Starting phenix.real_space_refine
on Fri Jul  3 02:00:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k41_62038/07_2026/9k41_62038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k41_62038/07_2026/9k41_62038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k41_62038/07_2026/9k41_62038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k41_62038/07_2026/9k41_62038.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k41_62038/07_2026/9k41_62038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k41_62038/07_2026/9k41_62038.map"
  }
  resolution = 2.81
  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      14      5.16       5
     C    6585      2.51       5
     N    2168      2.21       5
     O    2772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 11828
  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: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 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: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.23, per 1000 atoms: 0.19
  Number of scatterers: 11828
  At special positions: 0
  Unit cell: (121.136, 75.04, 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      14     16.00
     P     289     15.00
     O    2772      8.00
     N    2168      7.00
     C    6585      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: 0.79
  Conformation dependent library (CDL) restraints added in 248.7 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      72.3% alpha, 3.2% beta
      145 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.559A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.677A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.644A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 31
      removed outlier: 3.546A  pdb=" N   ALA C  30 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 55 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 99 through 106
    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 127 through 147
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.687A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.598A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 25 through 31
    Processing helix  chain 'G' and resid 35 through 46
    Processing helix  chain 'G' and resid 55 through 82
    Processing helix  chain 'G' and resid 88 through 98
    Processing helix  chain 'G' and resid 99 through 106
    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
      removed outlier: 3.528A  pdb=" N   ALA H 130 " --> pdb=" O   PRO H 126 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.044A  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 96 through 98
      removed outlier: 6.439A  pdb=" N   THR B  96 " --> pdb=" O   THR G 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52
      removed outlier: 7.447A  pdb=" N   ARG C  51 " --> 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 86 through 87
    Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.111A  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 51 through 52
      removed outlier: 7.241A  pdb=" N   ARG G  51 " --> 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 86 through 87

    405 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      696 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.15 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: 2177
        1.33 -     1.45: 4095
        1.45 -     1.57: 5758
        1.57 -     1.69: 577
        1.69 -     1.81: 26
  Bond restraints: 12633
  Sorted by residual:
  bond pdb=" C3'  DT I  22 "
       pdb=" C2'  DT I  22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DG I  61 "
       pdb=" C2'  DG I  61 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  bond pdb=" C3'  DC J  64 "
       pdb=" C2'  DC J  64 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.68e+00
  bond pdb=" C3'  DT I  52 "
       pdb=" C2'  DT I  52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.41e+00
  bond pdb=" O3'  DC J -26 "
       pdb=" P    DA J -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.50e-02 4.44e+03 9.38e+00
  ... (remaining 12628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 15994
        1.03 -     2.07: 1620
        2.07 -     3.10: 636
        3.10 -     4.13: 39
        4.13 -     5.17: 10
  Bond angle restraints: 18299
  Sorted by residual:
  angle pdb=" N3   DT I   8 "
        pdb=" C4   DT I   8 "
        pdb=" O4   DT I   8 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.02e+01
  angle pdb=" N3   DT J  51 "
        pdb=" C4   DT J  51 "
        pdb=" O4   DT J  51 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.92e+01
  angle pdb=" N3   DT J -42 "
        pdb=" C4   DT J -42 "
        pdb=" O4   DT J -42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.91e+01
  angle pdb=" N3   DT I -33 "
        pdb=" C4   DT I -33 "
        pdb=" O4   DT I -33 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  angle pdb=" N3   DT I  29 "
        pdb=" C4   DT I  29 "
        pdb=" O4   DT I  29 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  ... (remaining 18294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.84: 4451
       20.84 -    41.69: 1347
       41.69 -    62.53: 1084
       62.53 -    83.38: 50
       83.38 -   104.22: 3
  Dihedral angle restraints: 6935
    sinusoidal: 4785
      harmonic: 2150
  Sorted by residual:
  dihedral pdb=" CA  PRO H 126 "
           pdb=" C   PRO H 126 "
           pdb=" N   GLY H 127 "
           pdb=" CA  GLY H 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.93   16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CG  ARG A  49 "
           pdb=" CD  ARG A  49 "
           pdb=" NE  ARG A  49 "
           pdb=" CZ  ARG A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.97  -42.97     2      1.50e+01 4.44e-03 9.91e+00
  dihedral pdb=" C4'  DG J -17 "
           pdb=" C3'  DG J -17 "
           pdb=" O3'  DG J -17 "
           pdb=" P    DC J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -35.78 -104.22     1      3.50e+01 8.16e-04 9.76e+00
  ... (remaining 6932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1317
       0.038 -    0.077: 564
       0.077 -    0.115: 183
       0.115 -    0.153: 22
       0.153 -    0.192: 1
  Chirality restraints: 2087
  Sorted by residual:
  chirality pdb=" CA  ASP F  24 "
            pdb=" N   ASP F  24 "
            pdb=" C   ASP F  24 "
            pdb=" CB  ASP F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" P    DA I  -8 "
            pdb=" OP1  DA I  -8 "
            pdb=" OP2  DA I  -8 "
            pdb=" O5'  DA I  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.48   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" C3'  DC I -62 "
            pdb=" C4'  DC I -62 "
            pdb=" O3'  DC I -62 "
            pdb=" C2'  DC I -62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.60   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 2084 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 125 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO H 126 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  44 "    0.011 2.00e-02 2.50e+03   1.07e-02 2.60e+00
        pdb=" N1   DC J  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2   DC J  44 "    0.021 2.00e-02 2.50e+03
        pdb=" O2   DC J  44 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DC J  44 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC J  44 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC J  44 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DC J  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DC J  44 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.29e+00
        pdb=" N   PRO D 126 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1308
        2.75 -     3.29: 10382
        3.29 -     3.82: 23519
        3.82 -     4.36: 27964
        4.36 -     4.90: 39816
  Nonbonded interactions: 102989
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  55 "
            pdb=" OP1  DT I -46 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH2 ARG G  41 "
            pdb=" OE1 GLU H  58 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   SER G  85 "
            pdb=" OG  SER G  85 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.309 3.120
  ... (remaining 102984 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:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.030
  Find NCS groups from input model:        0.100
  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:7.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
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   0.046  12633  Z= 0.514
  Angle     :  0.733   5.167  18299  Z= 0.678
  Chirality :  0.045   0.192   2087
  Planarity :  0.004   0.041   1304
  Dihedral  : 28.881 104.221   5547
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 22.99 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.30), residues: 730
  helix:  1.71 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.08 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.010   0.002   TYR B  98 
 PHE   0.006   0.001   PHE C  34 
 HIS   0.002   0.000   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00588 /  0.51 (12633)
  covalent geometry    : angle       0.73337 /  0.68 (18299)
  hydrogen bonds       : bond        0.12474 /  8.56 (  753)
  hydrogen bonds       : angle       4.65008 /  3.36 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.290 
Fit side-chains
REVERT: C   81 ASP cc_start: 0.8800 (m-30) cc_final: 0.8594 (m-30)
REVERT: C   99 ASP cc_start: 0.8819 (t70) cc_final: 0.7685 (t0)
REVERT: C  121 ASN cc_start: 0.9301 (t0) cc_final: 0.8789 (t0)
REVERT: D   82 MET cc_start: 0.9307 (tpt) cc_final: 0.9096 (mmm)
REVERT: D   91 ASP cc_start: 0.9111 (t70) cc_final: 0.8801 (t0)
REVERT: G   81 ASP cc_start: 0.8985 (m-30) cc_final: 0.8775 (m-30)
REVERT: G   99 ASP cc_start: 0.8900 (t70) cc_final: 0.8635 (t0)
REVERT: G  121 ASN cc_start: 0.9264 (t0) cc_final: 0.8854 (t0)
REVERT: H   58 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: H   91 ASP cc_start: 0.9098 (t0) cc_final: 0.8782 (t0)
REVERT: H  128 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8131 (tm-30)
  outliers start: 8
  outliers final: 0
  residues processed: 148
  average time/residue: 0.8005
  time to fit residues: 125.1480
Evaluate side-chains
  110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0370
   overall best weight:    1.5864

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A 108 ASN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
B  27 GLN
B  75 HIS
C  33 GLN
C  82 ASN
D  56 ASN
E  68 GLN
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
G  33 GLN
G  77 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.054359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.037939 restraints weight = 52303.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.91
r_work: 0.2735 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12633  Z= 0.160
  Angle     :  0.643   7.811  18299  Z= 0.382
  Chirality :  0.044   0.216   2087
  Planarity :  0.005   0.040   1304
  Dihedral  : 31.382 114.057   4071
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 22.83 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.67 (0.31), residues: 730
  helix:  2.34 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.06 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  80 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.16 (12633)
  covalent geometry    : angle       0.64334 /  0.38 (18299)
  hydrogen bonds       : bond        0.05434 /  3.67 (  753)
  hydrogen bonds       : angle       3.07715 /  2.28 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.224 
Fit side-chains
REVERT: C   81 ASP cc_start: 0.9069 (m-30) cc_final: 0.8821 (m-30)
REVERT: C   99 ASP cc_start: 0.8710 (t70) cc_final: 0.7773 (t0)
REVERT: C  101 GLU cc_start: 0.8312 (pm20) cc_final: 0.7848 (pm20)
REVERT: C  121 ASN cc_start: 0.9304 (OUTLIER) cc_final: 0.8706 (t0)
REVERT: D   82 MET cc_start: 0.9353 (tpt) cc_final: 0.9102 (mmm)
REVERT: D   91 ASP cc_start: 0.9322 (t70) cc_final: 0.8962 (t0)
REVERT: D   98 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9094 (mm-40)
REVERT: D  128 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8385 (tp30)
REVERT: G   81 ASP cc_start: 0.9170 (m-30) cc_final: 0.8883 (m-30)
REVERT: G   99 ASP cc_start: 0.9181 (t70) cc_final: 0.8636 (t0)
REVERT: G  121 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8741 (t0)
REVERT: H   58 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8237 (mm-30)
REVERT: H   91 ASP cc_start: 0.9267 (t70) cc_final: 0.8899 (t0)
REVERT: H   94 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8416 (tm-30)
REVERT: H  128 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8380 (tm-30)
  outliers start: 13
  outliers final: 3
  residues processed: 130
  average time/residue: 0.7061
  time to fit residues: 97.2886
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 48 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
E 113 HIS
H 107 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.053211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.036915 restraints weight = 52935.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.92
r_work: 0.2707 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12633  Z= 0.179
  Angle     :  0.620   7.523  18299  Z= 0.368
  Chirality :  0.042   0.210   2087
  Planarity :  0.004   0.038   1304
  Dihedral  : 31.608 114.852   4071
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 21.70 %
    Favored  : 76.21 %
  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:  2.98 (0.31), residues: 730
  helix:  2.56 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.01 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  23 
 TYR   0.010   0.001   TYR H  63 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.18 (12633)
  covalent geometry    : angle       0.61987 /  0.37 (18299)
  hydrogen bonds       : bond        0.05384 /  3.61 (  753)
  hydrogen bonds       : angle       2.88815 /  2.14 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: C   81 ASP cc_start: 0.9114 (m-30) cc_final: 0.8878 (m-30)
REVERT: C   99 ASP cc_start: 0.8639 (t70) cc_final: 0.7835 (t0)
REVERT: C  101 GLU cc_start: 0.8302 (pm20) cc_final: 0.7792 (pm20)
REVERT: C  121 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.8717 (t0)
REVERT: D   82 MET cc_start: 0.9428 (tpt) cc_final: 0.9136 (mmm)
REVERT: D   91 ASP cc_start: 0.9346 (t70) cc_final: 0.8977 (t0)
REVERT: D   94 GLU cc_start: 0.9232 (tp30) cc_final: 0.8928 (tp30)
REVERT: D   98 GLN cc_start: 0.9417 (mm-40) cc_final: 0.9194 (mm-40)
REVERT: D  128 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8375 (tp30)
REVERT: E   69 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8819 (mtp180)
REVERT: F   92 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.9103 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9137 (m-30) cc_final: 0.8887 (m-30)
REVERT: G   83 LYS cc_start: 0.9460 (mttm) cc_final: 0.9079 (tptp)
REVERT: G   99 ASP cc_start: 0.9157 (t70) cc_final: 0.8383 (t0)
REVERT: G  121 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8705 (t0)
REVERT: H   58 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8190 (mm-30)
REVERT: H   91 ASP cc_start: 0.9296 (t0) cc_final: 0.8923 (t0)
REVERT: H   94 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8515 (tm-30)
REVERT: H  128 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8345 (tm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 125
  average time/residue: 0.7439
  time to fit residues: 98.0339
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   69 ARG
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9990
   chunk 85 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 97 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 90 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.053091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.036943 restraints weight = 52919.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 1.92
r_work: 0.2706 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12633  Z= 0.158
  Angle     :  0.607   7.462  18299  Z= 0.360
  Chirality :  0.041   0.208   2087
  Planarity :  0.004   0.039   1304
  Dihedral  : 31.649 116.346   4071
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 23.31 %
    Favored  : 75.24 %
  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:  3.11 (0.31), residues: 730
  helix:  2.66 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.06 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 105 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.16 (12633)
  covalent geometry    : angle       0.60734 /  0.36 (18299)
  hydrogen bonds       : bond        0.04818 /  3.24 (  753)
  hydrogen bonds       : angle       2.80606 /  2.09 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.284 
Fit side-chains
REVERT: C   81 ASP cc_start: 0.9097 (m-30) cc_final: 0.8865 (m-30)
REVERT: C   99 ASP cc_start: 0.8639 (t70) cc_final: 0.7787 (t0)
REVERT: C  101 GLU cc_start: 0.8228 (pm20) cc_final: 0.7695 (pm20)
REVERT: C  121 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.8692 (t0)
REVERT: D   82 MET cc_start: 0.9452 (tpt) cc_final: 0.9126 (mmm)
REVERT: D   91 ASP cc_start: 0.9348 (t70) cc_final: 0.8981 (t0)
REVERT: D   94 GLU cc_start: 0.9234 (tp30) cc_final: 0.8889 (tp30)
REVERT: D   98 GLN cc_start: 0.9395 (mm-40) cc_final: 0.9187 (mm-40)
REVERT: D  128 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8349 (tp30)
REVERT: F   92 ARG cc_start: 0.9474 (OUTLIER) cc_final: 0.9090 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9129 (m-30) cc_final: 0.8915 (m-30)
REVERT: G   99 ASP cc_start: 0.9006 (t70) cc_final: 0.8455 (t0)
REVERT: G  121 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8713 (t0)
REVERT: H   58 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: H   91 ASP cc_start: 0.9291 (t0) cc_final: 0.8924 (t0)
REVERT: H   94 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8484 (tm-30)
REVERT: H  128 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8343 (tm-30)
  outliers start: 9
  outliers final: 3
  residues processed: 123
  average time/residue: 0.8273
  time to fit residues: 107.1662
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 75 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 73 optimal weight:   40.0000
   chunk 86 optimal weight:   30.0000
   chunk 33 optimal weight:    0.9980
   overall best weight:    2.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
G  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.052450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.036280 restraints weight = 52989.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.92
r_work: 0.2689 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12633  Z= 0.180
  Angle     :  0.630   9.559  18299  Z= 0.367
  Chirality :  0.042   0.209   2087
  Planarity :  0.004   0.043   1304
  Dihedral  : 31.768 117.024   4071
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.19 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.17 (0.31), residues: 730
  helix:  2.70 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.05 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  23 
 TYR   0.009   0.001   TYR H  63 
 PHE   0.007   0.001   PHE C  34 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.18 (12633)
  covalent geometry    : angle       0.62989 /  0.37 (18299)
  hydrogen bonds       : bond        0.05098 /  3.44 (  753)
  hydrogen bonds       : angle       2.82723 /  2.10 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.377 
Fit side-chains
REVERT: B   53 GLU cc_start: 0.9099 (tp30) cc_final: 0.8875 (mm-30)
REVERT: C   81 ASP cc_start: 0.9108 (m-30) cc_final: 0.8891 (m-30)
REVERT: C   99 ASP cc_start: 0.8721 (t70) cc_final: 0.7873 (t70)
REVERT: C  101 GLU cc_start: 0.8312 (pm20) cc_final: 0.7754 (pm20)
REVERT: C  121 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.8706 (t0)
REVERT: D   82 MET cc_start: 0.9480 (tpt) cc_final: 0.9135 (mmm)
REVERT: D   91 ASP cc_start: 0.9368 (t70) cc_final: 0.8991 (t0)
REVERT: D   94 GLU cc_start: 0.9235 (tp30) cc_final: 0.8888 (tp30)
REVERT: D   98 GLN cc_start: 0.9397 (mm-40) cc_final: 0.9159 (mm-40)
REVERT: D  128 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8411 (tp30)
REVERT: F   92 ARG cc_start: 0.9471 (OUTLIER) cc_final: 0.9135 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9155 (m-30) cc_final: 0.8952 (m-30)
REVERT: G   99 ASP cc_start: 0.9096 (t70) cc_final: 0.8568 (t0)
REVERT: G  121 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8730 (t0)
REVERT: H   58 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8056 (mm-30)
REVERT: H   91 ASP cc_start: 0.9314 (t0) cc_final: 0.8940 (t0)
REVERT: H   94 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8515 (tm-30)
REVERT: H  128 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8370 (tm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 120
  average time/residue: 0.7637
  time to fit residues: 96.9765
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 92 optimal weight:   10.0000
   chunk 76 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9980
   chunk 90 optimal weight:   20.0000
   chunk 68 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.052230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.036115 restraints weight = 53121.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 1.92
r_work: 0.2688 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12633  Z= 0.158
  Angle     :  0.618   8.706  18299  Z= 0.361
  Chirality :  0.041   0.208   2087
  Planarity :  0.004   0.037   1304
  Dihedral  : 31.797 119.091   4071
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.19 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.25 (0.31), residues: 730
  helix:  2.76 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.09 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 105 
 TYR   0.009   0.001   TYR H  63 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.16 (12633)
  covalent geometry    : angle       0.61834 /  0.36 (18299)
  hydrogen bonds       : bond        0.04475 /  2.98 (  753)
  hydrogen bonds       : angle       2.72377 /  2.03 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 THR cc_start: 0.9600 (OUTLIER) cc_final: 0.9328 (m)
REVERT: B   53 GLU cc_start: 0.9095 (tp30) cc_final: 0.8852 (mm-30)
REVERT: C   28 MET cc_start: 0.9078 (ppp) cc_final: 0.8872 (ppp)
REVERT: C   81 ASP cc_start: 0.9105 (m-30) cc_final: 0.8883 (m-30)
REVERT: C   83 LYS cc_start: 0.9402 (tppp) cc_final: 0.9195 (tptp)
REVERT: C   99 ASP cc_start: 0.8719 (t70) cc_final: 0.7695 (t70)
REVERT: C  101 GLU cc_start: 0.8308 (pm20) cc_final: 0.7815 (pm20)
REVERT: C  121 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.8679 (t0)
REVERT: D   82 MET cc_start: 0.9496 (tpt) cc_final: 0.9107 (mmm)
REVERT: D   91 ASP cc_start: 0.9367 (t70) cc_final: 0.8993 (t0)
REVERT: D   94 GLU cc_start: 0.9238 (tp30) cc_final: 0.8824 (tp30)
REVERT: D   98 GLN cc_start: 0.9390 (mm-40) cc_final: 0.9125 (mm-40)
REVERT: D  128 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8407 (tp30)
REVERT: F   92 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.9105 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9166 (m-30) cc_final: 0.8947 (m-30)
REVERT: G   99 ASP cc_start: 0.9050 (t70) cc_final: 0.8480 (t0)
REVERT: G  100 GLU cc_start: 0.8632 (tp30) cc_final: 0.8431 (tp30)
REVERT: G  104 LYS cc_start: 0.9590 (ttmt) cc_final: 0.9312 (ttmm)
REVERT: G  121 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8701 (t0)
REVERT: H   58 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8129 (mm-30)
REVERT: H   91 ASP cc_start: 0.9306 (t0) cc_final: 0.8932 (t0)
REVERT: H   94 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8540 (tm-30)
REVERT: H  128 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8370 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 129
  average time/residue: 0.7320
  time to fit residues: 100.2024
Evaluate side-chains
  122 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 89 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9990
   chunk 88 optimal weight:   30.0000
   chunk 84 optimal weight:   20.0000
   chunk 3 optimal weight:    0.8980
   chunk 91 optimal weight:   20.0000
   chunk 2 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  82 ASN

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 = 0.051126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.035194 restraints weight = 52921.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.92
r_work: 0.2652 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12633  Z= 0.207
  Angle     :  0.672  11.990  18299  Z= 0.378
  Chirality :  0.043   0.213   2087
  Planarity :  0.004   0.043   1304
  Dihedral  : 31.984 119.761   4071
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.31 %
    Favored  : 74.92 %
  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:  3.17 (0.31), residues: 730
  helix:  2.73 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.06 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 105 
 TYR   0.012   0.002   TYR F  88 
 PHE   0.007   0.001   PHE D  65 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.21 (12633)
  covalent geometry    : angle       0.67183 /  0.38 (18299)
  hydrogen bonds       : bond        0.05924 /  4.03 (  753)
  hydrogen bonds       : angle       2.85590 /  2.12 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 THR cc_start: 0.9573 (OUTLIER) cc_final: 0.9292 (m)
REVERT: C   99 ASP cc_start: 0.8747 (t70) cc_final: 0.7805 (t0)
REVERT: C  101 GLU cc_start: 0.8307 (pm20) cc_final: 0.7687 (pm20)
REVERT: C  121 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8741 (t0)
REVERT: D   82 MET cc_start: 0.9521 (tpt) cc_final: 0.9167 (mmm)
REVERT: D   91 ASP cc_start: 0.9373 (t70) cc_final: 0.9002 (t0)
REVERT: D   94 GLU cc_start: 0.9238 (tp30) cc_final: 0.8602 (tm-30)
REVERT: D   98 GLN cc_start: 0.9399 (mm-40) cc_final: 0.9055 (mm-40)
REVERT: D  128 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8431 (tp30)
REVERT: E   79 LYS cc_start: 0.9175 (tptp) cc_final: 0.8910 (tttp)
REVERT: G   81 ASP cc_start: 0.9172 (m-30) cc_final: 0.8900 (m-30)
REVERT: G   99 ASP cc_start: 0.9124 (t70) cc_final: 0.8615 (t0)
REVERT: G  100 GLU cc_start: 0.8703 (tp30) cc_final: 0.8247 (tm-30)
REVERT: G  104 LYS cc_start: 0.9578 (ttmt) cc_final: 0.9262 (ttmm)
REVERT: G  121 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8749 (t0)
REVERT: H   58 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8083 (mm-30)
REVERT: H   91 ASP cc_start: 0.9325 (t0) cc_final: 0.8957 (t0)
REVERT: H   94 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8548 (tm-30)
REVERT: H  128 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8400 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 117
  average time/residue: 0.8041
  time to fit residues: 99.6304
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 99 optimal weight:   30.0000
   chunk 16 optimal weight:    3.9990
   chunk 75 optimal weight:   20.0000
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:   40.0000
   chunk 86 optimal weight:   30.0000
   chunk 40 optimal weight:    0.8980
   chunk 72 optimal weight:   30.0000
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.051629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.035463 restraints weight = 52976.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 1.95
r_work: 0.2666 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12633  Z= 0.150
  Angle     :  0.637  11.085  18299  Z= 0.365
  Chirality :  0.042   0.213   2087
  Planarity :  0.004   0.038   1304
  Dihedral  : 31.931 121.931   4071
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.79 %
    Favored  : 74.44 %
  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:  3.22 (0.31), residues: 730
  helix:  2.76 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.03 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 105 
 TYR   0.010   0.001   TYR F  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.001   HIS D  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.15 (12633)
  covalent geometry    : angle       0.63717 /  0.36 (18299)
  hydrogen bonds       : bond        0.04417 /  2.96 (  753)
  hydrogen bonds       : angle       2.71610 /  2.01 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.9114 (tptp) cc_final: 0.8829 (tttp)
REVERT: A   80 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9280 (m)
REVERT: C   82 ASN cc_start: 0.9415 (t0) cc_final: 0.9059 (t0)
REVERT: C   99 ASP cc_start: 0.8716 (t70) cc_final: 0.7837 (t0)
REVERT: C  100 GLU cc_start: 0.8138 (pm20) cc_final: 0.7936 (pm20)
REVERT: C  101 GLU cc_start: 0.8252 (pm20) cc_final: 0.7735 (pm20)
REVERT: C  121 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8734 (t0)
REVERT: D   82 MET cc_start: 0.9536 (tpt) cc_final: 0.9082 (mmm)
REVERT: D   91 ASP cc_start: 0.9371 (t70) cc_final: 0.9003 (t0)
REVERT: D   94 GLU cc_start: 0.9227 (tp30) cc_final: 0.8609 (tm-30)
REVERT: D   98 GLN cc_start: 0.9398 (mm-40) cc_final: 0.9060 (mm-40)
REVERT: D  128 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8219 (tm-30)
REVERT: E   80 THR cc_start: 0.9569 (m) cc_final: 0.9356 (p)
REVERT: F   92 ARG cc_start: 0.9451 (OUTLIER) cc_final: 0.9098 (mtp-110)
REVERT: G   28 MET cc_start: 0.9158 (ttp) cc_final: 0.8850 (ptt)
REVERT: G   81 ASP cc_start: 0.9167 (m-30) cc_final: 0.8902 (m-30)
REVERT: G   99 ASP cc_start: 0.9136 (t70) cc_final: 0.8529 (t0)
REVERT: G  121 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8751 (t0)
REVERT: H   58 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8100 (mm-30)
REVERT: H   91 ASP cc_start: 0.9329 (t0) cc_final: 0.8966 (t0)
REVERT: H   94 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8591 (tm-30)
REVERT: H  128 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8390 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 125
  average time/residue: 0.8113
  time to fit residues: 107.2984
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 89 optimal weight:   20.0000
   chunk 7 optimal weight:    3.9990
   chunk 91 optimal weight:   20.0000
   chunk 74 optimal weight:   30.0000
   chunk 9 optimal weight:    0.0570
   chunk 88 optimal weight:   30.0000
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0370
   overall best weight:    0.9580

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.052159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.036334 restraints weight = 52454.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 1.91
r_work: 0.2694 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12633  Z= 0.132
  Angle     :  0.634  12.085  18299  Z= 0.365
  Chirality :  0.041   0.206   2087
  Planarity :  0.004   0.043   1304
  Dihedral  : 31.731 124.318   4071
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 23.95 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.26 (0.31), residues: 730
  helix:  2.78 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.02 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H 105 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.13 (12633)
  covalent geometry    : angle       0.63355 /  0.36 (18299)
  hydrogen bonds       : bond        0.04053 /  2.70 (  753)
  hydrogen bonds       : angle       2.63815 /  1.96 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.9391 (t0) cc_final: 0.8953 (t0)
REVERT: C   99 ASP cc_start: 0.8721 (t70) cc_final: 0.7765 (t70)
REVERT: C  101 GLU cc_start: 0.8215 (pm20) cc_final: 0.7695 (pm20)
REVERT: C  121 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8697 (t0)
REVERT: D   82 MET cc_start: 0.9533 (tpt) cc_final: 0.9247 (mmm)
REVERT: D   91 ASP cc_start: 0.9357 (t70) cc_final: 0.8996 (t0)
REVERT: D   94 GLU cc_start: 0.9223 (tp30) cc_final: 0.8643 (tm-30)
REVERT: D  128 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8138 (tm-30)
REVERT: F   92 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.9088 (mtp-110)
REVERT: G   28 MET cc_start: 0.9190 (ttp) cc_final: 0.8864 (ptt)
REVERT: G   81 ASP cc_start: 0.9164 (m-30) cc_final: 0.8907 (m-30)
REVERT: G   99 ASP cc_start: 0.9100 (t70) cc_final: 0.8594 (t0)
REVERT: G  121 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8729 (t0)
REVERT: H   58 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8114 (mm-30)
REVERT: H   91 ASP cc_start: 0.9279 (t0) cc_final: 0.8900 (t0)
REVERT: H   94 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8606 (tm-30)
REVERT: H  128 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8385 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 125
  average time/residue: 0.7521
  time to fit residues: 99.7280
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0060
   chunk 86 optimal weight:   30.0000
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.1400

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A  76 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.052245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.036468 restraints weight = 52973.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 1.94
r_work: 0.2698 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12633  Z= 0.135
  Angle     :  0.629  12.222  18299  Z= 0.362
  Chirality :  0.041   0.205   2087
  Planarity :  0.004   0.038   1304
  Dihedral  : 31.701 125.271   4071
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 24.12 %
    Favored  : 74.76 %
  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:  3.36 (0.31), residues: 730
  helix:  2.87 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.02 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 105 
 TYR   0.008   0.001   TYR F  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.14 (12633)
  covalent geometry    : angle       0.62855 /  0.36 (18299)
  hydrogen bonds       : bond        0.04123 /  2.75 (  753)
  hydrogen bonds       : angle       2.61790 /  1.94 ( 1902)

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

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: C   99 ASP cc_start: 0.8710 (t70) cc_final: 0.7832 (t70)
REVERT: C  101 GLU cc_start: 0.8240 (pm20) cc_final: 0.7752 (pm20)
REVERT: C  121 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8679 (t0)
REVERT: D   82 MET cc_start: 0.9531 (tpt) cc_final: 0.9298 (mmm)
REVERT: D   91 ASP cc_start: 0.9362 (t70) cc_final: 0.8985 (t0)
REVERT: D   94 GLU cc_start: 0.9230 (tp30) cc_final: 0.8686 (tm-30)
REVERT: D  106 TYR cc_start: 0.8871 (m-10) cc_final: 0.8343 (m-10)
REVERT: D  128 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8125 (tm-30)
REVERT: F   92 ARG cc_start: 0.9408 (OUTLIER) cc_final: 0.9198 (mtp-110)
REVERT: G   28 MET cc_start: 0.9181 (ttp) cc_final: 0.8868 (ptt)
REVERT: G   81 ASP cc_start: 0.9160 (m-30) cc_final: 0.8934 (m-30)
REVERT: G   99 ASP cc_start: 0.9156 (t70) cc_final: 0.8676 (t0)
REVERT: G  121 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8710 (t0)
REVERT: H   58 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8137 (mm-30)
REVERT: H   91 ASP cc_start: 0.9283 (t0) cc_final: 0.8905 (t0)
REVERT: H   94 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8596 (tm-30)
REVERT: H  128 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8370 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 119
  average time/residue: 0.8053
  time to fit residues: 101.3130
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 90 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 83 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  82 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.052480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.036756 restraints weight = 52869.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.92
r_work: 0.2706 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8856
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      :  0.002   0.049  12633  Z= 0.133
  Angle     :  0.627  12.464  18299  Z= 0.362
  Chirality :  0.040   0.204   2087
  Planarity :  0.004   0.041   1304
  Dihedral  : 31.628 126.626   4071
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 24.44 %
    Favored  : 74.12 %
  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:  3.40 (0.31), residues: 730
  helix:  2.89 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.05 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 105 
 TYR   0.014   0.001   TYR B  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.000   HIS D  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.13 (12633)
  covalent geometry    : angle       0.62737 /  0.36 (18299)
  hydrogen bonds       : bond        0.03949 /  2.62 (  753)
  hydrogen bonds       : angle       2.56766 /  1.91 ( 1902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3241.54 seconds
wall clock time: 56 minutes 0.60 seconds (3360.60 seconds total)