Starting phenix.real_space_refine
on Wed Mar  4 05:04:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nl0_12453/03_2026/7nl0_12453.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nl0_12453/03_2026/7nl0_12453.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nl0_12453/03_2026/7nl0_12453.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nl0_12453/03_2026/7nl0_12453.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nl0_12453/03_2026/7nl0_12453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nl0_12453/03_2026/7nl0_12453.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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     262      5.49       5
     S      14      5.16       5
     C    6334      2.51       5
     N    2121      2.21       5
     O    2632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11363
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2715
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
    Chain: "J"
      Number of atoms: 2656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2656
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
  Time building chain proxies: 2.51, per 1000 atoms: 0.22
  Number of scatterers: 11363
  At special positions: 0
  Unit cell: (75.9676, 120.12, 116.873, 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     262     15.00
     O    2632      8.00
     N    2121      7.00
     C    6334      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: 0.90
  Conformation dependent library (CDL) restraints added in 286.4 milliseconds
  

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      73.0% alpha, 2.4% beta
      127 base pairs and 223 stacking pairs defined.
    Time for finding SS restraints: 1.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.820A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.671A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.802A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.505A  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 92 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 53 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.591A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.500A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    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: 3.787A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.638A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.727A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (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
      removed outlier: 3.513A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.350A  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
    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: 7.413A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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 101 through 102
      removed outlier: 6.676A  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: 7.283A  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

    409 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      307 hydrogen bonds
      614 hydrogen bond angles
      0 basepair planarities
      127 basepair parallelities
      223 stacking parallelities
  Total time for adding SS restraints: 2.28

  Time building geometry restraints manager: 1.21 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: 2176
        1.33 -     1.45: 3809
        1.45 -     1.57: 5564
        1.57 -     1.69: 522
        1.69 -     1.81: 24
  Bond restraints: 12095
  Sorted by residual:
  bond pdb=" C3'  DA I  58 "
       pdb=" O3'  DA I  58 "
    ideal  model  delta    sigma   weight residual
    1.422  1.481 -0.059 3.00e-02 1.11e+03 3.88e+00
  bond pdb=" CG1 ILE H  86 "
       pdb=" CD1 ILE H  86 "
    ideal  model  delta    sigma   weight residual
    1.513  1.446  0.067 3.90e-02 6.57e+02 2.94e+00
  bond pdb=" C3'  DA I  14 "
       pdb=" O3'  DA I  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.81e+00
  bond pdb=" CG1 ILE D  86 "
       pdb=" CD1 ILE D  86 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.49e+00
  bond pdb=" C3'  DC J -52 "
       pdb=" O3'  DC J -52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.78e+00
  ... (remaining 12090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 16646
        1.61 -     3.21: 753
        3.21 -     4.82: 36
        4.82 -     6.43: 15
        6.43 -     8.04: 1
  Bond angle restraints: 17451
  Sorted by residual:
  angle pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
      ideal   model   delta    sigma   weight residual
     113.71  107.75    5.96 9.50e-01 1.11e+00 3.94e+01
  angle pdb=" C   GLY G  37 "
        pdb=" N   ASN G  38 "
        pdb=" CA  ASN G  38 "
      ideal   model   delta    sigma   weight residual
     121.54  127.28   -5.74 1.91e+00 2.74e-01 9.04e+00
  angle pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
        pdb=" N   THR A 118 "
      ideal   model   delta    sigma   weight residual
     119.87  116.36    3.51 1.34e+00 5.57e-01 6.87e+00
  angle pdb=" C3'  DA I  58 "
        pdb=" O3'  DA I  58 "
        pdb=" P    DT I  59 "
      ideal   model   delta    sigma   weight residual
     120.20  124.04   -3.84 1.50e+00 4.44e-01 6.54e+00
  angle pdb=" C3'  DA I  14 "
        pdb=" O3'  DA I  14 "
        pdb=" P    DA I  15 "
      ideal   model   delta    sigma   weight residual
     120.20  123.98   -3.78 1.50e+00 4.44e-01 6.34e+00
  ... (remaining 17446 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.14: 5243
       35.14 -    70.28: 1400
       70.28 -   105.43: 23
      105.43 -   140.57: 3
      140.57 -   175.71: 9
  Dihedral angle restraints: 6678
    sinusoidal: 4495
      harmonic: 2183
  Sorted by residual:
  dihedral pdb=" CA  TYR G  39 "
           pdb=" C   TYR G  39 "
           pdb=" N   SER G  40 "
           pdb=" CA  SER G  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.30   20.70     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" C4'  DG J  30 "
           pdb=" C3'  DG J  30 "
           pdb=" O3'  DG J  30 "
           pdb=" P    DA J  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.71 -175.71     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT I -17 "
           pdb=" C3'  DT I -17 "
           pdb=" O3'  DT I -17 "
           pdb=" P    DG I -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.83 -173.83     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 6675 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1249
       0.032 -    0.065: 536
       0.065 -    0.097: 147
       0.097 -    0.129: 47
       0.129 -    0.161: 4
  Chirality restraints: 1983
  Sorted by residual:
  chirality pdb=" CA  ASN G  38 "
            pdb=" N   ASN G  38 "
            pdb=" C   ASN G  38 "
            pdb=" CB  ASN G  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" P    DT I  59 "
            pdb=" OP1  DT I  59 "
            pdb=" OP2  DT I  59 "
            pdb=" O5'  DT I  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL C 107 "
            pdb=" N   VAL C 107 "
            pdb=" C   VAL C 107 "
            pdb=" CB  VAL C 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 1980 not shown)

  Planarity restraints: 1305
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -24 "   -0.027 2.00e-02 2.50e+03   1.18e-02 3.80e+00
        pdb=" N9   DA I -24 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I -24 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -24 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I -24 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -24 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I -24 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -24 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -24 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -24 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -24 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  16 "    0.027 2.00e-02 2.50e+03   1.10e-02 3.66e+00
        pdb=" N9   DG I  16 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8   DG I  16 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  16 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DG I  16 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6   DG I  16 "    0.006 2.00e-02 2.50e+03
        pdb=" O6   DG I  16 "    0.013 2.00e-02 2.50e+03
        pdb=" N1   DG I  16 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DG I  16 "   -0.004 2.00e-02 2.50e+03
        pdb=" N2   DG I  16 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  16 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  16 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  28 "    0.025 2.00e-02 2.50e+03   1.08e-02 3.50e+00
        pdb=" N9   DG I  28 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DG I  28 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DG I  28 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I  28 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  28 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  28 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  28 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1302 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 559
        2.70 -     3.25: 9965
        3.25 -     3.80: 22342
        3.80 -     4.35: 27582
        4.35 -     4.90: 39438
  Nonbonded interactions: 99886
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  65 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OD1 ASP C  90 "
            pdb=" N   GLU C  91 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" NE  ARG A 131 "
            pdb=" OE2 GLU A 133 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.251 3.120
  ... (remaining 99881 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' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ 
e C or name O or name CB ))))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 24 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 13 through 117)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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 group one per residue
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:             3.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.980
  Find NCS groups from input model:        0.110
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
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   0.067  12095  Z= 0.272
  Angle     :  0.709   8.036  17451  Z= 0.428
  Chirality :  0.039   0.161   1983
  Planarity :  0.004   0.040   1305
  Dihedral  : 29.742 175.712   5272
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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:  0.67 (0.30), residues: 739
  helix:  1.29 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -1.90 (0.39), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  32 
 TYR   0.012   0.002   TYR F  51 
 PHE   0.024   0.003   PHE C  25 
 HIS   0.007   0.001   HIS H  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (12095)
  covalent geometry    : angle       0.70914 (17451)
  hydrogen bonds       : bond        0.11327 (  716)
  hydrogen bonds       : angle       4.81605 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.303 
Fit side-chains
REVERT: E   59 GLU cc_start: 0.7178 (pp20) cc_final: 0.6897 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1489
  time to fit residues: 25.5601
Evaluate side-chains
  121 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
D  92 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.141070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.102642 restraints weight = 18603.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.105109 restraints weight = 11814.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.106647 restraints weight = 9257.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.107462 restraints weight = 8152.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.107785 restraints weight = 7654.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.0597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12095  Z= 0.190
  Angle     :  0.661   8.865  17451  Z= 0.386
  Chirality :  0.038   0.159   1983
  Planarity :  0.005   0.040   1305
  Dihedral  : 32.919 174.565   3777
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  7.81 %
    Favored  : 90.75 %
  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:  1.23 (0.31), residues: 739
  helix:  1.69 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.75 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  29 
 TYR   0.013   0.002   TYR B  51 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (12095)
  covalent geometry    : angle       0.66079 (17451)
  hydrogen bonds       : bond        0.05447 (  716)
  hydrogen bonds       : angle       3.50553 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.298 
Fit side-chains
REVERT: E   59 GLU cc_start: 0.7252 (pp20) cc_final: 0.7005 (pm20)
  outliers start: 9
  outliers final: 8
  residues processed: 133
  average time/residue: 0.1553
  time to fit residues: 26.7712
Evaluate side-chains
  131 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 85 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.140974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.103084 restraints weight = 18766.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.105193 restraints weight = 12603.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.106493 restraints weight = 10197.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.107060 restraints weight = 9154.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.107060 restraints weight = 8674.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.0735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12095  Z= 0.202
  Angle     :  0.638   6.023  17451  Z= 0.374
  Chirality :  0.036   0.154   1983
  Planarity :  0.004   0.037   1305
  Dihedral  : 32.849 177.374   3777
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.53 %
    Favored  : 87.88 %
  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:  1.53 (0.31), residues: 739
  helix:  1.92 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.67 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  35 
 TYR   0.012   0.002   TYR C  57 
 PHE   0.013   0.002   PHE A  67 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (12095)
  covalent geometry    : angle       0.63806 (17451)
  hydrogen bonds       : bond        0.05307 (  716)
  hydrogen bonds       : angle       3.34527 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.330 
Fit side-chains
REVERT: E   59 GLU cc_start: 0.7268 (pp20) cc_final: 0.7055 (pm20)
  outliers start: 10
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1470
  time to fit residues: 24.4535
Evaluate side-chains
  132 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0370
   chunk 58 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.8064

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  38 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.140734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.101850 restraints weight = 18781.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.104311 restraints weight = 11987.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.105834 restraints weight = 9360.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.106693 restraints weight = 8224.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.106693 restraints weight = 7717.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.0832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  12095  Z= 0.218
  Angle     :  0.639   6.608  17451  Z= 0.375
  Chirality :  0.037   0.162   1983
  Planarity :  0.004   0.036   1305
  Dihedral  : 32.848 177.221   3777
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.32 %
    Favored  : 86.28 %
  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:  1.54 (0.31), residues: 739
  helix:  1.97 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.84 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 129 
 TYR   0.013   0.002   TYR C  57 
 PHE   0.015   0.002   PHE A  67 
 HIS   0.005   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (12095)
  covalent geometry    : angle       0.63906 (17451)
  hydrogen bonds       : bond        0.05016 (  716)
  hydrogen bonds       : angle       3.29093 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.251 
Fit side-chains
  outliers start: 15
  outliers final: 13
  residues processed: 131
  average time/residue: 0.1438
  time to fit residues: 24.4784
Evaluate side-chains
  133 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 85 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 94 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.141079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.102204 restraints weight = 18568.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.104692 restraints weight = 11731.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.106264 restraints weight = 9126.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.107115 restraints weight = 8010.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.107483 restraints weight = 7507.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12095  Z= 0.189
  Angle     :  0.618   6.458  17451  Z= 0.365
  Chirality :  0.036   0.149   1983
  Planarity :  0.004   0.039   1305
  Dihedral  : 32.810 178.275   3777
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.64 %
    Favored  : 86.28 %
  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:  1.72 (0.31), residues: 739
  helix:  2.10 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.78 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  71 
 TYR   0.019   0.002   TYR C  39 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.005   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (12095)
  covalent geometry    : angle       0.61768 (17451)
  hydrogen bonds       : bond        0.04721 (  716)
  hydrogen bonds       : angle       3.18470 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.315 
Fit side-chains
  outliers start: 13
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1311
  time to fit residues: 23.0430
Evaluate side-chains
  134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.141850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.102966 restraints weight = 18671.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.105597 restraints weight = 11565.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.107211 restraints weight = 8923.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.108010 restraints weight = 7790.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.108010 restraints weight = 7326.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12095  Z= 0.167
  Angle     :  0.610   6.436  17451  Z= 0.361
  Chirality :  0.036   0.147   1983
  Planarity :  0.004   0.042   1305
  Dihedral  : 32.778 178.608   3777
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.88 %
    Favored  : 84.37 %
  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:  1.91 (0.31), residues: 739
  helix:  2.21 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.68 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  83 
 TYR   0.011   0.001   TYR C  57 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (12095)
  covalent geometry    : angle       0.61026 (17451)
  hydrogen bonds       : bond        0.04481 (  716)
  hydrogen bonds       : angle       3.13200 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.236 
Fit side-chains
  outliers start: 11
  outliers final: 10
  residues processed: 134
  average time/residue: 0.1467
  time to fit residues: 25.7142
Evaluate side-chains
  136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.140978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102110 restraints weight = 18644.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.104715 restraints weight = 11606.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.106305 restraints weight = 8933.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.107138 restraints weight = 7851.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.107337 restraints weight = 7360.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  12095  Z= 0.200
  Angle     :  0.620   6.341  17451  Z= 0.365
  Chirality :  0.036   0.155   1983
  Planarity :  0.004   0.042   1305
  Dihedral  : 32.752 178.762   3777
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.19 %
    Favored  : 83.41 %
  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:  1.90 (0.31), residues: 739
  helix:  2.23 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.73 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  69 
 TYR   0.013   0.002   TYR C  57 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.006   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (12095)
  covalent geometry    : angle       0.62014 (17451)
  hydrogen bonds       : bond        0.04660 (  716)
  hydrogen bonds       : angle       3.11938 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.311 
Fit side-chains
REVERT: H   90 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7335 (mt-10)
  outliers start: 15
  outliers final: 11
  residues processed: 126
  average time/residue: 0.1422
  time to fit residues: 23.6644
Evaluate side-chains
  127 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 52 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.142193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.103751 restraints weight = 18606.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.106186 restraints weight = 11897.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.107721 restraints weight = 9307.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.108500 restraints weight = 8203.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.108691 restraints weight = 7709.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12095  Z= 0.160
  Angle     :  0.599   6.174  17451  Z= 0.356
  Chirality :  0.035   0.144   1983
  Planarity :  0.004   0.043   1305
  Dihedral  : 32.734 179.081   3777
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.51 %
    Favored  : 83.41 %
  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:  2.05 (0.31), residues: 739
  helix:  2.31 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.59 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  69 
 TYR   0.014   0.001   TYR C  57 
 PHE   0.019   0.002   PHE D  62 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (12095)
  covalent geometry    : angle       0.59884 (17451)
  hydrogen bonds       : bond        0.04333 (  716)
  hydrogen bonds       : angle       3.05236 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.355 
Fit side-chains
REVERT: H   90 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7336 (mt-10)
  outliers start: 13
  outliers final: 12
  residues processed: 127
  average time/residue: 0.1405
  time to fit residues: 23.3977
Evaluate side-chains
  130 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.3980
   chunk 52 optimal weight:   10.0000
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.142305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.104085 restraints weight = 18428.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.106569 restraints weight = 11657.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.108107 restraints weight = 9103.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.108782 restraints weight = 8018.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.108783 restraints weight = 7579.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  12095  Z= 0.160
  Angle     :  0.604  11.617  17451  Z= 0.355
  Chirality :  0.035   0.139   1983
  Planarity :  0.004   0.043   1305
  Dihedral  : 32.667 179.592   3777
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.88 %
    Favored  : 83.41 %
  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:  2.12 (0.31), residues: 739
  helix:  2.34 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.54 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  83 
 TYR   0.018   0.001   TYR C  57 
 PHE   0.015   0.002   PHE A  67 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12095)
  covalent geometry    : angle       0.60398 (17451)
  hydrogen bonds       : bond        0.04178 (  716)
  hydrogen bonds       : angle       3.04895 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.322 
Fit side-chains
REVERT: H   69 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8057 (mtm180)
REVERT: H   90 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7356 (mt-10)
  outliers start: 17
  outliers final: 13
  residues processed: 131
  average time/residue: 0.1471
  time to fit residues: 25.1895
Evaluate side-chains
  137 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 60 optimal weight:    0.5980
   chunk 76 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.142903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.104385 restraints weight = 18770.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.107034 restraints weight = 11537.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.108685 restraints weight = 8847.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.109583 restraints weight = 7718.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.109772 restraints weight = 7213.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12095  Z= 0.156
  Angle     :  0.590   6.671  17451  Z= 0.350
  Chirality :  0.035   0.140   1983
  Planarity :  0.004   0.044   1305
  Dihedral  : 32.595 179.797   3777
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.88 %
    Favored  : 83.73 %
  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:  2.24 (0.31), residues: 739
  helix:  2.42 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.42 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  83 
 TYR   0.018   0.001   TYR C  57 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (12095)
  covalent geometry    : angle       0.59016 (17451)
  hydrogen bonds       : bond        0.04096 (  716)
  hydrogen bonds       : angle       2.97985 ( 1826)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.309 
Fit side-chains
REVERT: H   69 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8055 (mtm180)
REVERT: H   90 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7332 (mt-10)
  outliers start: 15
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1403
  time to fit residues: 23.7507
Evaluate side-chains
  135 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 14 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.140746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102361 restraints weight = 18755.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.104459 restraints weight = 12660.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.105763 restraints weight = 10268.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.106428 restraints weight = 9225.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.106551 restraints weight = 8740.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  12095  Z= 0.231
  Angle     :  0.639   7.634  17451  Z= 0.371
  Chirality :  0.037   0.156   1983
  Planarity :  0.004   0.040   1305
  Dihedral  : 32.664 179.164   3777
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.19 %
    Favored  : 83.41 %
  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:  1.92 (0.30), residues: 739
  helix:  2.21 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.58 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.017   0.002   TYR C  57 
 PHE   0.014   0.003   PHE G  25 
 HIS   0.006   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (12095)
  covalent geometry    : angle       0.63908 (17451)
  hydrogen bonds       : bond        0.04865 (  716)
  hydrogen bonds       : angle       3.15665 ( 1826)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1617.89 seconds
wall clock time: 28 minutes 34.74 seconds (1714.74 seconds total)