Starting phenix.real_space_refine
on Tue Jun 10 08:46:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k43_62042/06_2025/9k43_62042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k43_62042/06_2025/9k43_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k43_62042/06_2025/9k43_62042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k43_62042/06_2025/9k43_62042.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k43_62042/06_2025/9k43_62042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k43_62042/06_2025/9k43_62042.cif"
  }
  resolution = 2.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.48, per 1000 atoms: 0.63
  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: 3.33
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 6.46
  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: 4.78

  Time building geometry restraints manager: 3.96 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=" 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
  bond pdb=" O3'  DA J -15 "
       pdb=" P    DA J -14 "
    ideal  model  delta    sigma   weight residual
    1.607  1.660 -0.053 1.50e-02 4.44e+03 1.25e+01
  bond pdb=" O3'  DA I -69 "
       pdb=" P    DG I -68 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.50e-02 4.44e+03 1.10e+01
  bond pdb=" O3'  DG J -69 "
       pdb=" P    DA J -68 "
    ideal  model  delta    sigma   weight residual
    1.607  1.655 -0.048 1.50e-02 4.44e+03 1.04e+01
  ... (remaining 12614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 17698
        1.60 -     3.19: 524
        3.19 -     4.79: 53
        4.79 -     6.39: 5
        6.39 -     7.98: 5
  Bond angle restraints: 18285
  Sorted by residual:
  angle pdb=" O3'  DG J   4 "
        pdb=" C3'  DG J   4 "
        pdb=" C2'  DG J   4 "
      ideal   model   delta    sigma   weight residual
     111.50  103.52    7.98 1.50e+00 4.44e-01 2.83e+01
  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=" O3'  DC J -26 "
        pdb=" C3'  DC J -26 "
        pdb=" C2'  DC J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  104.51    6.99 1.50e+00 4.44e-01 2.17e+01
  angle pdb=" N   GLY D 127 "
        pdb=" CA  GLY D 127 "
        pdb=" C   GLY D 127 "
      ideal   model   delta    sigma   weight residual
     111.02  118.02   -7.00 1.86e+00 2.89e-01 1.41e+01
  angle pdb=" N   GLY H 127 "
        pdb=" CA  GLY H 127 "
        pdb=" C   GLY H 127 "
      ideal   model   delta    sigma   weight residual
     110.77  117.84   -7.07 1.93e+00 2.68e-01 1.34e+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 -    0.049: 1803
       0.049 -    0.099: 242
       0.099 -    0.148: 42
       0.148 -    0.197: 8
       0.197 -    0.246: 2
  Chirality restraints: 2097
  Sorted by residual:
  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     -2.66   -2.91    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C3'  DC J -26 "
            pdb=" C4'  DC J -26 "
            pdb=" O3'  DC J -26 "
            pdb=" C2'  DC J -26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.87    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C3'  DG I -71 "
            pdb=" C4'  DG I -71 "
            pdb=" O3'  DG I -71 "
            pdb=" C2'  DG I -71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 9.45e-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:             2.950
  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:             0.040
  Extract box with map and model:          1.230
  Check model and map are aligned:         0.280
  Set scattering table:                    0.370
  Process input model:                     36.620
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  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:17.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
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   0.060  12619  Z= 0.204
  Angle     :  0.607   7.984  18285  Z= 0.380
  Chirality :  0.037   0.246   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.007   0.001   HIS C 121 
 PHE   0.007   0.001   PHE B 100 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.010   0.001   ARG C  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10775 (  785)
  hydrogen bonds       : angle       4.37290 ( 1969)
  covalent geometry    : bond        0.00413 (12619)
  covalent geometry    : angle       0.60731 (18285)

*********************** 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  : 0.949 
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: 1.4502
  time to fit residues: 280.7672
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  : 0.873 
-------------------------------------------------------------------------------
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 84 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
B  75 HIS
B  93 GLN
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 = 0.3399 r_free = 0.3399 target = 0.050259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.035524 restraints weight = 56894.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.24
r_work: 0.2689 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12619  Z= 0.243
  Angle     :  0.612   6.513  18285  Z= 0.367
  Chirality :  0.036   0.149   2097
  Planarity :  0.004   0.034   1296
  Dihedral  : 31.093  88.049   3979
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 25.56 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.17 (0.31), residues: 728
  helix:  2.85 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.55 (0.42), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  72 
 PHE   0.019   0.001   PHE H  88 
 TYR   0.012   0.001   TYR F  51 
 ARG   0.005   0.001   ARG F  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04515 (  785)
  hydrogen bonds       : angle       3.06942 ( 1969)
  covalent geometry    : bond        0.00541 (12619)
  covalent geometry    : angle       0.61249 (18285)

*********************** 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
  166 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   27 GLN cc_start: 0.9379 (mm-40) cc_final: 0.9169 (mm110)
REVERT: B   88 TYR cc_start: 0.9293 (m-10) cc_final: 0.8712 (m-10)
REVERT: C   54 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7241 (mtp180)
REVERT: C   68 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8854 (tt0)
REVERT: C  102 ASP cc_start: 0.8909 (t0) cc_final: 0.8637 (t0)
REVERT: D   91 ASP cc_start: 0.9332 (t0) cc_final: 0.8945 (t0)
REVERT: D  106 TYR cc_start: 0.9115 (m-10) cc_final: 0.8626 (m-10)
REVERT: D  136 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9060 (tp30)
REVERT: G  102 ASP cc_start: 0.9010 (t0) cc_final: 0.8111 (t0)
REVERT: G  110 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8923 (mmmm)
REVERT: H   85 MET cc_start: 0.9576 (mmm) cc_final: 0.9368 (mmm)
REVERT: H  106 TYR cc_start: 0.8967 (m-10) cc_final: 0.8625 (m-10)
REVERT: H  116 GLU cc_start: 0.9336 (mp0) cc_final: 0.9079 (mp0)
REVERT: H  136 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.9059 (tp30)
  outliers start: 27
  outliers final: 8
  residues processed: 158
  average time/residue: 1.3286
  time to fit residues: 225.3978
Evaluate side-chains
  136 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
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   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   27 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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   chunk 23 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
C 121 HIS
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.049573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.034850 restraints weight = 57929.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 2.29
r_work: 0.2675 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12619  Z= 0.202
  Angle     :  0.578   5.802  18285  Z= 0.348
  Chirality :  0.034   0.153   2097
  Planarity :  0.004   0.041   1296
  Dihedral  : 30.988  88.990   3978
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 28.30 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.34 (0.30), residues: 728
  helix:  3.03 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.57 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.006   0.001   PHE E  78 
 TYR   0.013   0.001   TYR F  51 
 ARG   0.002   0.000   ARG F  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  785)
  hydrogen bonds       : angle       2.93076 ( 1969)
  covalent geometry    : bond        0.00448 (12619)
  covalent geometry    : angle       0.57771 (18285)

*********************** 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
  160 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8349 (mp0)
REVERT: B   88 TYR cc_start: 0.9288 (m-10) cc_final: 0.8894 (m-10)
REVERT: C   54 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7307 (mtp180)
REVERT: C  102 ASP cc_start: 0.8909 (t0) cc_final: 0.8586 (t0)
REVERT: C  110 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8810 (mmmm)
REVERT: D   56 ASN cc_start: 0.9473 (m-40) cc_final: 0.9254 (m-40)
REVERT: D   91 ASP cc_start: 0.9354 (t0) cc_final: 0.8992 (t0)
REVERT: D  106 TYR cc_start: 0.9015 (m-10) cc_final: 0.8764 (m-10)
REVERT: D  136 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9039 (tp30)
REVERT: E   56 LYS cc_start: 0.9536 (ttpp) cc_final: 0.9142 (tmmt)
REVERT: F   84 MET cc_start: 0.9323 (mmm) cc_final: 0.9052 (mmm)
REVERT: G   48 ARG cc_start: 0.9319 (tpp80) cc_final: 0.9112 (tpp80)
REVERT: G  102 ASP cc_start: 0.8629 (t0) cc_final: 0.7990 (t0)
REVERT: G  110 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8883 (mmmm)
REVERT: H   85 MET cc_start: 0.9545 (mmm) cc_final: 0.9242 (mmm)
REVERT: H  116 GLU cc_start: 0.9339 (mp0) cc_final: 0.9016 (mp0)
REVERT: H  136 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9048 (tp30)
  outliers start: 20
  outliers final: 6
  residues processed: 153
  average time/residue: 1.3468
  time to fit residues: 221.4498
Evaluate side-chains
  140 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain D residue  136 GLU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0570
   overall best weight:    1.6104

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.049664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.035073 restraints weight = 57360.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.29
r_work: 0.2686 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12619  Z= 0.177
  Angle     :  0.564   5.982  18285  Z= 0.341
  Chirality :  0.034   0.148   2097
  Planarity :  0.004   0.042   1296
  Dihedral  : 30.824  89.841   3977
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 28.62 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.47 (0.31), residues: 728
  helix:  3.13 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.55 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 132 
 PHE   0.020   0.001   PHE D  88 
 TYR   0.021   0.002   TYR H 106 
 ARG   0.005   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03648 (  785)
  hydrogen bonds       : angle       2.80710 ( 1969)
  covalent geometry    : bond        0.00389 (12619)
  covalent geometry    : angle       0.56403 (18285)

*********************** 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
  165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8307 (mp0)
REVERT: C   54 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7452 (mtp180)
REVERT: C   68 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8803 (tt0)
REVERT: C  102 ASP cc_start: 0.8900 (t0) cc_final: 0.8580 (t0)
REVERT: C  110 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8686 (mmmm)
REVERT: D   56 ASN cc_start: 0.9554 (m-40) cc_final: 0.9319 (m-40)
REVERT: D   68 LEU cc_start: 0.9725 (tp) cc_final: 0.9522 (tm)
REVERT: D   91 ASP cc_start: 0.9338 (t0) cc_final: 0.8990 (t0)
REVERT: D  136 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.9058 (tp30)
REVERT: E   56 LYS cc_start: 0.9494 (ttpp) cc_final: 0.9139 (tmmt)
REVERT: G   30 SER cc_start: 0.9741 (OUTLIER) cc_final: 0.9457 (p)
REVERT: G  102 ASP cc_start: 0.8605 (t0) cc_final: 0.7946 (t0)
REVERT: G  106 ASP cc_start: 0.9368 (t0) cc_final: 0.9161 (t0)
REVERT: G  110 LYS cc_start: 0.9236 (mtmm) cc_final: 0.8839 (mmmm)
REVERT: H   85 MET cc_start: 0.9499 (mmm) cc_final: 0.9282 (mmm)
REVERT: H   91 ASP cc_start: 0.9369 (t0) cc_final: 0.9006 (t0)
REVERT: H  116 GLU cc_start: 0.9332 (mp0) cc_final: 0.8919 (mp0)
  outliers start: 24
  outliers final: 10
  residues processed: 154
  average time/residue: 1.3396
  time to fit residues: 221.6441
Evaluate side-chains
  145 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.046977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.032792 restraints weight = 57087.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 2.27
r_work: 0.2602 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  12619  Z= 0.294
  Angle     :  0.640   6.492  18285  Z= 0.379
  Chirality :  0.037   0.145   2097
  Planarity :  0.004   0.036   1296
  Dihedral  : 31.357  86.908   3977
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 30.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.21 (0.31), residues: 728
  helix:  2.97 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.74 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.009   0.001   PHE D  88 
 TYR   0.035   0.003   TYR H 106 
 ARG   0.005   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04826 (  785)
  hydrogen bonds       : angle       3.21601 ( 1969)
  covalent geometry    : bond        0.00663 (12619)
  covalent geometry    : angle       0.64030 (18285)

*********************** 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
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.9332 (mmm) cc_final: 0.9100 (mmm)
REVERT: C   68 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8848 (tt0)
REVERT: C  102 ASP cc_start: 0.8905 (t0) cc_final: 0.8588 (t0)
REVERT: D  128 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8280 (tm-30)
REVERT: D  136 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9059 (tp30)
REVERT: E   56 LYS cc_start: 0.9493 (ttpp) cc_final: 0.9148 (tmmt)
REVERT: G   30 SER cc_start: 0.9748 (OUTLIER) cc_final: 0.9447 (p)
REVERT: G  102 ASP cc_start: 0.8508 (t0) cc_final: 0.7938 (t0)
REVERT: G  106 ASP cc_start: 0.9398 (t0) cc_final: 0.9148 (t0)
REVERT: G  110 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8917 (mmmm)
REVERT: H   85 MET cc_start: 0.9553 (mmm) cc_final: 0.9297 (mmm)
REVERT: H  116 GLU cc_start: 0.9354 (mp0) cc_final: 0.8973 (mp0)
REVERT: H  136 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9087 (tp30)
  outliers start: 23
  outliers final: 10
  residues processed: 144
  average time/residue: 1.3661
  time to fit residues: 211.2600
Evaluate side-chains
  137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 33 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.048865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.035135 restraints weight = 57146.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.26
r_work: 0.2679 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12619  Z= 0.162
  Angle     :  0.581   7.021  18285  Z= 0.348
  Chirality :  0.034   0.158   2097
  Planarity :  0.004   0.039   1296
  Dihedral  : 30.781  89.653   3977
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 30.71 %
    Favored  : 66.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.38 (0.31), residues: 728
  helix:  3.08 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.65 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.021   0.001   PHE H  88 
 TYR   0.036   0.002   TYR H 106 
 ARG   0.002   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 (  785)
  hydrogen bonds       : angle       2.79335 ( 1969)
  covalent geometry    : bond        0.00354 (12619)
  covalent geometry    : angle       0.58135 (18285)

*********************** 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
  155 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8788 (tt0)
REVERT: C  102 ASP cc_start: 0.8911 (t0) cc_final: 0.8603 (t0)
REVERT: D   91 ASP cc_start: 0.9323 (t0) cc_final: 0.9022 (t0)
REVERT: D   98 GLN cc_start: 0.9222 (tp40) cc_final: 0.8993 (tp40)
REVERT: D  136 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.8948 (tp30)
REVERT: E   56 LYS cc_start: 0.9474 (ttpp) cc_final: 0.9114 (tmmt)
REVERT: F   30 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9193 (p)
REVERT: G   30 SER cc_start: 0.9753 (OUTLIER) cc_final: 0.9488 (p)
REVERT: G  102 ASP cc_start: 0.8412 (t0) cc_final: 0.7868 (t0)
REVERT: G  106 ASP cc_start: 0.9302 (t0) cc_final: 0.9017 (t0)
REVERT: G  109 ILE cc_start: 0.8943 (mt) cc_final: 0.8707 (mt)
REVERT: G  110 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8791 (mmmm)
REVERT: H   91 ASP cc_start: 0.9357 (t0) cc_final: 0.9049 (t0)
REVERT: H   98 GLN cc_start: 0.9211 (tp40) cc_final: 0.8999 (tp40)
REVERT: H  116 GLU cc_start: 0.9323 (mp0) cc_final: 0.8901 (mp0)
REVERT: H  136 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9043 (tp30)
  outliers start: 20
  outliers final: 8
  residues processed: 148
  average time/residue: 1.2762
  time to fit residues: 203.6244
Evaluate side-chains
  143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.048000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.033546 restraints weight = 58024.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 2.29
r_work: 0.2640 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8878
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12619  Z= 0.206
  Angle     :  0.610   9.276  18285  Z= 0.360
  Chirality :  0.034   0.151   2097
  Planarity :  0.004   0.033   1296
  Dihedral  : 30.935  89.262   3977
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 32.80 %
    Favored  : 64.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.31), residues: 728
  helix:  3.08 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.57 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 132 
 PHE   0.020   0.001   PHE D  88 
 TYR   0.046   0.002   TYR D 106 
 ARG   0.012   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  785)
  hydrogen bonds       : angle       2.92226 ( 1969)
  covalent geometry    : bond        0.00461 (12619)
  covalent geometry    : angle       0.60981 (18285)

*********************** 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: 17
    poor density    : 132
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8836 (tt0)
REVERT: C  102 ASP cc_start: 0.8904 (t0) cc_final: 0.8574 (t0)
REVERT: D   91 ASP cc_start: 0.9385 (t0) cc_final: 0.9062 (t0)
REVERT: D  128 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8159 (tm-30)
REVERT: D  136 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.8992 (tp30)
REVERT: E   56 LYS cc_start: 0.9476 (ttpp) cc_final: 0.9131 (tmmt)
REVERT: G   30 SER cc_start: 0.9755 (OUTLIER) cc_final: 0.9468 (p)
REVERT: G  102 ASP cc_start: 0.8440 (t0) cc_final: 0.7873 (t0)
REVERT: G  106 ASP cc_start: 0.9299 (t0) cc_final: 0.9018 (t0)
REVERT: G  109 ILE cc_start: 0.8997 (mt) cc_final: 0.8742 (mt)
REVERT: G  110 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8775 (mmmm)
REVERT: H   91 ASP cc_start: 0.9388 (t0) cc_final: 0.9070 (t0)
REVERT: H  116 GLU cc_start: 0.9346 (mp0) cc_final: 0.8937 (mp0)
REVERT: H  136 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9076 (tp30)
  outliers start: 17
  outliers final: 9
  residues processed: 144
  average time/residue: 1.3609
  time to fit residues: 210.6984
Evaluate side-chains
  141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.049566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.035674 restraints weight = 57365.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 2.28
r_work: 0.2712 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12619  Z= 0.151
  Angle     :  0.595  10.927  18285  Z= 0.352
  Chirality :  0.033   0.157   2097
  Planarity :  0.004   0.038   1296
  Dihedral  : 30.551  88.412   3977
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 33.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.41 (0.30), residues: 728
  helix:  3.05 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.44 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 132 
 PHE   0.024   0.001   PHE H  88 
 TYR   0.050   0.003   TYR D 106 
 ARG   0.006   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  785)
  hydrogen bonds       : angle       2.72763 ( 1969)
  covalent geometry    : bond        0.00329 (12619)
  covalent geometry    : angle       0.59549 (18285)

*********************** 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
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8783 (tt0)
REVERT: C  102 ASP cc_start: 0.8916 (t0) cc_final: 0.8597 (t0)
REVERT: D   68 LEU cc_start: 0.9711 (tp) cc_final: 0.9492 (tm)
REVERT: D   91 ASP cc_start: 0.9332 (t0) cc_final: 0.9034 (t0)
REVERT: D  128 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8038 (tm-30)
REVERT: D  136 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8923 (tp30)
REVERT: E   56 LYS cc_start: 0.9463 (ttpp) cc_final: 0.9129 (tmmt)
REVERT: F   30 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9185 (p)
REVERT: G   30 SER cc_start: 0.9759 (OUTLIER) cc_final: 0.9503 (p)
REVERT: G  102 ASP cc_start: 0.8279 (t0) cc_final: 0.7783 (t0)
REVERT: G  106 ASP cc_start: 0.9238 (t0) cc_final: 0.8961 (t0)
REVERT: G  109 ILE cc_start: 0.8743 (mt) cc_final: 0.8525 (mt)
REVERT: G  110 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8697 (mmmm)
REVERT: H   91 ASP cc_start: 0.9369 (t0) cc_final: 0.9087 (t0)
REVERT: H  116 GLU cc_start: 0.9320 (mp0) cc_final: 0.8802 (mp0)
REVERT: H  136 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.9067 (tp30)
  outliers start: 11
  outliers final: 3
  residues processed: 147
  average time/residue: 1.2544
  time to fit residues: 199.0066
Evaluate side-chains
  143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   82 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 79 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 86 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS
H 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.047462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.033012 restraints weight = 57642.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.30
r_work: 0.2617 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12619  Z= 0.255
  Angle     :  0.654  11.014  18285  Z= 0.379
  Chirality :  0.036   0.148   2097
  Planarity :  0.004   0.033   1296
  Dihedral  : 31.081  88.061   3977
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 33.92 %
    Favored  : 63.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.17 (0.31), residues: 728
  helix:  2.88 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.54 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 132 
 PHE   0.020   0.001   PHE D  88 
 TYR   0.069   0.003   TYR D 106 
 ARG   0.007   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  785)
  hydrogen bonds       : angle       3.12546 ( 1969)
  covalent geometry    : bond        0.00575 (12619)
  covalent geometry    : angle       0.65360 (18285)

*********************** 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
  140 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   68 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8834 (tt0)
REVERT: C  102 ASP cc_start: 0.8908 (t0) cc_final: 0.8573 (t0)
REVERT: D   91 ASP cc_start: 0.9415 (t0) cc_final: 0.9097 (t0)
REVERT: D  128 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8164 (tm-30)
REVERT: D  136 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8978 (tp30)
REVERT: E   56 LYS cc_start: 0.9467 (ttpp) cc_final: 0.9151 (tmmt)
REVERT: G   30 SER cc_start: 0.9752 (OUTLIER) cc_final: 0.9458 (p)
REVERT: G  102 ASP cc_start: 0.8392 (t0) cc_final: 0.7603 (t0)
REVERT: G  106 ASP cc_start: 0.9327 (t0) cc_final: 0.9081 (t0)
REVERT: G  109 ILE cc_start: 0.9099 (mt) cc_final: 0.8833 (mt)
REVERT: G  110 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8798 (mmmm)
REVERT: H   91 ASP cc_start: 0.9403 (t0) cc_final: 0.9067 (t0)
REVERT: H  116 GLU cc_start: 0.9379 (mp0) cc_final: 0.9004 (mp0)
REVERT: H  136 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9070 (tp30)
  outliers start: 16
  outliers final: 8
  residues processed: 135
  average time/residue: 1.4951
  time to fit residues: 218.2004
Evaluate side-chains
  134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
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   82 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.049065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.035203 restraints weight = 57218.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 2.31
r_work: 0.2694 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12619  Z= 0.160
  Angle     :  0.619  11.106  18285  Z= 0.363
  Chirality :  0.034   0.154   2097
  Planarity :  0.004   0.039   1296
  Dihedral  : 30.604  88.852   3977
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 36.01 %
    Favored  : 62.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.19 (0.30), residues: 728
  helix:  2.88 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.48 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 132 
 PHE   0.024   0.001   PHE H  88 
 TYR   0.036   0.002   TYR B  88 
 ARG   0.006   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  785)
  hydrogen bonds       : angle       2.85385 ( 1969)
  covalent geometry    : bond        0.00355 (12619)
  covalent geometry    : angle       0.61935 (18285)

********************** 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
  142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 ASP cc_start: 0.8902 (t0) cc_final: 0.8572 (t0)
REVERT: D   91 ASP cc_start: 0.9357 (t0) cc_final: 0.9058 (t0)
REVERT: D  128 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8043 (tm-30)
REVERT: D  136 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.8944 (tp30)
REVERT: E   56 LYS cc_start: 0.9463 (ttpp) cc_final: 0.9126 (tmmt)
REVERT: F   30 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9201 (p)
REVERT: G   30 SER cc_start: 0.9763 (OUTLIER) cc_final: 0.9505 (p)
REVERT: G  102 ASP cc_start: 0.8244 (t0) cc_final: 0.7479 (t0)
REVERT: G  106 ASP cc_start: 0.9210 (t0) cc_final: 0.8943 (t0)
REVERT: G  109 ILE cc_start: 0.8842 (mt) cc_final: 0.8600 (mt)
REVERT: G  110 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8672 (mmmm)
REVERT: H   91 ASP cc_start: 0.9345 (t0) cc_final: 0.9040 (t0)
REVERT: H  116 GLU cc_start: 0.9349 (mp0) cc_final: 0.8878 (mp0)
REVERT: H  136 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9053 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 138
  average time/residue: 2.0310
  time to fit residues: 301.5394
Evaluate side-chains
  139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0040
   chunk 15 optimal weight:    0.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    1.2000

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** D  98 GLN ** 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 = 0.3381 r_free = 0.3381 target = 0.048970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.035283 restraints weight = 57541.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 2.29
r_work: 0.2692 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12619  Z= 0.169
  Angle     :  0.618  10.549  18285  Z= 0.361
  Chirality :  0.034   0.151   2097
  Planarity :  0.004   0.034   1296
  Dihedral  : 30.648  89.354   3977
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 35.69 %
    Favored  : 63.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.04 (0.30), residues: 728
  helix:  2.75 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.42 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 132 
 PHE   0.024   0.001   PHE D  88 
 TYR   0.032   0.002   TYR B  88 
 ARG   0.006   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03626 (  785)
  hydrogen bonds       : angle       2.90646 ( 1969)
  covalent geometry    : bond        0.00376 (12619)
  covalent geometry    : angle       0.61790 (18285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8564.64 seconds
wall clock time: 150 minutes 43.53 seconds (9043.53 seconds total)