Starting phenix.real_space_refine
on Wed Feb  4 16:57:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k44_62044/02_2026/9k44_62044.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k44_62044/02_2026/9k44_62044.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k44_62044/02_2026/9k44_62044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k44_62044/02_2026/9k44_62044.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k44_62044/02_2026/9k44_62044.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k44_62044/02_2026/9k44_62044.cif"
  }
  resolution = 3.22
  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=   0.038
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     289      5.49       5
     S      12      5.16       5
     C    6587      2.51       5
     N    2172      2.21       5
     O    2780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11840
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.89, per 1000 atoms: 0.24
  Number of scatterers: 11840
  At special positions: 0
  Unit cell: (124.3, 95.7, 116.6, 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      12     16.00
     P     289     15.00
     O    2780      8.00
     N    2172      7.00
     C    6587      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: 0.96
  Conformation dependent library (CDL) restraints added in 380.7 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      72.9% alpha, 2.7% beta
      144 base pairs and 253 stacking pairs defined.
    Time for finding SS restraints: 1.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.767A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    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: 3.603A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.621A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 27 through 38
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 126 through 147
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.824A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   SER E  57 " --> pdb=" O   LYS E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.731A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.678A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.673A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 47 through 74
    Processing helix  chain 'G' and resid 80 through 91
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
      removed outlier: 3.512A  pdb=" N   ASN H 107 " --> pdb=" O   LEU H 103 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 146
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.133A  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 43 through 44
      removed outlier: 7.358A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103
      removed outlier: 6.969A  pdb=" N   THR C 102 " --> 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: 7.032A  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 43 through 44
      removed outlier: 7.437A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79

    403 hydrogen bonds defined for protein.
    1197 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      253 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 1.39 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: 2030
        1.33 -     1.45: 4175
        1.45 -     1.57: 5843
        1.57 -     1.68: 577
        1.68 -     1.80: 22
  Bond restraints: 12647
  Sorted by residual:
  bond pdb=" O3'  DG I -26 "
       pdb=" P    DT I -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.666 -0.059 1.50e-02 4.44e+03 1.53e+01
  bond pdb=" O3'  DT J -36 "
       pdb=" P    DG J -35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.659 -0.052 1.50e-02 4.44e+03 1.22e+01
  bond pdb=" O3'  DC I  47 "
       pdb=" P    DC I  48 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.50e-02 4.44e+03 9.20e+00
  bond pdb=" O3'  DA I -47 "
       pdb=" P    DT I -46 "
    ideal  model  delta    sigma   weight residual
    1.607  1.650 -0.043 1.50e-02 4.44e+03 8.21e+00
  bond pdb=" O3'  DC I  -6 "
       pdb=" P    DA I  -5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.645 -0.038 1.50e-02 4.44e+03 6.35e+00
  ... (remaining 12642 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 17763
        1.52 -     3.03: 509
        3.03 -     4.55: 47
        4.55 -     6.07: 7
        6.07 -     7.58: 3
  Bond angle restraints: 18329
  Sorted by residual:
  angle pdb=" O3'  DT I  45 "
        pdb=" C3'  DT I  45 "
        pdb=" C2'  DT I  45 "
      ideal   model   delta    sigma   weight residual
     111.50  104.16    7.34 1.50e+00 4.44e-01 2.40e+01
  angle pdb=" N   GLN C  25 "
        pdb=" CA  GLN C  25 "
        pdb=" C   GLN C  25 "
      ideal   model   delta    sigma   weight residual
     114.12  107.53    6.59 1.39e+00 5.18e-01 2.25e+01
  angle pdb=" CA  PHE C  26 "
        pdb=" C   PHE C  26 "
        pdb=" O   PHE C  26 "
      ideal   model   delta    sigma   weight residual
     120.19  116.98    3.21 8.40e-01 1.42e+00 1.46e+01
  angle pdb=" O3'  DG J -37 "
        pdb=" C3'  DG J -37 "
        pdb=" C2'  DG J -37 "
      ideal   model   delta    sigma   weight residual
     111.50  106.16    5.34 1.50e+00 4.44e-01 1.27e+01
  angle pdb=" N   PHE C  26 "
        pdb=" CA  PHE C  26 "
        pdb=" C   PHE C  26 "
      ideal   model   delta    sigma   weight residual
     110.07  113.94   -3.87 1.26e+00 6.30e-01 9.41e+00
  ... (remaining 18324 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 4244
       17.63 -    35.27: 1175
       35.27 -    52.90: 1148
       52.90 -    70.53: 344
       70.53 -    88.16: 28
  Dihedral angle restraints: 6939
    sinusoidal: 4779
      harmonic: 2160
  Sorted by residual:
  dihedral pdb=" CG  ARG A 128 "
           pdb=" CD  ARG A 128 "
           pdb=" NE  ARG A 128 "
           pdb=" CZ  ARG A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.67  -44.33     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  PRO H 126 "
           pdb=" C   PRO H 126 "
           pdb=" N   GLY H 127 "
           pdb=" CA  GLY H 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.87   16.13     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  PRO D 126 "
           pdb=" C   PRO D 126 "
           pdb=" N   GLY D 127 "
           pdb=" CA  GLY D 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.96   16.04     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 6936 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1808
       0.050 -    0.099: 228
       0.099 -    0.149: 49
       0.149 -    0.198: 4
       0.198 -    0.248: 2
  Chirality restraints: 2091
  Sorted by residual:
  chirality pdb=" C3'  DT I  45 "
            pdb=" C4'  DT I  45 "
            pdb=" O3'  DT I  45 "
            pdb=" C2'  DT I  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.91    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" C3'  DG I  -7 "
            pdb=" C4'  DG I  -7 "
            pdb=" O3'  DG I  -7 "
            pdb=" C2'  DG I  -7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.86    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" C3'  DG J -37 "
            pdb=" C4'  DG J -37 "
            pdb=" O3'  DG J -37 "
            pdb=" C2'  DG J -37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 8.70e-01
  ... (remaining 2088 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  69 "   -0.020 2.00e-02 2.50e+03   8.87e-03 2.17e+00
        pdb=" N9   DA I  69 "    0.019 2.00e-02 2.50e+03
        pdb=" C8   DA I  69 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I  69 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  69 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  69 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1   DA I  69 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I  69 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DA I  69 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DA I  69 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 125 "    0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO H 126 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -58 "    0.017 2.00e-02 2.50e+03   8.15e-03 1.83e+00
        pdb=" N9   DA I -58 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DA I -58 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DA I -58 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -58 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -58 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -58 "    0.004 2.00e-02 2.50e+03
        pdb=" N1   DA I -58 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -58 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -58 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -58 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1230
        2.74 -     3.28: 10389
        3.28 -     3.82: 23052
        3.82 -     4.36: 26952
        4.36 -     4.90: 39169
  Nonbonded interactions: 100792
  Sorted by model distance:
  nonbonded pdb=" O   ASP G  91 "
            pdb=" OG  SER G  95 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ASP C  91 "
            pdb=" OG  SER C  95 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" NH2 ARG G  30 "
            pdb=" OH  TYR H  63 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" N   GLU C  93 "
            pdb=" OE1 GLU C  93 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" N   GLU A  59 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.280 3.120
  ... (remaining 100787 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'
}

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=0.00 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:             1.380
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.720
  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:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
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      :  0.004   0.059  12647  Z= 0.185
  Angle     :  0.575   7.583  18329  Z= 0.355
  Chirality :  0.036   0.248   2091
  Planarity :  0.004   0.037   1312
  Dihedral  : 28.802  88.162   5543
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 14.68 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.01 (0.31), residues: 730
  helix:  2.85 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.48 (0.39), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  72 
 TYR   0.013   0.001   TYR B  98 
 PHE   0.010   0.001   PHE C  26 
 HIS   0.001   0.001   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (12647)
  covalent geometry    : angle       0.57480 (18329)
  hydrogen bonds       : bond        0.11223 (  750)
  hydrogen bonds       : angle       4.34034 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   98 GLN cc_start: 0.7888 (mm-40) cc_final: 0.6472 (mm-40)
  outliers start: 1
  outliers final: 1
  residues processed: 227
  average time/residue: 0.1335
  time to fit residues: 41.1219
Evaluate side-chains
  190 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   96 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
B  75 HIS
D  70 GLN
E  39 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.063481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.044818 restraints weight = 59626.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.58
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12647  Z= 0.149
  Angle     :  0.568   7.297  18329  Z= 0.340
  Chirality :  0.033   0.136   2091
  Planarity :  0.004   0.031   1312
  Dihedral  : 31.121  87.909   4074
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.06 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.27 (0.31), residues: 730
  helix:  2.88 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.16 (0.44), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 122 
 TYR   0.011   0.002   TYR H  63 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12647)
  covalent geometry    : angle       0.56813 (18329)
  hydrogen bonds       : bond        0.04095 (  750)
  hydrogen bonds       : angle       2.83590 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 202
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8790 (mmm) cc_final: 0.8321 (mmt)
REVERT: C   91 ASP cc_start: 0.7744 (t70) cc_final: 0.7338 (t70)
REVERT: C   93 GLU cc_start: 0.9188 (pm20) cc_final: 0.8986 (pm20)
REVERT: C  108 VAL cc_start: 0.8804 (m) cc_final: 0.8578 (p)
REVERT: C  109 MET cc_start: 0.6970 (mpp) cc_final: 0.6533 (mtp)
REVERT: D   58 GLU cc_start: 0.8150 (tp30) cc_final: 0.7914 (tp30)
REVERT: D   87 SER cc_start: 0.9568 (m) cc_final: 0.9291 (p)
REVERT: D   98 GLN cc_start: 0.9173 (mm110) cc_final: 0.8061 (mm-40)
REVERT: D  116 GLU cc_start: 0.8748 (mp0) cc_final: 0.8272 (mp0)
REVERT: F   84 MET cc_start: 0.8698 (mmm) cc_final: 0.8128 (mmt)
REVERT: F   88 TYR cc_start: 0.9116 (m-80) cc_final: 0.8076 (m-80)
REVERT: G   89 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8390 (tpp80)
REVERT: G   91 ASP cc_start: 0.7900 (t70) cc_final: 0.7364 (t70)
REVERT: G   93 GLU cc_start: 0.9222 (pm20) cc_final: 0.8987 (pm20)
REVERT: H   94 GLU cc_start: 0.8791 (tp30) cc_final: 0.8242 (tp30)
REVERT: H   98 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8282 (mm-40)
REVERT: H   99 GLU cc_start: 0.8953 (tp30) cc_final: 0.8464 (tp30)
REVERT: H  116 GLU cc_start: 0.8998 (mp0) cc_final: 0.8796 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 205
  average time/residue: 0.1184
  time to fit residues: 33.8699
Evaluate side-chains
  198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 191
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain H residue   57 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
D  70 GLN
D  98 GLN
D 107 ASN
F  75 HIS
G  74 ASN
H  70 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.059392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.040616 restraints weight = 61907.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.59
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032  12647  Z= 0.256
  Angle     :  0.602   5.741  18329  Z= 0.360
  Chirality :  0.035   0.160   2091
  Planarity :  0.004   0.039   1312
  Dihedral  : 31.629  89.806   4073
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.35 %
    Favored  : 78.39 %
  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:  3.28 (0.31), residues: 730
  helix:  2.90 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.16 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  72 
 TYR   0.019   0.002   TYR B  88 
 PHE   0.009   0.001   PHE C  26 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 (12647)
  covalent geometry    : angle       0.60179 (18329)
  hydrogen bonds       : bond        0.05737 (  750)
  hydrogen bonds       : angle       3.19879 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9342 (mtpp) cc_final: 0.9047 (mtmm)
REVERT: A  120 MET cc_start: 0.8530 (mmm) cc_final: 0.8291 (mmm)
REVERT: B   53 GLU cc_start: 0.8974 (tp30) cc_final: 0.8720 (tp30)
REVERT: B   84 MET cc_start: 0.8664 (mmm) cc_final: 0.8389 (tpp)
REVERT: C   91 ASP cc_start: 0.7966 (t70) cc_final: 0.7440 (t70)
REVERT: C   93 GLU cc_start: 0.9125 (pm20) cc_final: 0.8788 (pm20)
REVERT: C  109 MET cc_start: 0.7791 (mpp) cc_final: 0.7286 (mtm)
REVERT: D   87 SER cc_start: 0.9585 (m) cc_final: 0.9370 (p)
REVERT: D   94 GLU cc_start: 0.8864 (tp30) cc_final: 0.8526 (tp30)
REVERT: D   98 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8732 (mm110)
REVERT: D  116 GLU cc_start: 0.8900 (mp0) cc_final: 0.8372 (mp0)
REVERT: E   64 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8606 (mtmm)
REVERT: E  120 MET cc_start: 0.8516 (mmm) cc_final: 0.8296 (mmm)
REVERT: F   53 GLU cc_start: 0.8940 (tp30) cc_final: 0.8712 (tp30)
REVERT: G   72 ARG cc_start: 0.9230 (ttm-80) cc_final: 0.8912 (ttp80)
REVERT: G   89 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8452 (tpp80)
REVERT: G   91 ASP cc_start: 0.8025 (t70) cc_final: 0.7424 (t70)
REVERT: G   93 GLU cc_start: 0.9265 (pm20) cc_final: 0.8975 (pm20)
REVERT: H   94 GLU cc_start: 0.8908 (tp30) cc_final: 0.8397 (tp30)
REVERT: H   98 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8780 (mm110)
REVERT: H   99 GLU cc_start: 0.8922 (tp30) cc_final: 0.8715 (tp30)
  outliers start: 14
  outliers final: 7
  residues processed: 193
  average time/residue: 0.1161
  time to fit residues: 30.9698
Evaluate side-chains
  184 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue   70 GLN
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   89 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 62 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
D  70 GLN
E  85 GLN
G  74 ASN
G  90 ASN
H  70 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.059004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.039923 restraints weight = 62104.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.79
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  12647  Z= 0.246
  Angle     :  0.600   7.242  18329  Z= 0.359
  Chirality :  0.035   0.159   2091
  Planarity :  0.004   0.037   1312
  Dihedral  : 31.568  88.773   4073
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.16 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.38 (0.31), residues: 730
  helix:  2.96 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.06 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  30 
 TYR   0.024   0.002   TYR B  88 
 PHE   0.007   0.001   PHE D  65 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (12647)
  covalent geometry    : angle       0.59976 (18329)
  hydrogen bonds       : bond        0.05360 (  750)
  hydrogen bonds       : angle       3.09232 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9332 (mtpp) cc_final: 0.9035 (mtmm)
REVERT: A   76 GLN cc_start: 0.9218 (tt0) cc_final: 0.8803 (tm-30)
REVERT: A  120 MET cc_start: 0.8541 (mmm) cc_final: 0.8256 (mmm)
REVERT: B   53 GLU cc_start: 0.8979 (tp30) cc_final: 0.8771 (tp30)
REVERT: B   84 MET cc_start: 0.8621 (mmm) cc_final: 0.8352 (tpp)
REVERT: C  109 MET cc_start: 0.7662 (mpp) cc_final: 0.7399 (mtm)
REVERT: D   94 GLU cc_start: 0.8817 (tp30) cc_final: 0.8337 (tp30)
REVERT: D   98 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8514 (mm110)
REVERT: E  120 MET cc_start: 0.8537 (mmm) cc_final: 0.8312 (mmm)
REVERT: F   53 GLU cc_start: 0.8997 (tp30) cc_final: 0.8788 (tp30)
REVERT: F   84 MET cc_start: 0.8674 (mmm) cc_final: 0.8429 (tpp)
REVERT: F   88 TYR cc_start: 0.9036 (m-80) cc_final: 0.8693 (m-80)
REVERT: G   72 ARG cc_start: 0.9141 (ttm-80) cc_final: 0.8838 (ttp80)
REVERT: G   89 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8302 (tpp80)
REVERT: G   91 ASP cc_start: 0.8077 (t70) cc_final: 0.7508 (t70)
REVERT: G   93 GLU cc_start: 0.9290 (pm20) cc_final: 0.9030 (pm20)
REVERT: H   94 GLU cc_start: 0.8796 (tp30) cc_final: 0.8347 (tp30)
REVERT: H   98 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8666 (mm110)
REVERT: H   99 GLU cc_start: 0.8897 (tp30) cc_final: 0.8694 (tp30)
  outliers start: 16
  outliers final: 10
  residues processed: 188
  average time/residue: 0.1185
  time to fit residues: 31.1799
Evaluate side-chains
  182 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue  121 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
G  74 ASN
G 113 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.060381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.041729 restraints weight = 62327.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 2.73
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12647  Z= 0.153
  Angle     :  0.565   6.871  18329  Z= 0.341
  Chirality :  0.033   0.178   2091
  Planarity :  0.003   0.036   1312
  Dihedral  : 31.178  86.933   4073
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 21.94 %
    Favored  : 76.94 %
  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:  3.58 (0.31), residues: 730
  helix:  3.05 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.13 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  72 
 TYR   0.021   0.002   TYR B  88 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12647)
  covalent geometry    : angle       0.56452 (18329)
  hydrogen bonds       : bond        0.03807 (  750)
  hydrogen bonds       : angle       2.74907 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 197
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9297 (mtpp) cc_final: 0.8978 (mtmm)
REVERT: A   76 GLN cc_start: 0.9193 (tt0) cc_final: 0.8776 (tm-30)
REVERT: C   91 ASP cc_start: 0.8369 (t0) cc_final: 0.8126 (t0)
REVERT: D   85 MET cc_start: 0.9378 (mmt) cc_final: 0.9034 (mmt)
REVERT: D   94 GLU cc_start: 0.8755 (tp30) cc_final: 0.8148 (tp30)
REVERT: D   98 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8515 (mm110)
REVERT: D  116 GLU cc_start: 0.8773 (mp0) cc_final: 0.8395 (mp0)
REVERT: E   79 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8180 (tttm)
REVERT: F   84 MET cc_start: 0.8675 (mmm) cc_final: 0.8351 (tpp)
REVERT: F   88 TYR cc_start: 0.9058 (m-80) cc_final: 0.8719 (m-80)
REVERT: G   72 ARG cc_start: 0.9153 (ttm-80) cc_final: 0.8952 (ttp80)
REVERT: G   91 ASP cc_start: 0.8182 (t70) cc_final: 0.7820 (t0)
REVERT: G   93 GLU cc_start: 0.9309 (pm20) cc_final: 0.9035 (pm20)
REVERT: G  109 MET cc_start: 0.6906 (mpp) cc_final: 0.6626 (mtm)
REVERT: H   94 GLU cc_start: 0.8708 (tp30) cc_final: 0.8203 (tp30)
REVERT: H   98 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8505 (mm110)
REVERT: H   99 GLU cc_start: 0.8840 (tp30) cc_final: 0.8476 (tp30)
  outliers start: 7
  outliers final: 5
  residues processed: 199
  average time/residue: 0.1128
  time to fit residues: 31.5119
Evaluate side-chains
  189 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 184
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain F residue   49 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
G  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.060295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.041759 restraints weight = 61720.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 2.72
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12647  Z= 0.162
  Angle     :  0.573  10.341  18329  Z= 0.343
  Chirality :  0.033   0.162   2091
  Planarity :  0.003   0.034   1312
  Dihedral  : 31.196  86.933   4073
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.45 %
    Favored  : 76.45 %
  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:  3.50 (0.31), residues: 730
  helix:  3.01 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.08 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  30 
 TYR   0.018   0.002   TYR G  51 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (12647)
  covalent geometry    : angle       0.57319 (18329)
  hydrogen bonds       : bond        0.03985 (  750)
  hydrogen bonds       : angle       2.75031 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 190
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9275 (mtpp) cc_final: 0.8948 (mtmm)
REVERT: A   76 GLN cc_start: 0.9186 (tt0) cc_final: 0.8762 (tm-30)
REVERT: A  120 MET cc_start: 0.8345 (mmm) cc_final: 0.8077 (mmm)
REVERT: B   53 GLU cc_start: 0.8855 (tp30) cc_final: 0.8566 (tp30)
REVERT: C   91 ASP cc_start: 0.8232 (t0) cc_final: 0.7897 (t0)
REVERT: D   94 GLU cc_start: 0.8728 (tp30) cc_final: 0.8088 (tp30)
REVERT: D   98 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8427 (mm110)
REVERT: D  116 GLU cc_start: 0.8804 (mp0) cc_final: 0.8336 (mp0)
REVERT: F   53 GLU cc_start: 0.8868 (tp30) cc_final: 0.8583 (tp30)
REVERT: F   84 MET cc_start: 0.8662 (mmm) cc_final: 0.8306 (tpp)
REVERT: G   91 ASP cc_start: 0.8257 (t70) cc_final: 0.7865 (t0)
REVERT: G   93 GLU cc_start: 0.9315 (pm20) cc_final: 0.9038 (pm20)
REVERT: H   94 GLU cc_start: 0.8710 (tp30) cc_final: 0.8100 (tp30)
REVERT: H   98 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8360 (mm110)
REVERT: H   99 GLU cc_start: 0.8825 (tp30) cc_final: 0.8462 (tp30)
REVERT: H  116 GLU cc_start: 0.8849 (mp0) cc_final: 0.8632 (mp0)
  outliers start: 13
  outliers final: 7
  residues processed: 192
  average time/residue: 0.1259
  time to fit residues: 33.3481
Evaluate side-chains
  188 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 181
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    0.2980
   chunk 15 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
D  70 GLN
F  93 GLN
G  90 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.059929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.040947 restraints weight = 61836.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.77
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12647  Z= 0.178
  Angle     :  0.584  11.119  18329  Z= 0.348
  Chirality :  0.033   0.169   2091
  Planarity :  0.003   0.034   1312
  Dihedral  : 31.196  87.672   4073
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.77 %
    Favored  : 76.29 %
  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:  3.57 (0.31), residues: 730
  helix:  3.07 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.08 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  72 
 TYR   0.026   0.002   TYR H 106 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (12647)
  covalent geometry    : angle       0.58436 (18329)
  hydrogen bonds       : bond        0.04296 (  750)
  hydrogen bonds       : angle       2.80767 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8329 (mp10)
REVERT: A   64 LYS cc_start: 0.9306 (mtpp) cc_final: 0.8990 (mtmm)
REVERT: A   76 GLN cc_start: 0.9180 (tt0) cc_final: 0.8763 (tm-30)
REVERT: A  120 MET cc_start: 0.8340 (mmm) cc_final: 0.8083 (mmm)
REVERT: B   53 GLU cc_start: 0.8868 (tp30) cc_final: 0.8617 (tp30)
REVERT: C   91 ASP cc_start: 0.8220 (t0) cc_final: 0.7872 (t0)
REVERT: C  109 MET cc_start: 0.6652 (mpp) cc_final: 0.6313 (mtp)
REVERT: D   94 GLU cc_start: 0.8736 (tp30) cc_final: 0.8093 (tp30)
REVERT: D   98 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8457 (mm110)
REVERT: D  116 GLU cc_start: 0.8820 (mp0) cc_final: 0.8334 (mp0)
REVERT: E   53 LYS cc_start: 0.9495 (tmmt) cc_final: 0.9276 (tmtt)
REVERT: E   79 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8385 (mtpp)
REVERT: F   45 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8127 (mtt180)
REVERT: F   53 GLU cc_start: 0.8891 (tp30) cc_final: 0.8647 (tp30)
REVERT: G   91 ASP cc_start: 0.8272 (t70) cc_final: 0.7861 (t0)
REVERT: G   93 GLU cc_start: 0.9332 (pm20) cc_final: 0.9052 (pm20)
REVERT: H   94 GLU cc_start: 0.8706 (tp30) cc_final: 0.8066 (tp30)
REVERT: H   98 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8306 (mm110)
REVERT: H   99 GLU cc_start: 0.8818 (tp30) cc_final: 0.8603 (tp30)
REVERT: H  116 GLU cc_start: 0.8879 (mp0) cc_final: 0.8647 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 188
  average time/residue: 0.1243
  time to fit residues: 32.3002
Evaluate side-chains
  189 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 181
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue   70 GLN
Chi-restraints excluded: chain F residue   45 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
** G  74 ASN ** 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 = 0.3563 r_free = 0.3563 target = 0.060747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.042305 restraints weight = 61256.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.67
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12647  Z= 0.154
  Angle     :  0.586  11.447  18329  Z= 0.347
  Chirality :  0.033   0.162   2091
  Planarity :  0.003   0.034   1312
  Dihedral  : 31.031  86.827   4073
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 23.23 %
    Favored  : 75.97 %
  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:  3.46 (0.31), residues: 730
  helix:  2.99 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.04 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  72 
 TYR   0.029   0.002   TYR F  88 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12647)
  covalent geometry    : angle       0.58588 (18329)
  hydrogen bonds       : bond        0.03783 (  750)
  hydrogen bonds       : angle       2.80347 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 187
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8760 (mt0) cc_final: 0.8360 (mp10)
REVERT: A   76 GLN cc_start: 0.9167 (tt0) cc_final: 0.8728 (tm-30)
REVERT: A  120 MET cc_start: 0.8297 (mmm) cc_final: 0.8062 (mmm)
REVERT: C   91 ASP cc_start: 0.8302 (t0) cc_final: 0.7955 (t0)
REVERT: C  109 MET cc_start: 0.6432 (mpp) cc_final: 0.6014 (mtp)
REVERT: D   94 GLU cc_start: 0.8709 (tp30) cc_final: 0.8005 (tp30)
REVERT: D   98 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8408 (mm110)
REVERT: D  116 GLU cc_start: 0.8838 (mp0) cc_final: 0.8354 (mp0)
REVERT: E   53 LYS cc_start: 0.9460 (tmmt) cc_final: 0.9255 (tmtt)
REVERT: E   79 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8420 (tttp)
REVERT: F   88 TYR cc_start: 0.8600 (m-80) cc_final: 0.7990 (m-80)
REVERT: G   91 ASP cc_start: 0.8296 (t70) cc_final: 0.7909 (t0)
REVERT: G   93 GLU cc_start: 0.9334 (pm20) cc_final: 0.9062 (pm20)
REVERT: H   94 GLU cc_start: 0.8679 (tp30) cc_final: 0.7974 (tp30)
REVERT: H   98 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8239 (mm110)
REVERT: H   99 GLU cc_start: 0.8828 (tp30) cc_final: 0.8503 (tp30)
REVERT: H  106 TYR cc_start: 0.8322 (m-80) cc_final: 0.7968 (m-80)
REVERT: H  116 GLU cc_start: 0.8890 (mp0) cc_final: 0.8589 (mp0)
  outliers start: 5
  outliers final: 5
  residues processed: 187
  average time/residue: 0.1234
  time to fit residues: 31.9306
Evaluate side-chains
  186 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 181
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
G  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.060551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.042036 restraints weight = 60803.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.70
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12647  Z= 0.166
  Angle     :  0.601  11.394  18329  Z= 0.353
  Chirality :  0.033   0.170   2091
  Planarity :  0.003   0.034   1312
  Dihedral  : 31.064  86.999   4073
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 22.10 %
    Favored  : 77.10 %
  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:  3.55 (0.31), residues: 730
  helix:  3.05 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.07 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  72 
 TYR   0.026   0.002   TYR F  88 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (12647)
  covalent geometry    : angle       0.60051 (18329)
  hydrogen bonds       : bond        0.04043 (  750)
  hydrogen bonds       : angle       2.75629 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 182
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8759 (mt0) cc_final: 0.8340 (mp10)
REVERT: A   76 GLN cc_start: 0.9174 (tt0) cc_final: 0.8703 (tm-30)
REVERT: A  120 MET cc_start: 0.8353 (mmm) cc_final: 0.8121 (mmm)
REVERT: C   91 ASP cc_start: 0.8319 (t0) cc_final: 0.7840 (t0)
REVERT: C  109 MET cc_start: 0.6430 (mpp) cc_final: 0.6024 (mtp)
REVERT: D   58 GLU cc_start: 0.7906 (tp30) cc_final: 0.7646 (tp30)
REVERT: D   94 GLU cc_start: 0.8709 (tp30) cc_final: 0.8021 (tp30)
REVERT: D   98 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8446 (mm110)
REVERT: D  116 GLU cc_start: 0.8856 (mp0) cc_final: 0.8352 (mp0)
REVERT: G   91 ASP cc_start: 0.8216 (t70) cc_final: 0.7809 (t0)
REVERT: G   93 GLU cc_start: 0.9320 (pm20) cc_final: 0.9052 (pm20)
REVERT: H   94 GLU cc_start: 0.8701 (tp30) cc_final: 0.7973 (tp30)
REVERT: H   98 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8273 (mm110)
REVERT: H   99 GLU cc_start: 0.8820 (tp30) cc_final: 0.8512 (tp30)
REVERT: H  116 GLU cc_start: 0.8906 (mp0) cc_final: 0.8612 (mp0)
  outliers start: 5
  outliers final: 5
  residues processed: 182
  average time/residue: 0.1268
  time to fit residues: 31.8461
Evaluate side-chains
  181 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 176
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  70 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.057332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.038838 restraints weight = 61892.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.61
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058  12647  Z= 0.354
  Angle     :  0.697  11.577  18329  Z= 0.408
  Chirality :  0.039   0.177   2091
  Planarity :  0.004   0.035   1312
  Dihedral  : 31.824  92.641   4073
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 21.45 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.11 (0.31), residues: 730
  helix:  2.76 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.26 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  30 
 TYR   0.043   0.003   TYR H 106 
 PHE   0.011   0.002   PHE H  88 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00801 (12647)
  covalent geometry    : angle       0.69728 (18329)
  hydrogen bonds       : bond        0.06996 (  750)
  hydrogen bonds       : angle       3.52305 ( 1891)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.9078 (mt0) cc_final: 0.8452 (mp10)
REVERT: A   64 LYS cc_start: 0.9352 (mtpp) cc_final: 0.9049 (mtmm)
REVERT: A   76 GLN cc_start: 0.9216 (tt0) cc_final: 0.8745 (tm-30)
REVERT: A   79 LYS cc_start: 0.8667 (tttm) cc_final: 0.8398 (tttp)
REVERT: B   72 TYR cc_start: 0.9238 (m-80) cc_final: 0.8957 (m-80)
REVERT: C   91 ASP cc_start: 0.8450 (t0) cc_final: 0.8011 (t0)
REVERT: D   94 GLU cc_start: 0.8833 (tp30) cc_final: 0.8174 (tp30)
REVERT: D   98 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8585 (mm110)
REVERT: D  116 GLU cc_start: 0.8931 (mp0) cc_final: 0.8388 (mp0)
REVERT: F   88 TYR cc_start: 0.8959 (m-80) cc_final: 0.7978 (m-80)
REVERT: G   91 ASP cc_start: 0.8220 (t70) cc_final: 0.7810 (t0)
REVERT: G   93 GLU cc_start: 0.9307 (pm20) cc_final: 0.9012 (pm20)
REVERT: H   94 GLU cc_start: 0.8766 (tp30) cc_final: 0.8034 (tp30)
REVERT: H   98 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8233 (mm110)
REVERT: H  106 TYR cc_start: 0.8376 (m-80) cc_final: 0.7942 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 170
  average time/residue: 0.1216
  time to fit residues: 28.7316
Evaluate side-chains
  166 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
C  90 ASN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.058394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.040246 restraints weight = 61307.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.70
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12647  Z= 0.210
  Angle     :  0.638  11.845  18329  Z= 0.374
  Chirality :  0.035   0.174   2091
  Planarity :  0.004   0.035   1312
  Dihedral  : 31.429  92.406   4073
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 23.71 %
    Favored  : 75.48 %
  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:  3.33 (0.31), residues: 730
  helix:  2.94 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.17 (0.44), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  72 
 TYR   0.023   0.002   TYR H 106 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (12647)
  covalent geometry    : angle       0.63847 (18329)
  hydrogen bonds       : bond        0.04877 (  750)
  hydrogen bonds       : angle       3.07912 ( 1891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2340.84 seconds
wall clock time: 40 minutes 54.11 seconds (2454.11 seconds total)