA  ASN D 105 "
        pdb=" CB  ASN D 105 "
      ideal   model   delta    sigma   weight residual
     110.77  104.85    5.92 1.57e+00 4.06e-01 1.42e+01
  ... (remaining 5195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.17: 1765
       11.17 -    22.35: 255
       22.35 -    33.52: 125
       33.52 -    44.69: 40
       44.69 -    55.87: 30
  Dihedral angle restraints: 2215
    sinusoidal: 905
      harmonic: 1310
  Sorted by residual:
  dihedral pdb=" CA  TYR C  46 "
           pdb=" C   TYR C  46 "
           pdb=" N   GLN C  47 "
           pdb=" CA  GLN C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.03   15.97     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  TYR E  46 "
           pdb=" C   TYR E  46 "
           pdb=" N   GLN E  47 "
           pdb=" CA  GLN E  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.04   15.96     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  TYR D  46 "
           pdb=" C   TYR D  46 "
           pdb=" N   GLN D  47 "
           pdb=" CA  GLN D  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.06   15.94     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2212 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 262
       0.041 -    0.082: 128
       0.082 -    0.123: 10
       0.123 -    0.164: 0
       0.164 -    0.205: 5
  Chirality restraints: 405
  Sorted by residual:
  chirality pdb=" CA  GLN B  14 "
            pdb=" N   GLN B  14 "
            pdb=" C   GLN B  14 "
            pdb=" CB  GLN B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  GLN A  14 "
            pdb=" N   GLN A  14 "
            pdb=" C   GLN A  14 "
            pdb=" CB  GLN A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  GLN E  14 "
            pdb=" N   GLN E  14 "
            pdb=" C   GLN E  14 "
            pdb=" CB  GLN E  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 402 not shown)

  Planarity restraints: 775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  28 "   -0.154 9.50e-02 1.11e+02   6.95e-02 3.92e+00
        pdb=" NE  ARG C  28 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  28 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  28 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  28 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  28 "   -0.154 9.50e-02 1.11e+02   6.94e-02 3.91e+00
        pdb=" NE  ARG A  28 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  28 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  28 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  28 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  28 "   -0.154 9.50e-02 1.11e+02   6.94e-02 3.91e+00
        pdb=" NE  ARG E  28 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  28 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  28 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  28 "    0.000 2.00e-02 2.50e+03
  ... (remaining 772 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1364
        2.86 -     3.37: 2845
        3.37 -     3.88: 6928
        3.88 -     4.39: 8284
        4.39 -     4.90: 15000
  Nonbonded interactions: 34421
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  45 "
            pdb=" ND2 ASN E  27 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" ND2 ASN B  27 "
            pdb=" OH  TYR D  45 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OH  TYR A  45 "
            pdb=" ND2 ASN C  27 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" ND2 ASN A  27 "
            pdb=" OH  TYR B  45 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" O   GLY C  25 "
            pdb=" OD1 ASN C  27 "
     model   vdw
     2.514 3.040
  ... (remaining 34416 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 'D'
  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:             0.530
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.190
  Find NCS groups from input model:        0.030
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
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      :  0.003   0.031   3860  Z= 0.232
  Angle     :  0.699   6.548   5200  Z= 0.418
  Chirality :  0.046   0.205    405
  Planarity :  0.006   0.070    775
  Dihedral  : 15.070  55.866   1425
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.42 (0.21), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.16), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.009   ARG A  28 
 TYR   0.011   0.001   TYR C  63 
 PHE   0.006   0.001   PHE D 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 3860)
  covalent geometry    : angle       0.69939 ( 5200)
  hydrogen bonds       : bond        0.12764 (   74)
  hydrogen bonds       : angle      11.11301 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.138 
Fit side-chains
REVERT: B   52 TYR cc_start: 0.9430 (m-80) cc_final: 0.8876 (m-80)
REVERT: C   11 GLN cc_start: 0.8666 (tt0) cc_final: 0.8320 (tp40)
REVERT: D  121 SER cc_start: 0.8810 (p) cc_final: 0.8466 (p)
REVERT: E   13 TYR cc_start: 0.8933 (t80) cc_final: 0.8579 (t80)
REVERT: E   40 GLN cc_start: 0.8497 (tt0) cc_final: 0.7803 (mt0)
REVERT: E  122 GLN cc_start: 0.8686 (mt0) cc_final: 0.8472 (mt0)
REVERT: E  128 ASP cc_start: 0.8315 (t0) cc_final: 0.8062 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0654
  time to fit residues: 6.8006
Evaluate side-chains
  70 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN
B   5 ASN
B   9 ASN
B 127 ASN
C   9 ASN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 127 ASN
D   9 ASN
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 122 GLN
D 127 ASN
E   9 ASN
E  24 GLN
E  40 GLN
E 127 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.120324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.098594 restraints weight = 4696.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.90
r_work: 0.3358 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.042   3860  Z= 0.378
  Angle     :  0.576   4.013   5200  Z= 0.329
  Chirality :  0.038   0.094    405
  Planarity :  0.003   0.014    775
  Dihedral  :  4.720  20.929    525
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.65 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.59 (0.17), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.13), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  28 
 TYR   0.015   0.002   TYR C  32 
 PHE   0.010   0.002   PHE B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00858 ( 3860)
  covalent geometry    : angle       0.57605 ( 5200)
  hydrogen bonds       : bond        0.03397 (   74)
  hydrogen bonds       : angle       6.64590 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7975 (mm-40)
REVERT: A   28 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8176 (mtt90)
REVERT: A  113 TYR cc_start: 0.8918 (t80) cc_final: 0.8626 (t80)
REVERT: B   62 GLN cc_start: 0.8971 (tt0) cc_final: 0.8559 (tt0)
REVERT: B  104 PHE cc_start: 0.8773 (t80) cc_final: 0.8540 (t80)
REVERT: B  106 TYR cc_start: 0.9415 (t80) cc_final: 0.9065 (t80)
REVERT: C   28 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8102 (mtm-85)
REVERT: D  113 TYR cc_start: 0.8751 (t80) cc_final: 0.8478 (t80)
REVERT: D  121 SER cc_start: 0.8715 (p) cc_final: 0.8317 (p)
REVERT: E  122 GLN cc_start: 0.8546 (mt0) cc_final: 0.8255 (mt0)
  outliers start: 5
  outliers final: 3
  residues processed: 74
  average time/residue: 0.0835
  time to fit residues: 7.4281
Evaluate side-chains
  77 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain E residue   17 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
A   9 ASN
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 ASN
C   5 ASN
C   9 ASN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   9 ASN
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.123019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.100934 restraints weight = 4559.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.92
r_work: 0.3407 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   3860  Z= 0.250
  Angle     :  0.499   3.773   5200  Z= 0.285
  Chirality :  0.036   0.081    405
  Planarity :  0.002   0.016    775
  Dihedral  :  4.478  20.037    525
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  8.38 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.57 (0.18), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.14), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  28 
 TYR   0.023   0.002   TYR C  13 
 PHE   0.010   0.002   PHE B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 3860)
  covalent geometry    : angle       0.49897 ( 5200)
  hydrogen bonds       : bond        0.02713 (   74)
  hydrogen bonds       : angle       5.82048 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7465 (mm-40)
REVERT: A  113 TYR cc_start: 0.8891 (t80) cc_final: 0.8522 (t80)
REVERT: B   14 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7509 (mm-40)
REVERT: B   62 GLN cc_start: 0.8931 (tt0) cc_final: 0.8588 (tt0)
REVERT: B  104 PHE cc_start: 0.8845 (t80) cc_final: 0.8630 (t80)
REVERT: B  106 TYR cc_start: 0.9406 (t80) cc_final: 0.9026 (t80)
REVERT: C   28 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8210 (mtt-85)
REVERT: D   14 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8317 (mm-40)
REVERT: D  113 TYR cc_start: 0.8699 (t80) cc_final: 0.8321 (t80)
REVERT: D  121 SER cc_start: 0.8733 (p) cc_final: 0.8365 (p)
REVERT: E  122 GLN cc_start: 0.8511 (mt0) cc_final: 0.8241 (mt0)
  outliers start: 12
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0824
  time to fit residues: 7.9097
Evaluate side-chains
  81 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain D residue   14 GLN
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue   53 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    2.9984

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
A   9 ASN
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 ASN
C   9 ASN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   9 ASN
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.124760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.102876 restraints weight = 4580.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.91
r_work: 0.3431 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3860  Z= 0.192
  Angle     :  0.472   3.697   5200  Z= 0.269
  Chirality :  0.036   0.080    405
  Planarity :  0.002   0.024    775
  Dihedral  :  4.282  19.509    525
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  9.46 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.56 (0.18), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.14), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  28 
 TYR   0.013   0.002   TYR C  32 
 PHE   0.011   0.001   PHE B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 3860)
  covalent geometry    : angle       0.47172 ( 5200)
  hydrogen bonds       : bond        0.02317 (   74)
  hydrogen bonds       : angle       5.44692 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7485 (mm-40)
REVERT: A   28 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8222 (mtm-85)
REVERT: A   62 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8690 (tt0)
REVERT: A  113 TYR cc_start: 0.8847 (t80) cc_final: 0.8481 (t80)
REVERT: B   14 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7698 (mm-40)
REVERT: B   28 ARG cc_start: 0.8550 (mtt-85) cc_final: 0.7824 (mtm180)
REVERT: B   62 GLN cc_start: 0.8868 (tt0) cc_final: 0.8520 (tt0)
REVERT: B  104 PHE cc_start: 0.8840 (t80) cc_final: 0.8623 (t80)
REVERT: B  106 TYR cc_start: 0.9392 (t80) cc_final: 0.9002 (t80)
REVERT: C   28 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8079 (mtm-85)
REVERT: D  113 TYR cc_start: 0.8669 (t80) cc_final: 0.8285 (t80)
REVERT: D  121 SER cc_start: 0.8710 (p) cc_final: 0.8342 (p)
REVERT: E  110 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8946 (tt)
REVERT: E  122 GLN cc_start: 0.8512 (mt0) cc_final: 0.8259 (mt0)
  outliers start: 10
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0626
  time to fit residues: 5.9072
Evaluate side-chains
  78 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ASN
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain E residue   53 SER
Chi-restraints excluded: chain E residue  110 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 ASN
C   9 ASN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   9 ASN
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.118252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.095803 restraints weight = 4642.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.91
r_work: 0.3324 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.040   3860  Z= 0.411
  Angle     :  0.568   3.953   5200  Z= 0.324
  Chirality :  0.037   0.090    405
  Planarity :  0.003   0.019    775
  Dihedral  :  4.589  21.779    525
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  :  9.19 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.69 (0.17), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.13), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  28 
 TYR   0.013   0.002   TYR C  32 
 PHE   0.012   0.003   PHE B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00928 ( 3860)
  covalent geometry    : angle       0.56814 ( 5200)
  hydrogen bonds       : bond        0.02893 (   74)
  hydrogen bonds       : angle       5.64358 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.7782 (mm-40)
REVERT: A   62 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8719 (tt0)
REVERT: A  113 TYR cc_start: 0.8897 (t80) cc_final: 0.8568 (t80)
REVERT: B   14 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7931 (mm-40)
REVERT: B  104 PHE cc_start: 0.8878 (t80) cc_final: 0.8641 (t80)
REVERT: C   13 TYR cc_start: 0.8480 (t80) cc_final: 0.7747 (t80)
REVERT: C   14 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.7714 (mm-40)
REVERT: C   28 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8248 (mtt-85)
REVERT: C  110 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8808 (tt)
REVERT: D  113 TYR cc_start: 0.8714 (t80) cc_final: 0.8407 (t80)
REVERT: D  121 SER cc_start: 0.8692 (p) cc_final: 0.8343 (p)
REVERT: E  110 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8995 (tt)
  outliers start: 14
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0519
  time to fit residues: 4.9285
Evaluate side-chains
  85 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain C residue   14 GLN
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  110 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 122 GLN
C  62 GLN
D  40 GLN
E  40 GLN
E  62 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.131666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.110176 restraints weight = 4470.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 1.91
r_work: 0.3549 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3860  Z= 0.093
  Angle     :  0.430   3.457   5200  Z= 0.245
  Chirality :  0.035   0.078    405
  Planarity :  0.002   0.038    775
  Dihedral  :  3.974  17.513    525
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  :  9.19 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.53 (0.18), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.14), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG B  28 
 TYR   0.010   0.001   TYR A  32 
 PHE   0.010   0.001   PHE B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 3860)
  covalent geometry    : angle       0.43036 ( 5200)
  hydrogen bonds       : bond        0.01953 (   74)
  hydrogen bonds       : angle       5.03602 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7425 (mm-40)
REVERT: A   28 ARG cc_start: 0.8646 (mtt90) cc_final: 0.8170 (mtm-85)
REVERT: A   62 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8667 (tt0)
REVERT: A  113 TYR cc_start: 0.8878 (t80) cc_final: 0.8548 (t80)
REVERT: B   14 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7818 (mm-40)
REVERT: B   28 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.7915 (mtm180)
REVERT: B   62 GLN cc_start: 0.8886 (tt0) cc_final: 0.8501 (tt0)
REVERT: B  104 PHE cc_start: 0.8826 (t80) cc_final: 0.8611 (t80)
REVERT: C   13 TYR cc_start: 0.8511 (t80) cc_final: 0.8266 (t80)
REVERT: C   28 ARG cc_start: 0.8425 (mtt180) cc_final: 0.8064 (mtm-85)
REVERT: C  110 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8785 (tt)
REVERT: D  113 TYR cc_start: 0.8672 (t80) cc_final: 0.8251 (t80)
REVERT: D  121 SER cc_start: 0.8736 (p) cc_final: 0.8389 (p)
REVERT: E  124 MET cc_start: 0.8802 (mtm) cc_final: 0.8388 (ptp)
  outliers start: 14
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0492
  time to fit residues: 4.9237
Evaluate side-chains
  84 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue   28 ARG
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue   53 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   chunk 3 optimal weight:   30.0000
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    5.1386

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 ASN
C   9 ASN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 127 ASN
E   9 ASN
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.119893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.097499 restraints weight = 4663.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.91
r_work: 0.3341 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   3860  Z= 0.317
  Angle     :  0.527   3.858   5200  Z= 0.300
  Chirality :  0.036   0.083    405
  Planarity :  0.003   0.030    775
  Dihedral  :  4.392  21.516    525
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 10.00 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.68 (0.17), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.13), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  28 
 TYR   0.011   0.002   TYR B  46 
 PHE   0.013   0.002   PHE B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00715 ( 3860)
  covalent geometry    : angle       0.52743 ( 5200)
  hydrogen bonds       : bond        0.02483 (   74)
  hydrogen bonds       : angle       5.39489 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7597 (mm-40)
REVERT: A   28 ARG cc_start: 0.8685 (mtt90) cc_final: 0.8243 (mtm-85)
REVERT: A   62 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8779 (tt0)
REVERT: A  113 TYR cc_start: 0.8831 (t80) cc_final: 0.8469 (t80)
REVERT: B   14 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7852 (mm-40)
REVERT: B   28 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.7883 (mtm180)
REVERT: C   13 TYR cc_start: 0.8479 (t80) cc_final: 0.8130 (t80)
REVERT: C   28 ARG cc_start: 0.8538 (mtt180) cc_final: 0.8150 (mtm-85)
REVERT: C  110 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8837 (tt)
REVERT: D  113 TYR cc_start: 0.8678 (t80) cc_final: 0.8420 (t80)
REVERT: D  121 SER cc_start: 0.8714 (p) cc_final: 0.8368 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0849
  time to fit residues: 7.3969
Evaluate side-chains
  76 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue   53 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 9 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 130 GLN
B   9 ASN
C   9 ASN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
D  40 GLN
E   9 ASN
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.130203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.107814 restraints weight = 4507.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.95
r_work: 0.3503 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3860  Z= 0.095
  Angle     :  0.435   3.473   5200  Z= 0.246
  Chirality :  0.035   0.076    405
  Planarity :  0.002   0.029    775
  Dihedral  :  3.957  17.902    525
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  :  9.46 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.54 (0.18), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.14), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  28 
 TYR   0.009   0.001   TYR C  63 
 PHE   0.014   0.001   PHE B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 3860)
  covalent geometry    : angle       0.43472 ( 5200)
  hydrogen bonds       : bond        0.01854 (   74)
  hydrogen bonds       : angle       4.93259 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7467 (mm-40)
REVERT: A   28 ARG cc_start: 0.8635 (mtt90) cc_final: 0.8154 (mtm-85)
REVERT: A   62 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (tt0)
REVERT: A  113 TYR cc_start: 0.8845 (t80) cc_final: 0.8494 (t80)
REVERT: B   14 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7773 (mm-40)
REVERT: B   28 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.7898 (mtm180)
REVERT: B   62 GLN cc_start: 0.8884 (tt0) cc_final: 0.8505 (tt0)
REVERT: C   13 TYR cc_start: 0.8503 (t80) cc_final: 0.8230 (t80)
REVERT: C   28 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8046 (mtm-85)
REVERT: C  110 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8760 (tt)
REVERT: D  113 TYR cc_start: 0.8638 (t80) cc_final: 0.8392 (t80)
REVERT: D  121 SER cc_start: 0.8734 (p) cc_final: 0.8396 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0847
  time to fit residues: 7.8146
Evaluate side-chains
  81 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue   28 ARG
Chi-restraints excluded: chain E residue   17 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.121758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.099223 restraints weight = 4565.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.91
r_work: 0.3376 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   3860  Z= 0.272
  Angle     :  0.506   3.766   5200  Z= 0.287
  Chirality :  0.036   0.080    405
  Planarity :  0.003   0.027    775
  Dihedral  :  4.281  21.057    525
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  9.19 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.62 (0.17), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.13), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  28 
 TYR   0.011   0.002   TYR B  46 
 PHE   0.026   0.002   PHE B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 3860)
  covalent geometry    : angle       0.50615 ( 5200)
  hydrogen bonds       : bond        0.02295 (   74)
  hydrogen bonds       : angle       5.21300 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7555 (mm-40)
REVERT: A   28 ARG cc_start: 0.8699 (mtt90) cc_final: 0.8184 (mtm-85)
REVERT: A   62 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8828 (tt0)
REVERT: A  113 TYR cc_start: 0.8847 (t80) cc_final: 0.8481 (t80)
REVERT: B   14 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7812 (mm-40)
REVERT: B   28 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.7922 (mtm180)
REVERT: C   13 TYR cc_start: 0.8495 (t80) cc_final: 0.8105 (t80)
REVERT: C   28 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8096 (mtm-85)
REVERT: C  110 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8848 (tt)
REVERT: D  113 TYR cc_start: 0.8691 (t80) cc_final: 0.8435 (t80)
REVERT: D  121 SER cc_start: 0.8704 (p) cc_final: 0.8365 (p)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.0772
  time to fit residues: 6.4817
Evaluate side-chains
  75 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   62 GLN
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue   28 ARG
Chi-restraints excluded: chain E residue   17 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:   20.0000
   chunk 28 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 27 optimal weight:    0.4980
   chunk 29 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    3.6988

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.123035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.100799 restraints weight = 4615.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.91
r_work: 0.3401 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3860  Z= 0.232
  Angle     :  0.487   3.709   5200  Z= 0.276
  Chirality :  0.035   0.076    405
  Planarity :  0.003   0.027    775
  Dihedral  :  4.247  20.522    525
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  8.92 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.63 (0.17), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.13), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  28 
 TYR   0.010   0.002   TYR B  46 
 PHE   0.022   0.002   PHE B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 3860)
  covalent geometry    : angle       0.48716 ( 5200)
  hydrogen bonds       : bond        0.02110 (   74)
  hydrogen bonds       : angle       5.16481 (  222)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7567 (mm-40)
REVERT: A   28 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8184 (mtm-85)
REVERT: A  113 TYR cc_start: 0.8833 (t80) cc_final: 0.8466 (t80)
REVERT: B   14 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7779 (mm-40)
REVERT: B   28 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.7904 (mtm180)
REVERT: C   13 TYR cc_start: 0.8524 (t80) cc_final: 0.8178 (t80)
REVERT: C   28 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8096 (mtm-85)
REVERT: C  110 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8824 (tt)
REVERT: C  124 MET cc_start: 0.8365 (ptp) cc_final: 0.8086 (ptp)
REVERT: D  113 TYR cc_start: 0.8645 (t80) cc_final: 0.8348 (t80)
REVERT: D  121 SER cc_start: 0.8715 (p) cc_final: 0.8379 (p)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0841
  time to fit residues: 7.3380
Evaluate side-chains
  77 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLN
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 GLN
Chi-restraints excluded: chain C residue   53 SER
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue   28 ARG
Chi-restraints excluded: chain E residue   17 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A  40 GLN
B   9 ASN
C   9 ASN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   9 ASN
D  40 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   9 ASN
E  40 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.122320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.099922 restraints weight = 4508.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.89
r_work: 0.3396 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   3860  Z= 0.273
  Angle     :  0.506   3.774   5200  Z= 0.288
  Chirality :  0.036   0.079    405
  Planarity :  0.003   0.027    775
  Dihedral  :  4.311  21.009    525
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  8.65 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.65 (0.17), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.13), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  28 
 TYR   0.016   0.002   TYR B  60 
 PHE   0.020   0.002   PHE B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 3860)
  covalent geometry    : angle       0.50564 ( 5200)
  hydrogen bonds       : bond        0.02227 (   74)
  hydrogen bonds       : angle       5.19954 (  222)

===============================================================================
Job complete
usr+sys time: 1055.82 seconds
wall clock time: 18 minutes 53.14 seconds (1133.14 seconds total)