Starting phenix.real_space_refine
on Fri Sep 11 22:32:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jla_36390/09_2026/8jla_36390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jla_36390/09_2026/8jla_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_36390/09_2026/8jla_36390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jla_36390/09_2026/8jla_36390.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jla_36390/09_2026/8jla_36390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jla_36390/09_2026/8jla_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-2.2.1-6174/lib/python3.11/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: 3.16, per 1000 atoms: 0.26
  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: 0.92
  Conformation dependent library (CDL) restraints added in 355.5 milliseconds
  

  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: 1.87
  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: 2.44

  Time building geometry restraints manager: 1.26 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=" C3'  DG J -53 "
       pdb=" C2'  DG J -53 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 8.00e-03 1.56e+04 2.26e+01
  bond pdb=" C3'  DT I -76 "
       pdb=" C2'  DT I -76 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 8.00e-03 1.56e+04 2.21e+01
  bond pdb=" C3'  DG I -53 "
       pdb=" C2'  DG I -53 "
    ideal  model  delta    sigma   weight residual
    1.516  1.552 -0.036 8.00e-03 1.56e+04 2.00e+01
  bond pdb=" C3'  DT J  72 "
       pdb=" C2'  DT J  72 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 8.00e-03 1.56e+04 1.82e+01
  bond pdb=" C3'  DC J -68 "
       pdb=" C2'  DC J -68 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 8.00e-03 1.56e+04 1.75e+01
  ... (remaining 13167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 16687
        1.42 -     2.84: 1964
        2.84 -     4.26: 374
        4.26 -     5.68: 90
        5.68 -     7.10: 15
  Bond angle restraints: 19130
  Sorted by residual:
  angle pdb=" O4'  DA I  47 "
        pdb=" C1'  DA I  47 "
        pdb=" N9   DA I  47 "
      ideal   model   delta    sigma   weight residual
     108.00  103.46    4.54 7.00e-01 2.04e+00 4.21e+01
  angle pdb=" C4'  DG J -53 "
        pdb=" O4'  DG J -53 "
        pdb=" C1'  DG J -53 "
      ideal   model   delta    sigma   weight residual
     110.10  103.73    6.37 1.00e+00 1.00e+00 4.05e+01
  angle pdb=" O4'  DA I -54 "
        pdb=" C1'  DA I -54 "
        pdb=" N9   DA I -54 "
      ideal   model   delta    sigma   weight residual
     108.00  103.80    4.20 7.00e-01 2.04e+00 3.59e+01
  angle pdb=" C4'  DC J  37 "
        pdb=" O4'  DC J  37 "
        pdb=" C1'  DC J  37 "
      ideal   model   delta    sigma   weight residual
     110.10  104.35    5.75 1.00e+00 1.00e+00 3.30e+01
  angle pdb=" O4'  DA J  71 "
        pdb=" C1'  DA J  71 "
        pdb=" N9   DA J  71 "
      ideal   model   delta    sigma   weight residual
     108.00  112.00   -4.00 7.00e-01 2.04e+00 3.27e+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 -    0.069: 1684
       0.069 -    0.138: 401
       0.138 -    0.208: 83
       0.208 -    0.277: 4
       0.277 -    0.346: 2
  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   -0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" C3'  DT J  54 "
            pdb=" C4'  DT J  54 "
            pdb=" O3'  DT J  54 "
            pdb=" C2'  DT J  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.44   -0.29 2.00e-01 2.50e+01 2.05e+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   -0.24 2.00e-01 2.50e+01 1.42e+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:             1.180
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.860
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
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      :  0.007   0.069  13172  Z= 0.631
  Angle     :  1.010   7.104  19130  Z= 0.830
  Chirality :  0.062   0.346   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 are 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/Z
  covalent geometry    : bond        0.00709 /  0.63 (13172)
  covalent geometry    : angle       1.00974 /  0.83 (19130)
  hydrogen bonds       : bond        0.10438 /  7.10 (  804)
  hydrogen bonds       : angle       3.79437 /  2.76 ( 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  : 0.349 
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: 0.7753 (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: 0.8649 (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: 0.5999 (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: 0.2127
  time to fit residues: 62.3701
Evaluate side-chains
  208 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  75 HIS
C  73 ASN
D  47 GLN
D  82 HIS
D  84 ASN
E 125 GLN
F  27 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.102289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.086261 restraints weight = 21588.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 1.27
r_work: 0.2969 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13172  Z= 0.162
  Angle     :  0.689  11.058  19130  Z= 0.405
  Chirality :  0.048   0.218   2174
  Planarity :  0.005   0.059   1340
  Dihedral  : 30.799 165.176   4238
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.32 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.97 (0.30), residues: 732
  helix:  2.75 (0.22), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.23 (0.37), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  99 
 TYR   0.026   0.003   TYR H  42 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.16 (13172)
  covalent geometry    : angle       0.68883 /  0.41 (19130)
  hydrogen bonds       : bond        0.05278 /  3.55 (  804)
  hydrogen bonds       : angle       2.92121 /  2.14 ( 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: 21
    poor density    : 228
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8218 (pm20) cc_final: 0.7691 (pm20)
REVERT: A   90 MET cc_start: 0.8579 (mmm) cc_final: 0.8315 (mmm)
REVERT: A   96 CYS cc_start: 0.8567 (t) cc_final: 0.8197 (m)
REVERT: C   50 TYR cc_start: 0.8618 (t80) cc_final: 0.8324 (t80)
REVERT: C   57 TYR cc_start: 0.8887 (t80) cc_final: 0.8515 (t80)
REVERT: C   68 ASN cc_start: 0.8678 (m-40) cc_final: 0.8279 (m-40)
REVERT: C   71 ARG cc_start: 0.6994 (ttp-110) cc_final: 0.6530 (ttp-110)
REVERT: D   54 ILE cc_start: 0.8890 (tt) cc_final: 0.8463 (pt)
REVERT: D  120 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8554 (mtpp)
REVERT: E   59 GLU cc_start: 0.8080 (pm20) cc_final: 0.7813 (pm20)
REVERT: F   35 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8585 (mmm-85)
REVERT: G   73 ASN cc_start: 0.8460 (t0) cc_final: 0.8119 (t0)
REVERT: H   35 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7630 (mt-10)
REVERT: H   64 SER cc_start: 0.8949 (m) cc_final: 0.8741 (t)
REVERT: H   83 TYR cc_start: 0.8031 (m-10) cc_final: 0.7803 (m-10)
  outliers start: 21
  outliers final: 13
  residues processed: 235
  average time/residue: 0.1848
  time to fit residues: 55.0970
Evaluate side-chains
  219 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 206
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
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 B residue   59 LYS
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   58 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   82 THR
Chi-restraints excluded: chain G residue   85 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0870
   chunk 77 optimal weight:    9.9990
   chunk 82 optimal weight:    8.9990
   chunk 71 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  82 HIS
D  84 ASN
E  68 GLN
G  31 HIS
H  49 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.100287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.084270 restraints weight = 21547.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.30
r_work: 0.2928 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13172  Z= 0.162
  Angle     :  0.654   9.801  19130  Z= 0.386
  Chirality :  0.047   0.244   2174
  Planarity :  0.005   0.056   1340
  Dihedral  : 30.670 163.950   4236
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 18.23 %
    Favored  : 78.06 %
  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 are not related in a simple way.
  whole:  3.52 (0.30), residues: 732
  helix:  3.15 (0.22), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.03 (0.39), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  99 
 TYR   0.034   0.002   TYR D  83 
 PHE   0.028   0.002   PHE F 100 
 HIS   0.005   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.16 (13172)
  covalent geometry    : angle       0.65432 /  0.39 (19130)
  hydrogen bonds       : bond        0.05066 /  3.40 (  804)
  hydrogen bonds       : angle       2.69986 /  1.97 ( 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
  237 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 214
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8199 (pm20) cc_final: 0.7617 (pm20)
REVERT: A  117 VAL cc_start: 0.8856 (m) cc_final: 0.8603 (t)
REVERT: B  100 PHE cc_start: 0.8387 (m-10) cc_final: 0.8093 (m-10)
REVERT: C   57 TYR cc_start: 0.8904 (t80) cc_final: 0.8536 (t80)
REVERT: C   61 GLU cc_start: 0.7887 (tp30) cc_final: 0.7551 (tp30)
REVERT: C   68 ASN cc_start: 0.8782 (m-40) cc_final: 0.8122 (m-40)
REVERT: C   71 ARG cc_start: 0.7222 (ttp-110) cc_final: 0.6360 (ttp-110)
REVERT: C   99 ARG cc_start: 0.7753 (mmm160) cc_final: 0.7484 (mmm160)
REVERT: C  110 ASN cc_start: 0.8318 (t0) cc_final: 0.8096 (p0)
REVERT: D   42 TYR cc_start: 0.8099 (t80) cc_final: 0.7891 (t80)
REVERT: D  120 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8540 (mtpp)
REVERT: E   42 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7587 (ttm-80)
REVERT: E   59 GLU cc_start: 0.7910 (pm20) cc_final: 0.7516 (pm20)
REVERT: G   73 ASN cc_start: 0.8516 (t0) cc_final: 0.8184 (t0)
REVERT: H   83 TYR cc_start: 0.8147 (m-10) cc_final: 0.7800 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 223
  average time/residue: 0.1707
  time to fit residues: 49.1223
Evaluate side-chains
  221 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 207
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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   73 THR
Chi-restraints excluded: chain E residue   87 SER
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 G residue   85 LEU
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
D  82 HIS
F  75 HIS
H  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.100016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.082841 restraints weight = 21085.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 1.39
r_work: 0.2903 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13172  Z= 0.153
  Angle     :  0.627   8.541  19130  Z= 0.373
  Chirality :  0.045   0.226   2174
  Planarity :  0.005   0.056   1340
  Dihedral  : 30.595 164.414   4236
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.19 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.52 (0.30), residues: 732
  helix:  3.14 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.05 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  99 
 TYR   0.038   0.002   TYR D  83 
 PHE   0.017   0.001   PHE F 100 
 HIS   0.005   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.15 (13172)
  covalent geometry    : angle       0.62718 /  0.37 (19130)
  hydrogen bonds       : bond        0.04733 /  3.19 (  804)
  hydrogen bonds       : angle       2.58892 /  1.90 ( 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
  234 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.7918 (t)
REVERT: A   59 GLU cc_start: 0.8115 (pm20) cc_final: 0.7114 (pm20)
REVERT: A  117 VAL cc_start: 0.8951 (m) cc_final: 0.8689 (t)
REVERT: B  100 PHE cc_start: 0.8434 (m-10) cc_final: 0.8149 (m-10)
REVERT: C   57 TYR cc_start: 0.8922 (t80) cc_final: 0.8579 (t80)
REVERT: C   68 ASN cc_start: 0.8710 (m-40) cc_final: 0.7972 (m-40)
REVERT: C   71 ARG cc_start: 0.7061 (ttp-110) cc_final: 0.6181 (ttp-110)
REVERT: D   42 TYR cc_start: 0.8021 (t80) cc_final: 0.7817 (t80)
REVERT: D  120 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8585 (mtpp)
REVERT: E   59 GLU cc_start: 0.7838 (pm20) cc_final: 0.7483 (pm20)
REVERT: G   73 ASN cc_start: 0.8454 (t0) cc_final: 0.8139 (t0)
REVERT: H   83 TYR cc_start: 0.8157 (m-10) cc_final: 0.7912 (m-10)
  outliers start: 21
  outliers final: 16
  residues processed: 221
  average time/residue: 0.1700
  time to fit residues: 48.3419
Evaluate side-chains
  222 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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   74 ILE
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   73 THR
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   74 GLU
Chi-restraints excluded: chain F residue   79 LYS
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   56 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 97 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    1.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
B  75 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3257 r_free = 0.3257 target = 0.095763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.080316 restraints weight = 21791.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.29
r_work: 0.2857 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13172  Z= 0.203
  Angle     :  0.686  10.937  19130  Z= 0.395
  Chirality :  0.048   0.239   2174
  Planarity :  0.005   0.070   1340
  Dihedral  : 30.637 164.167   4236
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 19.19 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.26 (0.30), residues: 732
  helix:  3.01 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  99 
 TYR   0.031   0.003   TYR D  83 
 PHE   0.021   0.002   PHE F 100 
 HIS   0.008   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.20 (13172)
  covalent geometry    : angle       0.68649 /  0.39 (19130)
  hydrogen bonds       : bond        0.05527 /  3.73 (  804)
  hydrogen bonds       : angle       2.65961 /  1.95 ( 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
  265 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 233
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.7915 (t)
REVERT: A   59 GLU cc_start: 0.8135 (pm20) cc_final: 0.7214 (pm20)
REVERT: A  117 VAL cc_start: 0.9011 (m) cc_final: 0.8781 (t)
REVERT: B   25 ASN cc_start: 0.7326 (m-40) cc_final: 0.7062 (m-40)
REVERT: C   57 TYR cc_start: 0.8896 (t80) cc_final: 0.8545 (t80)
REVERT: D   42 TYR cc_start: 0.8131 (t80) cc_final: 0.7869 (t80)
REVERT: D   91 SER cc_start: 0.8772 (p) cc_final: 0.8516 (p)
REVERT: D  120 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8585 (mtpp)
REVERT: E   59 GLU cc_start: 0.7960 (pm20) cc_final: 0.7642 (pm20)
REVERT: G   73 ASN cc_start: 0.8483 (t0) cc_final: 0.8127 (t0)
REVERT: H   83 TYR cc_start: 0.8171 (m-10) cc_final: 0.7771 (m-10)
  outliers start: 32
  outliers final: 25
  residues processed: 244
  average time/residue: 0.1682
  time to fit residues: 52.9399
Evaluate side-chains
  253 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 227
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
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   74 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   80 THR
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 G residue   19 SER
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3272 r_free = 0.3272 target = 0.096589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.081201 restraints weight = 21646.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.26
r_work: 0.2876 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13172  Z= 0.164
  Angle     :  0.640  10.738  19130  Z= 0.377
  Chirality :  0.045   0.230   2174
  Planarity :  0.005   0.054   1340
  Dihedral  : 30.546 164.518   4236
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.23 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.48 (0.30), residues: 732
  helix:  3.19 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.16 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  99 
 TYR   0.029   0.002   TYR D  83 
 PHE   0.015   0.002   PHE F 100 
 HIS   0.005   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.16 (13172)
  covalent geometry    : angle       0.64030 /  0.38 (19130)
  hydrogen bonds       : bond        0.04832 /  3.26 (  804)
  hydrogen bonds       : angle       2.57685 /  1.89 ( 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
  244 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 224
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.7860 (t)
REVERT: A   59 GLU cc_start: 0.8170 (pm20) cc_final: 0.7241 (pm20)
REVERT: A  117 VAL cc_start: 0.9002 (m) cc_final: 0.8766 (t)
REVERT: B   25 ASN cc_start: 0.7325 (m-40) cc_final: 0.7074 (m-40)
REVERT: B   88 TYR cc_start: 0.8592 (m-80) cc_final: 0.8018 (m-10)
REVERT: C   57 TYR cc_start: 0.8927 (t80) cc_final: 0.8551 (t80)
REVERT: D   42 TYR cc_start: 0.8063 (t80) cc_final: 0.7777 (t80)
REVERT: D   54 ILE cc_start: 0.8827 (tt) cc_final: 0.8593 (mt)
REVERT: D   91 SER cc_start: 0.8736 (p) cc_final: 0.8471 (p)
REVERT: E   59 GLU cc_start: 0.7871 (pm20) cc_final: 0.7516 (pm20)
REVERT: G   73 ASN cc_start: 0.8519 (t0) cc_final: 0.8178 (t0)
REVERT: H   37 TYR cc_start: 0.8898 (m-80) cc_final: 0.8604 (m-80)
REVERT: H   83 TYR cc_start: 0.8150 (m-10) cc_final: 0.7840 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 230
  average time/residue: 0.1734
  time to fit residues: 51.5773
Evaluate side-chains
  239 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 223
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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  109 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
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  120 LYS
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:    0.6980
   chunk 89 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3291 r_free = 0.3291 target = 0.097678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.082272 restraints weight = 21530.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.27
r_work: 0.2893 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13172  Z= 0.147
  Angle     :  0.618  12.188  19130  Z= 0.367
  Chirality :  0.044   0.230   2174
  Planarity :  0.005   0.059   1340
  Dihedral  : 30.471 164.460   4236
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.23 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.60 (0.30), residues: 732
  helix:  3.28 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.12 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  99 
 TYR   0.023   0.002   TYR D  83 
 PHE   0.015   0.002   PHE B 100 
 HIS   0.004   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.15 (13172)
  covalent geometry    : angle       0.61757 /  0.37 (19130)
  hydrogen bonds       : bond        0.04552 /  3.06 (  804)
  hydrogen bonds       : angle       2.51162 /  1.83 ( 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: 20
    poor density    : 228
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.7784 (t)
REVERT: A   59 GLU cc_start: 0.8092 (pm20) cc_final: 0.7178 (pm20)
REVERT: B   25 ASN cc_start: 0.7294 (m-40) cc_final: 0.7047 (m-40)
REVERT: B   88 TYR cc_start: 0.8596 (m-80) cc_final: 0.7986 (m-10)
REVERT: B   97 LEU cc_start: 0.8502 (tt) cc_final: 0.8230 (tp)
REVERT: C   64 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7758 (tp30)
REVERT: D   45 LEU cc_start: 0.8838 (tp) cc_final: 0.8613 (tp)
REVERT: D   91 SER cc_start: 0.8725 (p) cc_final: 0.8459 (p)
REVERT: E   59 GLU cc_start: 0.7883 (pm20) cc_final: 0.7549 (pm20)
REVERT: G   73 ASN cc_start: 0.8520 (t0) cc_final: 0.8187 (t0)
REVERT: H   39 ILE cc_start: 0.9190 (mm) cc_final: 0.8988 (mm)
REVERT: H   83 TYR cc_start: 0.8140 (m-10) cc_final: 0.7846 (m-10)
  outliers start: 20
  outliers final: 14
  residues processed: 238
  average time/residue: 0.1722
  time to fit residues: 52.8926
Evaluate side-chains
  244 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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   74 ILE
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
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   56 SER
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 70 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 71 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3220 r_free = 0.3220 target = 0.093729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.076802 restraints weight = 21271.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 1.36
r_work: 0.2782 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13172  Z= 0.259
  Angle     :  0.754  10.961  19130  Z= 0.421
  Chirality :  0.051   0.244   2174
  Planarity :  0.005   0.062   1340
  Dihedral  : 30.699 163.773   4236
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 22.74 %
    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 are not related in a simple way.
  whole:  2.87 (0.30), residues: 732
  helix:  2.76 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.43 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  99 
 TYR   0.025   0.003   TYR G  39 
 PHE   0.025   0.003   PHE F 100 
 HIS   0.009   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00519 /  0.26 (13172)
  covalent geometry    : angle       0.75392 /  0.42 (19130)
  hydrogen bonds       : bond        0.06261 /  4.25 (  804)
  hydrogen bonds       : angle       2.83779 /  2.07 ( 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
  258 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 232
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.7859 (t)
REVERT: A   59 GLU cc_start: 0.8126 (pm20) cc_final: 0.7229 (pm20)
REVERT: B   25 ASN cc_start: 0.7476 (m-40) cc_final: 0.7188 (m-40)
REVERT: B   88 TYR cc_start: 0.8743 (m-80) cc_final: 0.8219 (m-10)
REVERT: B   97 LEU cc_start: 0.8527 (tt) cc_final: 0.8277 (tp)
REVERT: C   64 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7822 (tp30)
REVERT: D   91 SER cc_start: 0.8887 (p) cc_final: 0.8642 (p)
REVERT: D  120 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8767 (ttmm)
REVERT: E   59 GLU cc_start: 0.8064 (pm20) cc_final: 0.7757 (pm20)
REVERT: E   73 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: G   73 ASN cc_start: 0.8508 (t0) cc_final: 0.8145 (t0)
REVERT: H   83 TYR cc_start: 0.8225 (m-10) cc_final: 0.7626 (m-10)
REVERT: H  113 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8004 (mm-30)
  outliers start: 26
  outliers final: 19
  residues processed: 241
  average time/residue: 0.1748
  time to fit residues: 54.3477
Evaluate side-chains
  250 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 229
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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   74 ILE
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   56 LYS
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 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   55 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 94 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 82 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3252 r_free = 0.3252 target = 0.095845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.079188 restraints weight = 21237.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.36
r_work: 0.2826 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13172  Z= 0.169
  Angle     :  0.661  13.383  19130  Z= 0.383
  Chirality :  0.046   0.230   2174
  Planarity :  0.006   0.109   1340
  Dihedral  : 30.555 165.031   4236
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 24.68 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.25 (0.31), residues: 732
  helix:  3.06 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.37 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  99 
 TYR   0.019   0.002   TYR G  39 
 PHE   0.015   0.002   PHE F 100 
 HIS   0.006   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.17 (13172)
  covalent geometry    : angle       0.66100 /  0.38 (19130)
  hydrogen bonds       : bond        0.04994 /  3.37 (  804)
  hydrogen bonds       : angle       2.61674 /  1.91 ( 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
  246 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 228
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.7768 (t)
REVERT: A   59 GLU cc_start: 0.8120 (pm20) cc_final: 0.7137 (pm20)
REVERT: A   60 LEU cc_start: 0.8769 (mp) cc_final: 0.8487 (mt)
REVERT: B   25 ASN cc_start: 0.7364 (m-40) cc_final: 0.7078 (m-40)
REVERT: B   88 TYR cc_start: 0.8713 (m-80) cc_final: 0.8082 (m-10)
REVERT: C   64 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7853 (tp30)
REVERT: D   91 SER cc_start: 0.8764 (p) cc_final: 0.8509 (p)
REVERT: E   59 GLU cc_start: 0.7980 (pm20) cc_final: 0.7670 (pm20)
REVERT: E   73 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: G   73 ASN cc_start: 0.8528 (t0) cc_final: 0.8203 (t0)
REVERT: H   71 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8173 (tm-30)
REVERT: H   83 TYR cc_start: 0.8193 (m-10) cc_final: 0.7854 (m-10)
  outliers start: 18
  outliers final: 11
  residues processed: 234
  average time/residue: 0.1731
  time to fit residues: 52.1435
Evaluate side-chains
  238 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 225
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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   74 ILE
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   55 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0670
   overall best weight:    0.9520

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
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 = 0.3263 r_free = 0.3263 target = 0.096574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.079959 restraints weight = 21250.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.36
r_work: 0.2840 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13172  Z= 0.159
  Angle     :  0.650  14.044  19130  Z= 0.378
  Chirality :  0.045   0.225   2174
  Planarity :  0.005   0.054   1340
  Dihedral  : 30.520 164.913   4236
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 25.48 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.31 (0.31), residues: 732
  helix:  3.11 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.40 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  99 
 TYR   0.016   0.002   TYR B  88 
 PHE   0.015   0.002   PHE F 100 
 HIS   0.006   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.16 (13172)
  covalent geometry    : angle       0.65028 /  0.38 (19130)
  hydrogen bonds       : bond        0.04826 /  3.26 (  804)
  hydrogen bonds       : angle       2.60385 /  1.90 ( 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
  239 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 222
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.7718 (t)
REVERT: A   59 GLU cc_start: 0.8104 (pm20) cc_final: 0.7112 (pm20)
REVERT: A   60 LEU cc_start: 0.8764 (mp) cc_final: 0.8469 (mt)
REVERT: B   25 ASN cc_start: 0.7395 (m-40) cc_final: 0.7180 (m-40)
REVERT: B   88 TYR cc_start: 0.8702 (m-80) cc_final: 0.8061 (m-10)
REVERT: C   99 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7779 (mtt180)
REVERT: D   91 SER cc_start: 0.8770 (p) cc_final: 0.8511 (p)
REVERT: E   42 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7910 (ttm-80)
REVERT: E   59 GLU cc_start: 0.7970 (pm20) cc_final: 0.7634 (pm20)
REVERT: E   73 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: G   73 ASN cc_start: 0.8534 (t0) cc_final: 0.8197 (t0)
REVERT: H   71 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8211 (tm-30)
REVERT: H   83 TYR cc_start: 0.8176 (m-10) cc_final: 0.7863 (m-10)
  outliers start: 17
  outliers final: 12
  residues processed: 230
  average time/residue: 0.1724
  time to fit residues: 50.6986
Evaluate side-chains
  233 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 220
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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   74 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   81 VAL
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   56 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0040
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 93 optimal weight:   10.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5852

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
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 = 0.3289 r_free = 0.3289 target = 0.097640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.082227 restraints weight = 21472.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.27
r_work: 0.2895 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  13172  Z= 0.142
  Angle     :  0.627  12.935  19130  Z= 0.367
  Chirality :  0.043   0.223   2174
  Planarity :  0.005   0.052   1340
  Dihedral  : 30.472 164.606   4236
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 26.13 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.39 (0.31), residues: 732
  helix:  3.19 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -0.37 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  99 
 TYR   0.015   0.002   TYR B  88 
 PHE   0.013   0.001   PHE F 100 
 HIS   0.003   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.14 (13172)
  covalent geometry    : angle       0.62725 /  0.37 (19130)
  hydrogen bonds       : bond        0.04413 /  2.98 (  804)
  hydrogen bonds       : angle       2.53539 /  1.85 ( 1987)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2975.56 seconds
wall clock time: 51 minutes 44.71 seconds (3104.71 seconds total)