Starting phenix.real_space_refine
on Sat Aug 23 12:21:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jla_36390/08_2025/8jla_36390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jla_36390/08_2025/8jla_36390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jla_36390/08_2025/8jla_36390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jla_36390/08_2025/8jla_36390.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jla_36390/08_2025/8jla_36390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jla_36390/08_2025/8jla_36390.map"
  }
  resolution = 3.44
  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=   0.003 sd=   0.033
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: 5
    Type Number    sf(0)   Gaussians
     P     312      5.49       5
     S      14      5.16       5
     C    6761      2.51       5
     N    2309      2.21       5
     O    2918      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  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: 12314
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 3200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 3200
          Classifications: {'DNA': 156}
          Link IDs: {'rna3p': 155}
    Chain: "J"
      Number of atoms: 3196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 3196
          Classifications: {'DNA': 156}
          Link IDs: {'rna3p': 155}
  Time building chain proxies: 2.68, per 1000 atoms: 0.22
  Number of scatterers: 12314
  At special positions: 0
  Unit cell: (74.2, 121.9, 129.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     312     15.00
     O    2918      8.00
     N    2309      7.00
     C    6761      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: 1.05
  Conformation dependent library (CDL) restraints added in 265.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      73.7% alpha, 2.7% beta
      156 base pairs and 283 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.557A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.558A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.716A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.559A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.528A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.763A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 4.024A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.545A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.714A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.481A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 3.761A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.854A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.500A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.334A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.765A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.085A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    403 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      401 hydrogen bonds
      802 hydrogen bond angles
      0 basepair planarities
      156 basepair parallelities
      283 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2149
        1.33 -     1.45: 4573
        1.45 -     1.57: 5804
        1.57 -     1.69: 622
        1.69 -     1.81: 24
  Bond restraints: 13172
  Sorted by residual:
  bond pdb=" CZ  ARG C  88 "
       pdb=" NH2 ARG C  88 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 9.83e+00
  bond pdb=" CZ  ARG G  88 "
       pdb=" NH2 ARG G  88 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.58e+00
  bond pdb=" CZ  ARG B  78 "
       pdb=" NH2 ARG B  78 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.02e+00
  bond pdb=" CZ  ARG B  35 "
       pdb=" NH2 ARG B  35 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.69e+00
  bond pdb=" CZ  ARG B  67 "
       pdb=" NH2 ARG B  67 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.09e+00
  ... (remaining 13167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 17148
        1.42 -     2.84: 1692
        2.84 -     4.26: 242
        4.26 -     5.68: 37
        5.68 -     7.10: 11
  Bond angle restraints: 19130
  Sorted by residual:
  angle pdb=" CA  LEU A  65 "
        pdb=" C   LEU A  65 "
        pdb=" N   PRO A  66 "
      ideal   model   delta    sigma   weight residual
     120.52  124.12   -3.60 8.30e-01 1.45e+00 1.88e+01
  angle pdb=" C4'  DG J -53 "
        pdb=" O4'  DG J -53 "
        pdb=" C1'  DG J -53 "
      ideal   model   delta    sigma   weight residual
     109.70  103.73    5.97 1.50e+00 4.44e-01 1.58e+01
  angle pdb=" CD  ARG B  35 "
        pdb=" NE  ARG B  35 "
        pdb=" CZ  ARG B  35 "
      ideal   model   delta    sigma   weight residual
     124.40  129.76   -5.36 1.40e+00 5.10e-01 1.46e+01
  angle pdb=" C   GLN E  93 "
        pdb=" N   GLU E  94 "
        pdb=" CA  GLU E  94 "
      ideal   model   delta    sigma   weight residual
     120.44  125.22   -4.78 1.30e+00 5.92e-01 1.35e+01
  angle pdb=" C4'  DC J  37 "
        pdb=" O4'  DC J  37 "
        pdb=" C1'  DC J  37 "
      ideal   model   delta    sigma   weight residual
     109.70  104.35    5.35 1.50e+00 4.44e-01 1.27e+01
  ... (remaining 19125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.00: 5506
       33.00 -    65.99: 1547
       65.99 -    98.99: 39
       98.99 -   131.98: 0
      131.98 -   164.98: 2
  Dihedral angle restraints: 7094
    sinusoidal: 4936
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" C4'  DT J  54 "
           pdb=" C3'  DT J  54 "
           pdb=" O3'  DT J  54 "
           pdb=" P    DC J  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   55.02  164.98     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   68.92  151.08     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" C   LYS C  74 "
           pdb=" N   LYS C  74 "
           pdb=" CA  LYS C  74 "
           pdb=" CB  LYS C  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.76    9.16     0      2.50e+00 1.60e-01 1.34e+01
  ... (remaining 7091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1830
       0.068 -    0.136: 307
       0.136 -    0.204: 31
       0.204 -    0.272: 5
       0.272 -    0.340: 1
  Chirality restraints: 2174
  Sorted by residual:
  chirality pdb=" C4'  DG J -53 "
            pdb=" C5'  DG J -53 "
            pdb=" O4'  DG J -53 "
            pdb=" C3'  DG J -53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.19   -0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" CA  ILE G 102 "
            pdb=" N   ILE G 102 "
            pdb=" C   ILE G 102 "
            pdb=" CB  ILE G 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" C4'  DC J  37 "
            pdb=" C5'  DC J  37 "
            pdb=" O4'  DC J  37 "
            pdb=" C3'  DC J  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.29   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 2171 not shown)

  Planarity restraints: 1340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  43 "    0.003 2.00e-02 2.50e+03   2.73e-02 2.05e+01
        pdb=" N9   DA I  43 "   -0.064 2.00e-02 2.50e+03
        pdb=" C8   DA I  43 "    0.060 2.00e-02 2.50e+03
        pdb=" N7   DA I  43 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DA I  43 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DA I  43 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I  43 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I  43 "    0.006 2.00e-02 2.50e+03
        pdb=" C2   DA I  43 "    0.010 2.00e-02 2.50e+03
        pdb=" N3   DA I  43 "    0.010 2.00e-02 2.50e+03
        pdb=" C4   DA I  43 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  42 "   -0.059 2.00e-02 2.50e+03   3.14e-02 1.97e+01
        pdb=" CG  TYR H  42 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  42 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  42 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  42 "    0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  42 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  42 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H  42 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I -59 "    0.040 2.00e-02 2.50e+03   2.45e-02 1.51e+01
        pdb=" N1   DT I -59 "   -0.064 2.00e-02 2.50e+03
        pdb=" C2   DT I -59 "    0.015 2.00e-02 2.50e+03
        pdb=" O2   DT I -59 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DT I -59 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT I -59 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT I -59 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DT I -59 "    0.003 2.00e-02 2.50e+03
        pdb=" C7   DT I -59 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DT I -59 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1337 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 4
        2.27 -     2.92: 4692
        2.92 -     3.58: 19109
        3.58 -     4.24: 33457
        4.24 -     4.90: 49191
  Nonbonded interactions: 106453
  Sorted by model distance:
  nonbonded pdb=" O   THR A  80 "
            pdb=" OD1 ASP A  81 "
     model   vdw
     1.607 3.040
  nonbonded pdb=" O   GLN G  24 "
            pdb=" CD1 TYR H  40 "
     model   vdw
     1.896 3.340
  nonbonded pdb=" OH  TYR H  40 "
            pdb=" OP1  DG I  48 "
     model   vdw
     1.950 3.040
  nonbonded pdb=" OG1 THR F  82 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" C   THR A  80 "
            pdb=" OD1 ASP A  81 "
     model   vdw
     2.335 3.270
  ... (remaining 106448 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77))
  selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77))
}

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:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.990
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
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      :  0.006   0.069  13172  Z= 0.308
  Angle     :  0.884   7.104  19130  Z= 0.570
  Chirality :  0.052   0.340   2174
  Planarity :  0.010   0.135   1340
  Dihedral  : 28.206 164.979   5706
  Min Nonbonded Distance : 1.607

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 11.94 %
    Favored  : 87.90 %
  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:  0.68 (0.27), residues: 732
  helix:  0.81 (0.20), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.18 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  29 
 TYR   0.059   0.004   TYR H  42 
 PHE   0.027   0.002   PHE E  84 
 HIS   0.010   0.002   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (13172)
  covalent geometry    : angle       0.88371 (19130)
  hydrogen bonds       : bond        0.10438 (  804)
  hydrogen bonds       : angle       3.79437 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 236
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8487 (mmm) cc_final: 0.8263 (mmm)
REVERT: C   42 ARG cc_start: 0.8239 (mtp85) cc_final: 0.8034 (mtp85)
REVERT: C   68 ASN cc_start: 0.8046 (m-40) cc_final: 0.7754 (m-40)
REVERT: C   74 LYS cc_start: 0.7782 (mttt) cc_final: 0.7574 (mttt)
REVERT: C   95 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8650 (ttmm)
REVERT: C   99 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7569 (mmm160)
REVERT: D   57 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8632 (mmmm)
REVERT: E   59 GLU cc_start: 0.7810 (pm20) cc_final: 0.7477 (pm20)
REVERT: F   25 ASN cc_start: 0.6886 (m-40) cc_final: 0.5997 (m-40)
REVERT: G   13 LYS cc_start: 0.8298 (mmmm) cc_final: 0.8036 (mmmm)
REVERT: G   18 SER cc_start: 0.8832 (m) cc_final: 0.8608 (p)
REVERT: G   63 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8157 (mt)
REVERT: G   73 ASN cc_start: 0.8198 (t0) cc_final: 0.7842 (t0)
REVERT: H   57 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8410 (mmmm)
  outliers start: 1
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1877
  time to fit residues: 54.2560
Evaluate side-chains
  207 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
C  73 ASN
D  47 GLN
D  84 ASN
E 125 GLN
F  27 GLN
G  31 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.103351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.087095 restraints weight = 21667.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.17
r_work: 0.3000 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13172  Z= 0.174
  Angle     :  0.586   5.714  19130  Z= 0.358
  Chirality :  0.035   0.132   2174
  Planarity :  0.004   0.041   1340
  Dihedral  : 30.159 161.075   4238
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.26 %
    Favored  : 80.16 %
  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 (0.30), residues: 732
  helix:  3.00 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop :  0.20 (0.39), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  99 
 TYR   0.016   0.002   TYR F  88 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (13172)
  covalent geometry    : angle       0.58562 (19130)
  hydrogen bonds       : bond        0.04263 (  804)
  hydrogen bonds       : angle       2.66237 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 233
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8070 (pm20) cc_final: 0.7534 (pm20)
REVERT: A  117 VAL cc_start: 0.8865 (m) cc_final: 0.8606 (t)
REVERT: C   57 TYR cc_start: 0.8859 (t80) cc_final: 0.8577 (t80)
REVERT: C   61 GLU cc_start: 0.7828 (tp30) cc_final: 0.7558 (tp30)
REVERT: C   68 ASN cc_start: 0.8759 (m-40) cc_final: 0.8175 (m-40)
REVERT: C   71 ARG cc_start: 0.7084 (ttp-110) cc_final: 0.6337 (ttp-110)
REVERT: C   95 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8779 (ttmm)
REVERT: D   42 TYR cc_start: 0.8053 (t80) cc_final: 0.7828 (t80)
REVERT: D   52 THR cc_start: 0.8846 (m) cc_final: 0.8481 (p)
REVERT: D   79 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8329 (ttm-80)
REVERT: D   91 SER cc_start: 0.8583 (p) cc_final: 0.8336 (p)
REVERT: D   99 ARG cc_start: 0.8712 (mtt90) cc_final: 0.8477 (mtt-85)
REVERT: D  120 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8512 (mtpp)
REVERT: E   59 GLU cc_start: 0.7959 (pm20) cc_final: 0.7685 (pm20)
REVERT: F   79 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8520 (mtmm)
REVERT: G   73 ASN cc_start: 0.8442 (t0) cc_final: 0.8130 (t0)
REVERT: H   35 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7494 (mt-10)
  outliers start: 16
  outliers final: 8
  residues processed: 238
  average time/residue: 0.1522
  time to fit residues: 46.0508
Evaluate side-chains
  218 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 209
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   82 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  47 GLN
D  84 ASN
F  75 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.096661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.081253 restraints weight = 21744.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.28
r_work: 0.2873 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13172  Z= 0.211
  Angle     :  0.600   9.279  19130  Z= 0.361
  Chirality :  0.037   0.151   2174
  Planarity :  0.005   0.040   1340
  Dihedral  : 29.977 163.521   4236
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 20.97 %
    Favored  : 74.68 %
  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:  3.67 (0.30), residues: 732
  helix:  3.29 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop :  0.06 (0.37), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  99 
 TYR   0.035   0.002   TYR D  83 
 PHE   0.016   0.002   PHE F 100 
 HIS   0.006   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (13172)
  covalent geometry    : angle       0.59956 (19130)
  hydrogen bonds       : bond        0.04667 (  804)
  hydrogen bonds       : angle       2.60839 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 237
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.8931 (m-80) cc_final: 0.8716 (m-80)
REVERT: A   59 GLU cc_start: 0.8011 (pm20) cc_final: 0.7543 (pm20)
REVERT: A  117 VAL cc_start: 0.9008 (m) cc_final: 0.8803 (t)
REVERT: B   88 TYR cc_start: 0.8820 (m-80) cc_final: 0.7732 (m-10)
REVERT: C   40 SER cc_start: 0.8826 (m) cc_final: 0.8579 (p)
REVERT: C   57 TYR cc_start: 0.8844 (t80) cc_final: 0.8607 (t80)
REVERT: D   42 TYR cc_start: 0.8105 (t80) cc_final: 0.7824 (t80)
REVERT: D   83 TYR cc_start: 0.8121 (m-10) cc_final: 0.7418 (m-80)
REVERT: D   91 SER cc_start: 0.8732 (p) cc_final: 0.8510 (p)
REVERT: D  120 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8612 (mtpp)
REVERT: E   58 THR cc_start: 0.9197 (m) cc_final: 0.8859 (m)
REVERT: E   59 GLU cc_start: 0.7939 (pm20) cc_final: 0.7372 (pm20)
REVERT: G   73 ASN cc_start: 0.8444 (t0) cc_final: 0.8115 (t0)
REVERT: H   83 TYR cc_start: 0.8142 (m-10) cc_final: 0.7899 (m-10)
  outliers start: 27
  outliers final: 17
  residues processed: 247
  average time/residue: 0.1429
  time to fit residues: 45.3251
Evaluate side-chains
  247 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 230
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   64 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue  118 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  47 GLN
D  82 HIS
D  84 ASN
F  27 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.095059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.079657 restraints weight = 21738.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.28
r_work: 0.2841 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13172  Z= 0.238
  Angle     :  0.591   6.832  19130  Z= 0.359
  Chirality :  0.037   0.144   2174
  Planarity :  0.005   0.041   1340
  Dihedral  : 30.082 163.872   4236
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 22.10 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.49 (0.30), residues: 732
  helix:  3.16 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.04 (0.38), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  99 
 TYR   0.023   0.002   TYR D  83 
 PHE   0.018   0.002   PHE F 100 
 HIS   0.005   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (13172)
  covalent geometry    : angle       0.59089 (19130)
  hydrogen bonds       : bond        0.04699 (  804)
  hydrogen bonds       : angle       2.61523 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 222
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7987 (pm20) cc_final: 0.7498 (pm20)
REVERT: B   25 ASN cc_start: 0.7340 (m-40) cc_final: 0.7107 (m-40)
REVERT: C   57 TYR cc_start: 0.8847 (t80) cc_final: 0.8593 (t80)
REVERT: D   46 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8767 (mmtp)
REVERT: D   83 TYR cc_start: 0.8222 (m-10) cc_final: 0.7831 (m-80)
REVERT: D   91 SER cc_start: 0.8735 (p) cc_final: 0.8513 (p)
REVERT: D  120 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8713 (ttmm)
REVERT: E   58 THR cc_start: 0.9096 (m) cc_final: 0.8837 (m)
REVERT: E   59 GLU cc_start: 0.7979 (pm20) cc_final: 0.7704 (pm20)
REVERT: G   73 ASN cc_start: 0.8511 (t0) cc_final: 0.8174 (t0)
REVERT: H   87 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.7906 (p)
  outliers start: 30
  outliers final: 24
  residues processed: 234
  average time/residue: 0.1605
  time to fit residues: 47.7617
Evaluate side-chains
  245 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 220
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue  118 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 86 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  47 GLN
D  82 HIS
D  84 ASN
H  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.096985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.081530 restraints weight = 21745.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.29
r_work: 0.2877 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13172  Z= 0.183
  Angle     :  0.562   9.608  19130  Z= 0.341
  Chirality :  0.035   0.188   2174
  Planarity :  0.004   0.044   1340
  Dihedral  : 29.951 164.283   4236
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.87 %
    Favored  : 71.61 %
  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:  3.58 (0.30), residues: 732
  helix:  3.27 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.14 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  99 
 TYR   0.021   0.002   TYR D  83 
 PHE   0.016   0.001   PHE F 100 
 HIS   0.006   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (13172)
  covalent geometry    : angle       0.56218 (19130)
  hydrogen bonds       : bond        0.04137 (  804)
  hydrogen bonds       : angle       2.49213 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 223
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8068 (pm20) cc_final: 0.7524 (pm20)
REVERT: B   25 ASN cc_start: 0.7338 (m-40) cc_final: 0.7115 (m-40)
REVERT: B   73 THR cc_start: 0.8809 (m) cc_final: 0.8580 (t)
REVERT: C   57 TYR cc_start: 0.8877 (t80) cc_final: 0.8592 (t80)
REVERT: D   42 TYR cc_start: 0.8032 (t80) cc_final: 0.7811 (t80)
REVERT: D   52 THR cc_start: 0.8915 (m) cc_final: 0.8561 (p)
REVERT: D   80 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8129 (tt)
REVERT: D   91 SER cc_start: 0.8705 (p) cc_final: 0.8484 (p)
REVERT: E   58 THR cc_start: 0.9079 (m) cc_final: 0.8823 (m)
REVERT: E   59 GLU cc_start: 0.7884 (pm20) cc_final: 0.7596 (pm20)
REVERT: G   73 ASN cc_start: 0.8511 (t0) cc_final: 0.8178 (t0)
REVERT: H   83 TYR cc_start: 0.8057 (m-10) cc_final: 0.7803 (m-10)
  outliers start: 28
  outliers final: 20
  residues processed: 234
  average time/residue: 0.1643
  time to fit residues: 48.6355
Evaluate side-chains
  239 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0270
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.098256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.082812 restraints weight = 21546.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.26
r_work: 0.2903 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13172  Z= 0.170
  Angle     :  0.554  11.730  19130  Z= 0.336
  Chirality :  0.034   0.155   2174
  Planarity :  0.004   0.045   1340
  Dihedral  : 29.900 164.505   4236
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 23.55 %
    Favored  : 72.26 %
  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:  3.60 (0.31), residues: 732
  helix:  3.29 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  99 
 TYR   0.054   0.002   TYR D  83 
 PHE   0.015   0.001   PHE F 100 
 HIS   0.003   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13172)
  covalent geometry    : angle       0.55357 (19130)
  hydrogen bonds       : bond        0.03935 (  804)
  hydrogen bonds       : angle       2.45886 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 230
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8065 (pm20) cc_final: 0.7527 (pm20)
REVERT: B   25 ASN cc_start: 0.7335 (m-40) cc_final: 0.7110 (m-40)
REVERT: D   42 TYR cc_start: 0.8013 (t80) cc_final: 0.7756 (t80)
REVERT: D   91 SER cc_start: 0.8673 (p) cc_final: 0.8413 (p)
REVERT: E   58 THR cc_start: 0.9066 (m) cc_final: 0.8804 (m)
REVERT: E   59 GLU cc_start: 0.7892 (pm20) cc_final: 0.7588 (pm20)
REVERT: G   73 ASN cc_start: 0.8508 (t0) cc_final: 0.8192 (t0)
REVERT: H   83 TYR cc_start: 0.8039 (m-10) cc_final: 0.7783 (m-10)
  outliers start: 26
  outliers final: 21
  residues processed: 238
  average time/residue: 0.1554
  time to fit residues: 46.5463
Evaluate side-chains
  243 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 222
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 125 GLN
B  75 HIS
C  73 ASN
D  82 HIS
D  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.097701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.082217 restraints weight = 21507.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.25
r_work: 0.2892 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13172  Z= 0.184
  Angle     :  0.562   9.687  19130  Z= 0.340
  Chirality :  0.034   0.163   2174
  Planarity :  0.004   0.048   1340
  Dihedral  : 29.901 165.235   4236
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 24.19 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.31), residues: 732
  helix:  3.22 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  99 
 TYR   0.075   0.002   TYR D  83 
 PHE   0.016   0.001   PHE F 100 
 HIS   0.011   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (13172)
  covalent geometry    : angle       0.56249 (19130)
  hydrogen bonds       : bond        0.04092 (  804)
  hydrogen bonds       : angle       2.49502 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 219
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8051 (pm20) cc_final: 0.7521 (pm20)
REVERT: B   25 ASN cc_start: 0.7398 (m-40) cc_final: 0.7180 (m-40)
REVERT: B   88 TYR cc_start: 0.8573 (m-10) cc_final: 0.8228 (m-80)
REVERT: D   42 TYR cc_start: 0.7956 (t80) cc_final: 0.7707 (t80)
REVERT: E   58 THR cc_start: 0.9107 (m) cc_final: 0.8904 (m)
REVERT: E   59 GLU cc_start: 0.7892 (pm20) cc_final: 0.7618 (pm20)
REVERT: G   73 ASN cc_start: 0.8499 (t0) cc_final: 0.8187 (t0)
REVERT: H   83 TYR cc_start: 0.8039 (m-10) cc_final: 0.7746 (m-10)
REVERT: H  113 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7954 (mm-30)
  outliers start: 29
  outliers final: 24
  residues processed: 231
  average time/residue: 0.1865
  time to fit residues: 54.4473
Evaluate side-chains
  241 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
C  73 ASN
D  82 HIS
D  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.093562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.078166 restraints weight = 21697.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.27
r_work: 0.2815 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  13172  Z= 0.286
  Angle     :  0.628  11.658  19130  Z= 0.376
  Chirality :  0.040   0.174   2174
  Planarity :  0.005   0.052   1340
  Dihedral  : 30.138 167.321   4236
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 23.71 %
    Favored  : 70.81 %
  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:  3.15 (0.30), residues: 732
  helix:  2.96 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.33 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  99 
 TYR   0.063   0.003   TYR D  83 
 PHE   0.021   0.002   PHE F 100 
 HIS   0.006   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 (13172)
  covalent geometry    : angle       0.62771 (19130)
  hydrogen bonds       : bond        0.05170 (  804)
  hydrogen bonds       : angle       2.67352 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 231
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.7782 (t)
REVERT: A   59 GLU cc_start: 0.8111 (pm20) cc_final: 0.7072 (pm20)
REVERT: A   70 LEU cc_start: 0.8837 (tt) cc_final: 0.8629 (tp)
REVERT: B   25 ASN cc_start: 0.7457 (m-40) cc_final: 0.7214 (m-40)
REVERT: B   88 TYR cc_start: 0.8721 (m-10) cc_final: 0.8284 (m-10)
REVERT: C   64 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7930 (tp30)
REVERT: D   42 TYR cc_start: 0.8063 (t80) cc_final: 0.7841 (t80)
REVERT: D   51 ASP cc_start: 0.8498 (p0) cc_final: 0.8035 (p0)
REVERT: D   52 THR cc_start: 0.9072 (t) cc_final: 0.8821 (p)
REVERT: D  120 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8657 (ttmm)
REVERT: E   59 GLU cc_start: 0.7995 (pm20) cc_final: 0.7746 (pm20)
REVERT: F   77 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8774 (mtmm)
REVERT: G   73 ASN cc_start: 0.8551 (t0) cc_final: 0.8190 (t0)
REVERT: H   83 TYR cc_start: 0.8114 (m-10) cc_final: 0.7521 (m-10)
REVERT: H   87 SER cc_start: 0.8452 (m) cc_final: 0.8047 (p)
REVERT: H  113 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7961 (mm-30)
  outliers start: 34
  outliers final: 30
  residues processed: 242
  average time/residue: 0.1826
  time to fit residues: 56.1437
Evaluate side-chains
  257 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 225
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 125 GLN
C  73 ASN
D  82 HIS
D  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.094282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.078884 restraints weight = 21717.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.27
r_work: 0.2830 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13172  Z= 0.244
  Angle     :  0.624  13.065  19130  Z= 0.368
  Chirality :  0.038   0.175   2174
  Planarity :  0.005   0.055   1340
  Dihedral  : 30.109 167.924   4236
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 24.52 %
    Favored  : 69.84 %
  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 aren not related in a simple way.
  whole:  3.13 (0.31), residues: 732
  helix:  2.96 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.41 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  99 
 TYR   0.068   0.002   TYR D  83 
 PHE   0.018   0.002   PHE F 100 
 HIS   0.006   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 (13172)
  covalent geometry    : angle       0.62427 (19130)
  hydrogen bonds       : bond        0.04764 (  804)
  hydrogen bonds       : angle       2.62247 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 224
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   57 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.7770 (t)
REVERT: A   59 GLU cc_start: 0.8122 (pm20) cc_final: 0.7084 (pm20)
REVERT: B   25 ASN cc_start: 0.7388 (m-40) cc_final: 0.7123 (m-40)
REVERT: B   88 TYR cc_start: 0.8840 (m-10) cc_final: 0.7583 (m-10)
REVERT: C   64 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7904 (tp30)
REVERT: D   51 ASP cc_start: 0.8464 (p0) cc_final: 0.8012 (p0)
REVERT: D   52 THR cc_start: 0.9042 (t) cc_final: 0.8840 (p)
REVERT: D   83 TYR cc_start: 0.8158 (m-10) cc_final: 0.7220 (m-80)
REVERT: D  120 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8663 (ttmm)
REVERT: E   59 GLU cc_start: 0.7967 (pm20) cc_final: 0.7731 (pm20)
REVERT: F   77 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8784 (mtmm)
REVERT: G   73 ASN cc_start: 0.8553 (t0) cc_final: 0.8195 (t0)
REVERT: H   83 TYR cc_start: 0.8085 (m-10) cc_final: 0.7567 (m-10)
REVERT: H   87 SER cc_start: 0.8445 (m) cc_final: 0.8048 (p)
REVERT: H  113 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7981 (mm-30)
  outliers start: 35
  outliers final: 27
  residues processed: 236
  average time/residue: 0.1846
  time to fit residues: 54.9696
Evaluate side-chains
  252 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 19 optimal weight:    0.4980
   chunk 50 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
C 104 GLN
D  82 HIS
D  84 ASN
F  25 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.098520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.083072 restraints weight = 21573.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.27
r_work: 0.2905 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13172  Z= 0.168
  Angle     :  0.579  12.618  19130  Z= 0.343
  Chirality :  0.033   0.168   2174
  Planarity :  0.005   0.046   1340
  Dihedral  : 29.951 168.564   4236
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 26.13 %
    Favored  : 70.81 %
  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:  3.36 (0.31), residues: 732
  helix:  3.15 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.37 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  99 
 TYR   0.051   0.002   TYR D  83 
 PHE   0.015   0.001   PHE F 100 
 HIS   0.009   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13172)
  covalent geometry    : angle       0.57944 (19130)
  hydrogen bonds       : bond        0.03897 (  804)
  hydrogen bonds       : angle       2.47107 ( 1987)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 223
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8109 (pm20) cc_final: 0.7556 (pm20)
REVERT: B   88 TYR cc_start: 0.8775 (m-10) cc_final: 0.7513 (m-10)
REVERT: C   64 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7957 (tp30)
REVERT: D   48 VAL cc_start: 0.8903 (t) cc_final: 0.8690 (p)
REVERT: D   51 ASP cc_start: 0.8441 (p0) cc_final: 0.7987 (p0)
REVERT: D   52 THR cc_start: 0.9031 (t) cc_final: 0.8812 (p)
REVERT: D   83 TYR cc_start: 0.7982 (m-10) cc_final: 0.7205 (m-80)
REVERT: E   59 GLU cc_start: 0.7933 (pm20) cc_final: 0.7654 (pm20)
REVERT: F   77 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8780 (mtmm)
REVERT: G   73 ASN cc_start: 0.8545 (t0) cc_final: 0.8254 (t0)
REVERT: H   83 TYR cc_start: 0.8028 (m-10) cc_final: 0.7773 (m-10)
REVERT: H   87 SER cc_start: 0.8431 (m) cc_final: 0.8083 (p)
  outliers start: 19
  outliers final: 18
  residues processed: 232
  average time/residue: 0.1819
  time to fit residues: 53.5202
Evaluate side-chains
  239 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 220
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.0370
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.1862

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
D  82 HIS
D  84 ASN
H  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.096771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.081338 restraints weight = 21542.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.27
r_work: 0.2874 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13172  Z= 0.207
  Angle     :  0.604  12.457  19130  Z= 0.356
  Chirality :  0.036   0.174   2174
  Planarity :  0.005   0.102   1340
  Dihedral  : 30.021 170.002   4236
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 26.29 %
    Favored  : 69.35 %
  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:  3.30 (0.31), residues: 732
  helix:  3.09 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.39 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  99 
 TYR   0.056   0.002   TYR D  83 
 PHE   0.015   0.002   PHE F 100 
 HIS   0.009   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (13172)
  covalent geometry    : angle       0.60445 (19130)
  hydrogen bonds       : bond        0.04334 (  804)
  hydrogen bonds       : angle       2.56293 ( 1987)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2628.53 seconds
wall clock time: 45 minutes 39.43 seconds (2739.43 seconds total)