Starting phenix.real_space_refine
on Fri Jul  3 01:55:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k43_62042/07_2026/9k43_62042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k43_62042/07_2026/9k43_62042.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k43_62042/07_2026/9k43_62042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k43_62042/07_2026/9k43_62042.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k43_62042/07_2026/9k43_62042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k43_62042/07_2026/9k43_62042.map"
  }
  resolution = 2.87
  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=   0.002 sd=   0.052
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      10      5.16       5
     C    6542      2.51       5
     N    2197      2.21       5
     O    2776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11814
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          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: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    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: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          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: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    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: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2985
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.45, per 1000 atoms: 0.21
  Number of scatterers: 11814
  At special positions: 0
  Unit cell: (118.992, 97.552, 114.704, 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      10     16.00
     P     289     15.00
     O    2776      8.00
     N    2197      7.00
     C    6542      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: 0.77
  Conformation dependent library (CDL) restraints added in 220.3 milliseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      75.8% alpha, 2.7% beta
      143 base pairs and 244 stacking pairs defined.
    Time for finding SS restraints: 1.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.601A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.944A  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 131
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.508A  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
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 27 through 33
    Processing helix  chain 'C' and resid 37 through 49
    Processing helix  chain 'C' and resid 56 through 85
    Processing helix  chain 'C' and resid 91 through 102
      removed outlier: 3.572A  pdb=" N   ASP C 102 " --> pdb=" O   ALA C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 109
    Processing helix  chain 'C' and resid 123 through 127
      removed outlier: 3.560A  pdb=" N   ILE C 127 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
    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 146
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.541A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.927A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.661A  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
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.647A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 33
    Processing helix  chain 'G' and resid 37 through 49
    Processing helix  chain 'G' and resid 56 through 85
    Processing helix  chain 'G' and resid 91 through 102
      removed outlier: 3.573A  pdb=" N   ASP G 102 " --> pdb=" O   ALA G  98 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 109
    Processing helix  chain 'G' and resid 123 through 127
      removed outlier: 3.560A  pdb=" N   ILE G 127 " --> pdb=" O   LYS G 124 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.092A  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 54 through 55
      removed outlier: 7.031A  pdb=" N   ARG C  54 " --> 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 89 through 90
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113
      removed outlier: 6.451A  pdb=" N   THR C 112 " --> 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: 7.269A  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 54 through 55
      removed outlier: 6.753A  pdb=" N   ARG G  54 " --> 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 89 through 90

    417 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      244 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2090
        1.33 -     1.45: 4235
        1.45 -     1.57: 5699
        1.57 -     1.69: 577
        1.69 -     1.81: 18
  Bond restraints: 12619
  Sorted by residual:
  bond pdb=" C1'  DC J -72 "
       pdb=" N1   DC J -72 "
    ideal  model  delta    sigma   weight residual
    1.468  1.550 -0.082 1.40e-02 5.10e+03 3.43e+01
  bond pdb=" C1'  DC I  70 "
       pdb=" N1   DC I  70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.548 -0.080 1.40e-02 5.10e+03 3.23e+01
  bond pdb=" C1'  DC J  70 "
       pdb=" N1   DC J  70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.547 -0.079 1.40e-02 5.10e+03 3.15e+01
  bond pdb=" O3'  DG J  23 "
       pdb=" P    DC J  24 "
    ideal  model  delta    sigma   weight residual
    1.607  1.664 -0.057 1.50e-02 4.44e+03 1.45e+01
  bond pdb=" O3'  DT J  15 "
       pdb=" P    DA J  16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.662 -0.055 1.50e-02 4.44e+03 1.37e+01
  ... (remaining 12614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 17069
        1.47 -     2.95: 1126
        2.95 -     4.42: 78
        4.42 -     5.89: 8
        5.89 -     7.37: 4
  Bond angle restraints: 18285
  Sorted by residual:
  angle pdb=" N   ASN F  25 "
        pdb=" CA  ASN F  25 "
        pdb=" C   ASN F  25 "
      ideal   model   delta    sigma   weight residual
     113.15  107.42    5.73 1.19e+00 7.06e-01 2.32e+01
  angle pdb=" N3   DT I  60 "
        pdb=" C4   DT I  60 "
        pdb=" O4   DT I  60 "
      ideal   model   delta    sigma   weight residual
     119.90  122.58   -2.68 6.00e-01 2.78e+00 2.00e+01
  angle pdb=" N3   DT J   9 "
        pdb=" C4   DT J   9 "
        pdb=" O4   DT J   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.56   -2.66 6.00e-01 2.78e+00 1.97e+01
  angle pdb=" N3   DT I -39 "
        pdb=" C4   DT I -39 "
        pdb=" O4   DT I -39 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.90e+01
  angle pdb=" N3   DT I  43 "
        pdb=" C4   DT I  43 "
        pdb=" O4   DT I  43 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  ... (remaining 18280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 4190
       17.37 -    34.75: 1117
       34.75 -    52.12: 1125
       52.12 -    69.49: 375
       69.49 -    86.87: 18
  Dihedral angle restraints: 6825
    sinusoidal: 4679
      harmonic: 2146
  Sorted by residual:
  dihedral pdb=" CA  ASN F  64 "
           pdb=" CB  ASN F  64 "
           pdb=" CG  ASN F  64 "
           pdb=" OD1 ASN F  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -163.56   73.56     2      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CG  ARG F  39 "
           pdb=" CD  ARG F  39 "
           pdb=" NE  ARG F  39 "
           pdb=" CZ  ARG F  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.84  -43.84     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG C  54 "
           pdb=" CD  ARG C  54 "
           pdb=" NE  ARG C  54 "
           pdb=" CZ  ARG C  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.42  -43.58     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 6822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1339
       0.037 -    0.075: 531
       0.075 -    0.112: 182
       0.112 -    0.149: 38
       0.149 -    0.186: 7
  Chirality restraints: 2097
  Sorted by residual:
  chirality pdb=" P    DA J -71 "
            pdb=" OP1  DA J -71 "
            pdb=" OP2  DA J -71 "
            pdb=" O5'  DA J -71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.52   -0.19 2.00e-01 2.50e+01 8.67e-01
  chirality pdb=" C3'  DG J   4 "
            pdb=" C4'  DG J   4 "
            pdb=" O3'  DG J   4 "
            pdb=" C2'  DG J   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.91    0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" C1'  DC J  70 "
            pdb=" O4'  DC J  70 "
            pdb=" C2'  DC J  70 "
            pdb=" N1   DC J  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.38e-01
  ... (remaining 2094 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.48e+00
        pdb=" N   PRO D 126 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.025 5.00e-02 4.00e+02   3.78e-02 2.29e+00
        pdb=" N   PRO E  43 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  31 "    0.024 5.00e-02 4.00e+02   3.60e-02 2.08e+00
        pdb=" N   PRO B  32 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1806
        2.77 -     3.30: 10340
        3.30 -     3.83: 23767
        3.83 -     4.37: 27537
        4.37 -     4.90: 39377
  Nonbonded interactions: 102827
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  59 "
            pdb=" OE2 GLU B  63 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" NH2 ARG C  43 "
            pdb=" OE1 GLU D  58 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NH2 ARG G  43 "
            pdb=" OE1 GLU H  58 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.328 3.120
  ... (remaining 102822 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:             1.630
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.890
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:6.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
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   0.082  12619  Z= 0.517
  Angle     :  0.735   7.369  18285  Z= 0.647
  Chirality :  0.045   0.186   2097
  Planarity :  0.004   0.039   1296
  Dihedral  : 28.505  86.868   5437
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 24.60 %
    Favored  : 74.60 %
  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:  2.81 (0.30), residues: 728
  helix:  2.61 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.51 (0.40), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  48 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.007   0.001   PHE B 100 
 HIS   0.007   0.001   HIS C 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00591 /  0.52 (12619)
  covalent geometry    : angle       0.73543 /  0.65 (18285)
  hydrogen bonds       : bond        0.10775 /  6.98 (  785)
  hydrogen bonds       : angle       4.37290 /  3.16 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 177
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8627 (m-10) cc_final: 0.8137 (m-10)
REVERT: D  106 TYR cc_start: 0.8802 (m-10) cc_final: 0.8577 (m-10)
REVERT: H   85 MET cc_start: 0.8612 (mmm) cc_final: 0.8392 (tpp)
  outliers start: 5
  outliers final: 2
  residues processed: 181
  average time/residue: 0.6018
  time to fit residues: 116.3388
Evaluate side-chains
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   87 VAL
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:   20.0000
   chunk 53 optimal weight:    0.0030
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0670
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6130

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 ASN
B  75 HIS
C 121 HIS
C 123 HIS
E  39 HIS
E  68 GLN
F  64 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.054073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.039416 restraints weight = 56812.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 2.09
r_work: 0.2791 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12619  Z= 0.152
  Angle     :  0.638   7.507  18285  Z= 0.386
  Chirality :  0.045   0.243   2097
  Planarity :  0.004   0.037   1296
  Dihedral  : 30.833  86.873   3979
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 28.30 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.94 (0.30), residues: 728
  helix:  2.64 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.49 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 122 
 TYR   0.014   0.002   TYR B  51 
 PHE   0.019   0.001   PHE H  88 
 HIS   0.004   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.15 (12619)
  covalent geometry    : angle       0.63785 /  0.39 (18285)
  hydrogen bonds       : bond        0.04853 /  3.24 (  785)
  hydrogen bonds       : angle       3.07307 /  2.29 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.9241 (m-10) cc_final: 0.8478 (m-10)
REVERT: C  102 ASP cc_start: 0.8759 (t0) cc_final: 0.8525 (t0)
REVERT: D  106 TYR cc_start: 0.9012 (m-10) cc_final: 0.8478 (m-10)
REVERT: D  136 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8997 (tp30)
REVERT: G  102 ASP cc_start: 0.8791 (t0) cc_final: 0.7873 (t0)
REVERT: G  110 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8671 (mmmm)
REVERT: H   85 MET cc_start: 0.9501 (mmm) cc_final: 0.9173 (tpp)
  outliers start: 18
  outliers final: 8
  residues processed: 153
  average time/residue: 0.5642
  time to fit residues: 92.7682
Evaluate side-chains
  137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 73 optimal weight:   30.0000
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 97 optimal weight:   20.0000
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 83 optimal weight:   20.0000
   chunk 67 optimal weight:    6.9990
   overall best weight:    3.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.051224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.036540 restraints weight = 58352.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.12
r_work: 0.2699 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12619  Z= 0.251
  Angle     :  0.693  13.110  18285  Z= 0.400
  Chirality :  0.045   0.220   2097
  Planarity :  0.004   0.040   1296
  Dihedral  : 31.363  87.889   3979
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 27.33 %
    Favored  : 69.45 %
  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:  3.10 (0.31), residues: 728
  helix:  2.76 (0.22), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.45 (0.43), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  28 
 TYR   0.017   0.002   TYR H 106 
 PHE   0.011   0.001   PHE D  88 
 HIS   0.004   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00497 /  0.25 (12619)
  covalent geometry    : angle       0.69252 /  0.40 (18285)
  hydrogen bonds       : bond        0.05849 /  3.93 (  785)
  hydrogen bonds       : angle       3.17675 /  2.40 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9301 (mt-10) cc_final: 0.9099 (mt-10)
REVERT: A  120 MET cc_start: 0.8652 (mtt) cc_final: 0.8278 (mtm)
REVERT: B   88 TYR cc_start: 0.9274 (m-10) cc_final: 0.8546 (m-10)
REVERT: C  102 ASP cc_start: 0.8861 (t0) cc_final: 0.8556 (t0)
REVERT: D  106 TYR cc_start: 0.9089 (m-10) cc_final: 0.8613 (m-10)
REVERT: D  136 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.9005 (tp30)
REVERT: E  120 MET cc_start: 0.8799 (mmm) cc_final: 0.8288 (mtm)
REVERT: F   88 TYR cc_start: 0.9333 (m-10) cc_final: 0.8944 (m-10)
REVERT: G   30 SER cc_start: 0.9741 (OUTLIER) cc_final: 0.9465 (p)
REVERT: G  103 GLU cc_start: 0.8701 (tp30) cc_final: 0.8269 (tp30)
REVERT: G  106 ASP cc_start: 0.9421 (t0) cc_final: 0.9178 (t0)
REVERT: G  110 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8745 (mmmm)
REVERT: H  136 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.9016 (tp30)
  outliers start: 20
  outliers final: 8
  residues processed: 142
  average time/residue: 0.5530
  time to fit residues: 84.1552
Evaluate side-chains
  131 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:   20.0000
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 89 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 73 optimal weight:   30.0000
   chunk 36 optimal weight:   10.0000
   chunk 72 optimal weight:   30.0000
   chunk 8 optimal weight:    2.9990
   chunk 87 optimal weight:   30.0000
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.050822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.036004 restraints weight = 57998.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 2.13
r_work: 0.2698 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12619  Z= 0.190
  Angle     :  0.628   7.402  18285  Z= 0.372
  Chirality :  0.043   0.228   2097
  Planarity :  0.004   0.033   1296
  Dihedral  : 31.428  88.955   3978
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 28.14 %
    Favored  : 68.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.31), residues: 728
  helix:  2.91 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.44 (0.43), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  40 
 TYR   0.012   0.002   TYR D  63 
 PHE   0.018   0.001   PHE H  88 
 HIS   0.005   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.19 (12619)
  covalent geometry    : angle       0.62798 /  0.37 (18285)
  hydrogen bonds       : bond        0.04493 /  2.99 (  785)
  hydrogen bonds       : angle       2.99559 /  2.26 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9094 (mt-10)
REVERT: B   88 TYR cc_start: 0.9272 (m-10) cc_final: 0.8529 (m-10)
REVERT: C  102 ASP cc_start: 0.8903 (t0) cc_final: 0.8557 (t0)
REVERT: D   56 ASN cc_start: 0.9417 (m-40) cc_final: 0.9140 (m-40)
REVERT: D  106 TYR cc_start: 0.8999 (m-10) cc_final: 0.8592 (m-10)
REVERT: D  136 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8995 (tp30)
REVERT: E   56 LYS cc_start: 0.9322 (ttpp) cc_final: 0.9048 (tmmt)
REVERT: G  102 ASP cc_start: 0.8843 (t0) cc_final: 0.8627 (t0)
REVERT: G  110 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8731 (mmmm)
REVERT: H  136 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8990 (tp30)
  outliers start: 20
  outliers final: 12
  residues processed: 145
  average time/residue: 0.5291
  time to fit residues: 82.4677
Evaluate side-chains
  140 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  101 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:   20.0000
   chunk 88 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 85 optimal weight:   30.0000
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0670
   chunk 56 optimal weight:    3.9990
   chunk 95 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.4126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.050147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.035367 restraints weight = 58281.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.16
r_work: 0.2687 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12619  Z= 0.187
  Angle     :  0.639   7.305  18285  Z= 0.373
  Chirality :  0.043   0.225   2097
  Planarity :  0.004   0.036   1296
  Dihedral  : 31.443  88.332   3978
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 28.14 %
    Favored  : 67.85 %
  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:  3.34 (0.31), residues: 728
  helix:  2.97 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.49 (0.43), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  40 
 TYR   0.025   0.002   TYR H 106 
 PHE   0.023   0.001   PHE D  88 
 HIS   0.006   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.19 (12619)
  covalent geometry    : angle       0.63857 /  0.37 (18285)
  hydrogen bonds       : bond        0.04702 /  3.13 (  785)
  hydrogen bonds       : angle       2.98584 /  2.27 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9102 (mt-10)
REVERT: B   88 TYR cc_start: 0.9270 (m-10) cc_final: 0.8725 (m-10)
REVERT: C  102 ASP cc_start: 0.8932 (t0) cc_final: 0.8603 (t0)
REVERT: D   56 ASN cc_start: 0.9391 (m-40) cc_final: 0.9078 (m-40)
REVERT: D   91 ASP cc_start: 0.9310 (t0) cc_final: 0.8943 (t0)
REVERT: D  136 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8995 (tp30)
REVERT: E   56 LYS cc_start: 0.9327 (ttpp) cc_final: 0.9052 (tmmt)
REVERT: G  102 ASP cc_start: 0.9075 (t0) cc_final: 0.8543 (t0)
REVERT: G  106 ASP cc_start: 0.9418 (t0) cc_final: 0.9193 (t0)
REVERT: G  110 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8788 (mmmm)
REVERT: H  116 GLU cc_start: 0.9229 (mp0) cc_final: 0.9011 (mp0)
REVERT: H  136 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.9049 (tp30)
  outliers start: 25
  outliers final: 12
  residues processed: 145
  average time/residue: 0.5697
  time to fit residues: 88.9585
Evaluate side-chains
  139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 86 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.050882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.036259 restraints weight = 58156.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.13
r_work: 0.2714 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12619  Z= 0.138
  Angle     :  0.609   9.572  18285  Z= 0.360
  Chirality :  0.042   0.225   2097
  Planarity :  0.004   0.031   1296
  Dihedral  : 31.365  88.138   3978
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 29.74 %
    Favored  : 67.04 %
  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:  3.42 (0.31), residues: 728
  helix:  3.01 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.41 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  95 
 TYR   0.030   0.002   TYR H 106 
 PHE   0.020   0.001   PHE H  88 
 HIS   0.007   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.14 (12619)
  covalent geometry    : angle       0.60886 /  0.36 (18285)
  hydrogen bonds       : bond        0.03998 /  2.67 (  785)
  hydrogen bonds       : angle       2.82745 /  2.14 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9075 (mt-10)
REVERT: B   88 TYR cc_start: 0.9261 (m-10) cc_final: 0.8828 (m-10)
REVERT: C  102 ASP cc_start: 0.8865 (t0) cc_final: 0.8538 (t0)
REVERT: D   56 ASN cc_start: 0.9410 (m-40) cc_final: 0.9061 (m-40)
REVERT: D   68 LEU cc_start: 0.9707 (tp) cc_final: 0.9494 (tm)
REVERT: D   91 ASP cc_start: 0.9301 (t0) cc_final: 0.8935 (t0)
REVERT: D  128 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8115 (tm-30)
REVERT: D  136 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8977 (tp30)
REVERT: E   56 LYS cc_start: 0.9302 (ttpp) cc_final: 0.9017 (tmmt)
REVERT: F   85 ASP cc_start: 0.9127 (m-30) cc_final: 0.8896 (m-30)
REVERT: G  102 ASP cc_start: 0.8827 (t0) cc_final: 0.8518 (t0)
REVERT: G  106 ASP cc_start: 0.9373 (t0) cc_final: 0.9128 (t0)
REVERT: G  110 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8746 (mmmm)
REVERT: H  116 GLU cc_start: 0.9193 (mp0) cc_final: 0.8904 (mp0)
REVERT: H  136 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.9025 (tp30)
  outliers start: 20
  outliers final: 12
  residues processed: 152
  average time/residue: 0.5578
  time to fit residues: 91.4093
Evaluate side-chains
  144 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:   20.0000
   chunk 40 optimal weight:    0.0060
   chunk 88 optimal weight:   20.0000
   chunk 70 optimal weight:    0.0770
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 73 optimal weight:   30.0000
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 81 optimal weight:   20.0000
   overall best weight:    3.0160

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  39 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.049315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.034711 restraints weight = 58298.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 2.14
r_work: 0.2668 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12619  Z= 0.215
  Angle     :  0.673   8.826  18285  Z= 0.384
  Chirality :  0.043   0.221   2097
  Planarity :  0.004   0.036   1296
  Dihedral  : 31.510  89.847   3978
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 29.74 %
    Favored  : 66.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.39 (0.31), residues: 728
  helix:  3.01 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.47 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.022   0.002   TYR D 106 
 PHE   0.026   0.001   PHE D  88 
 HIS   0.006   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.22 (12619)
  covalent geometry    : angle       0.67287 /  0.38 (18285)
  hydrogen bonds       : bond        0.05177 /  3.48 (  785)
  hydrogen bonds       : angle       3.08419 /  2.34 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 ASP cc_start: 0.8912 (t0) cc_final: 0.8632 (t0)
REVERT: D   56 ASN cc_start: 0.9405 (m-40) cc_final: 0.9025 (m-40)
REVERT: D   91 ASP cc_start: 0.9325 (t0) cc_final: 0.8960 (t0)
REVERT: D  136 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.9043 (tp30)
REVERT: E   56 LYS cc_start: 0.9317 (ttpp) cc_final: 0.9037 (tmmt)
REVERT: G   86 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9202 (tppp)
REVERT: G  102 ASP cc_start: 0.9030 (t0) cc_final: 0.8750 (t0)
REVERT: G  110 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8782 (mmmm)
REVERT: H  116 GLU cc_start: 0.9229 (mp0) cc_final: 0.8997 (mp0)
REVERT: H  136 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.9067 (tp30)
  outliers start: 25
  outliers final: 13
  residues processed: 139
  average time/residue: 0.5759
  time to fit residues: 85.7843
Evaluate side-chains
  137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  101 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 90 optimal weight:   20.0000
   chunk 96 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 77 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 82 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.7788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.050030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.035307 restraints weight = 57231.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.22
r_work: 0.2693 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12619  Z= 0.159
  Angle     :  0.636  10.909  18285  Z= 0.368
  Chirality :  0.042   0.226   2097
  Planarity :  0.004   0.031   1296
  Dihedral  : 31.476  89.896   3977
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 31.35 %
    Favored  : 65.43 %
  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: 728
  helix:  3.01 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.51 (0.43), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.041   0.002   TYR D 106 
 PHE   0.026   0.001   PHE H  88 
 HIS   0.007   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.16 (12619)
  covalent geometry    : angle       0.63590 /  0.37 (18285)
  hydrogen bonds       : bond        0.04176 /  2.79 (  785)
  hydrogen bonds       : angle       2.94693 /  2.23 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 ASP cc_start: 0.8871 (t0) cc_final: 0.8577 (t0)
REVERT: D   56 ASN cc_start: 0.9385 (m-40) cc_final: 0.8980 (m-40)
REVERT: D   91 ASP cc_start: 0.9331 (t0) cc_final: 0.8971 (t0)
REVERT: D  128 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8043 (tm-30)
REVERT: D  136 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9078 (tp30)
REVERT: E   40 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8037 (tpt90)
REVERT: E   56 LYS cc_start: 0.9318 (ttpp) cc_final: 0.9030 (tmmt)
REVERT: G   86 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9213 (tppp)
REVERT: G  102 ASP cc_start: 0.8958 (t0) cc_final: 0.8526 (t0)
REVERT: G  106 ASP cc_start: 0.9362 (t0) cc_final: 0.9125 (t0)
REVERT: G  110 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8782 (mmmm)
REVERT: H  116 GLU cc_start: 0.9233 (mp0) cc_final: 0.8929 (mp0)
REVERT: H  128 GLU cc_start: 0.8718 (tp30) cc_final: 0.8155 (tm-30)
REVERT: H  136 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.9126 (tp30)
  outliers start: 20
  outliers final: 11
  residues processed: 139
  average time/residue: 0.5603
  time to fit residues: 83.7179
Evaluate side-chains
  138 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   40 ARG
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  101 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 72 optimal weight:   30.0000
   chunk 47 optimal weight:    0.2980
   chunk 2 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   overall best weight:    1.6386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.049963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.035306 restraints weight = 56755.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.22
r_work: 0.2695 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12619  Z= 0.159
  Angle     :  0.645  10.757  18285  Z= 0.372
  Chirality :  0.042   0.222   2097
  Planarity :  0.004   0.033   1296
  Dihedral  : 31.409  89.817   3977
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 31.83 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.31), residues: 728
  helix:  2.99 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.50 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  40 
 TYR   0.034   0.002   TYR D 106 
 PHE   0.020   0.001   PHE D  88 
 HIS   0.005   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.16 (12619)
  covalent geometry    : angle       0.64535 /  0.37 (18285)
  hydrogen bonds       : bond        0.04217 /  2.83 (  785)
  hydrogen bonds       : angle       2.95583 /  2.23 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 ASP cc_start: 0.8907 (t0) cc_final: 0.8619 (t0)
REVERT: D   56 ASN cc_start: 0.9385 (m-40) cc_final: 0.8984 (m-40)
REVERT: D   58 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8474 (tp30)
REVERT: D   91 ASP cc_start: 0.9331 (t0) cc_final: 0.8977 (t0)
REVERT: D  128 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8073 (tm-30)
REVERT: D  136 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9076 (tp30)
REVERT: E   40 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8048 (tpt90)
REVERT: E   56 LYS cc_start: 0.9314 (ttpp) cc_final: 0.9021 (tmmt)
REVERT: G   86 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9217 (tppp)
REVERT: G  102 ASP cc_start: 0.8909 (t0) cc_final: 0.8552 (t0)
REVERT: G  106 ASP cc_start: 0.9345 (t0) cc_final: 0.9095 (t0)
REVERT: G  110 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8784 (mmmm)
REVERT: H  116 GLU cc_start: 0.9236 (mp0) cc_final: 0.8927 (mp0)
REVERT: H  128 GLU cc_start: 0.8717 (tp30) cc_final: 0.8144 (tm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 142
  average time/residue: 0.6169
  time to fit residues: 93.9800
Evaluate side-chains
  138 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   40 ARG
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue  101 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 72 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 91 optimal weight:   20.0000
   chunk 11 optimal weight:    0.7980
   chunk 89 optimal weight:   20.0000
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.9386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.049729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.035145 restraints weight = 57534.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 2.24
r_work: 0.2689 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12619  Z= 0.169
  Angle     :  0.663  11.548  18285  Z= 0.380
  Chirality :  0.042   0.221   2097
  Planarity :  0.004   0.051   1296
  Dihedral  : 31.437  89.548   3977
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 33.28 %
    Favored  : 64.31 %
  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:  3.16 (0.31), residues: 728
  helix:  2.86 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.51 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  92 
 TYR   0.059   0.003   TYR F  88 
 PHE   0.023   0.001   PHE H  88 
 HIS   0.005   0.001   HIS D 132 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.17 (12619)
  covalent geometry    : angle       0.66303 /  0.38 (18285)
  hydrogen bonds       : bond        0.04284 /  2.88 (  785)
  hydrogen bonds       : angle       3.02578 /  2.27 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 ASP cc_start: 0.8891 (t0) cc_final: 0.8579 (t0)
REVERT: D   56 ASN cc_start: 0.9389 (m-40) cc_final: 0.8977 (m-40)
REVERT: D   91 ASP cc_start: 0.9339 (t0) cc_final: 0.8989 (t0)
REVERT: D  128 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8076 (tm-30)
REVERT: D  136 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9079 (tp30)
REVERT: E   40 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8081 (tpt90)
REVERT: E   56 LYS cc_start: 0.9319 (ttpp) cc_final: 0.9027 (tmmt)
REVERT: G   86 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9224 (tppp)
REVERT: G  102 ASP cc_start: 0.8915 (t0) cc_final: 0.8532 (t0)
REVERT: G  106 ASP cc_start: 0.9281 (t0) cc_final: 0.8947 (t0)
REVERT: G  110 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8745 (mmmm)
REVERT: H  116 GLU cc_start: 0.9253 (mp0) cc_final: 0.8942 (mp0)
REVERT: H  128 GLU cc_start: 0.8714 (tp30) cc_final: 0.8134 (tm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 138
  average time/residue: 0.6552
  time to fit residues: 96.9909
Evaluate side-chains
  139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   40 ARG
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue  101 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 96 optimal weight:   20.0000
   chunk 63 optimal weight:    5.9990
   chunk 92 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    3.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.048347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.034419 restraints weight = 57868.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.23
r_work: 0.2648 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8903
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  12619  Z= 0.244
  Angle     :  0.724  11.257  18285  Z= 0.403
  Chirality :  0.044   0.225   2097
  Planarity :  0.004   0.035   1296
  Dihedral  : 31.663  88.100   3977
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 33.76 %
    Favored  : 63.99 %
  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:  2.78 (0.31), residues: 728
  helix:  2.56 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.63 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  92 
 TYR   0.069   0.003   TYR F  88 
 PHE   0.023   0.002   PHE D  88 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00498 /  0.24 (12619)
  covalent geometry    : angle       0.72408 /  0.40 (18285)
  hydrogen bonds       : bond        0.05561 /  3.77 (  785)
  hydrogen bonds       : angle       3.33574 /  2.49 ( 1969)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3157.41 seconds
wall clock time: 54 minutes 28.20 seconds (3268.20 seconds total)