Starting phenix.real_space_refine
on Wed Mar  4 05:04:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pii_13437/03_2026/7pii_13437_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pii_13437/03_2026/7pii_13437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pii_13437/03_2026/7pii_13437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pii_13437/03_2026/7pii_13437.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pii_13437/03_2026/7pii_13437_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pii_13437/03_2026/7pii_13437_neut.cif"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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     244      5.49       5
     S       8      5.16       5
     C    6321      2.51       5
     N    2070      2.21       5
     O    2549      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11192
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 799
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 755
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 770
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 784
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 2506
          Classifications: {'DNA': 122}
          Link IDs: {'rna3p': 121}
    Chain: "J"
      Number of atoms: 2514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 2514
          Classifications: {'DNA': 123}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 122}
    Chain: "K"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 178
          Classifications: {'peptide': 21}
          Link IDs: {'PTRANS': 1, 'TRANS': 19}
    Chain: "L"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 185
          Classifications: {'peptide': 22}
          Link IDs: {'PTRANS': 1, 'TRANS': 20}
  Time building chain proxies: 2.11, per 1000 atoms: 0.19
  Number of scatterers: 11192
  At special positions: 0
  Unit cell: (80.607, 114.678, 123.819, 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       8     16.00
     P     244     15.00
     O    2549      8.00
     N    2070      7.00
     C    6321      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: 0.88
  Conformation dependent library (CDL) restraints added in 315.9 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1450

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      68.9% alpha, 2.6% beta
      121 base pairs and 220 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.629A  pdb=" N   LYS A  49 " --> pdb=" O   GLN A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.618A  pdb=" N   LEU A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 138
      removed outlier: 5.628A  pdb=" N   LEU A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   GLU A 136 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLU A 137 " --> pdb=" O   ARG A 133 " (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 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.409A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 47 through 55
    Processing helix  chain 'E' and resid 63 through 78
    Processing helix  chain 'E' and resid 87 through 116
    Processing helix  chain 'E' and resid 122 through 134
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.479A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.727A  pdb=" N   ASN A  85 " --> 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 120 through 121
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.452A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86
      removed outlier: 6.916A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.180A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'L' and resid 516 through 517

    408 hydrogen bonds defined for protein.
    1221 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      282 hydrogen bonds
      564 hydrogen bond angles
      0 basepair planarities
      121 basepair parallelities
      220 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1668
        1.32 -     1.45: 4128
        1.45 -     1.57: 5598
        1.57 -     1.69: 487
        1.69 -     1.81: 14
  Bond restraints: 11895
  Sorted by residual:
  bond pdb=" N   ILE D  54 "
       pdb=" CA  ILE D  54 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.18e-02 7.18e+03 1.04e+01
  bond pdb=" N   VAL K 517 "
       pdb=" CA  VAL K 517 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.20e-02 6.94e+03 9.56e+00
  bond pdb=" N   VAL K 533 "
       pdb=" CA  VAL K 533 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.17e-02 7.31e+03 9.22e+00
  bond pdb=" N   THR K 518 "
       pdb=" CA  THR K 518 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.17e-02 7.31e+03 9.20e+00
  bond pdb=" N   VAL K 532 "
       pdb=" CA  VAL K 532 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.037 1.24e-02 6.50e+03 8.70e+00
  ... (remaining 11890 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 16152
        1.63 -     3.27: 871
        3.27 -     4.90: 83
        4.90 -     6.54: 9
        6.54 -     8.17: 1
  Bond angle restraints: 17116
  Sorted by residual:
  angle pdb=" N   LEU F  49 "
        pdb=" CA  LEU F  49 "
        pdb=" C   LEU F  49 "
      ideal   model   delta    sigma   weight residual
     113.18  108.67    4.51 1.21e+00 6.83e-01 1.39e+01
  angle pdb=" N   GLN B  27 "
        pdb=" CA  GLN B  27 "
        pdb=" C   GLN B  27 "
      ideal   model   delta    sigma   weight residual
     113.01  108.59    4.42 1.20e+00 6.94e-01 1.36e+01
  angle pdb=" N   VAL E 119 "
        pdb=" CA  VAL E 119 "
        pdb=" C   VAL E 119 "
      ideal   model   delta    sigma   weight residual
     113.10  109.53    3.57 9.70e-01 1.06e+00 1.36e+01
  angle pdb=" CA  SER K 524 "
        pdb=" C   SER K 524 "
        pdb=" O   SER K 524 "
      ideal   model   delta    sigma   weight residual
     122.37  118.26    4.11 1.15e+00 7.56e-01 1.28e+01
  angle pdb=" N   TYR H  37 "
        pdb=" CA  TYR H  37 "
        pdb=" C   TYR H  37 "
      ideal   model   delta    sigma   weight residual
     113.21  109.43    3.78 1.15e+00 7.56e-01 1.08e+01
  ... (remaining 17111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.25: 5305
       35.25 -    70.50: 1265
       70.50 -   105.75: 23
      105.75 -   141.01: 1
      141.01 -   176.26: 2
  Dihedral angle restraints: 6596
    sinusoidal: 4351
      harmonic: 2245
  Sorted by residual:
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.05  -25.95     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  HIS F  75 "
           pdb=" C   HIS F  75 "
           pdb=" N   ALA F  76 "
           pdb=" CA  ALA F  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  ARG E 133 "
           pdb=" C   ARG E 133 "
           pdb=" N   GLY E 134 "
           pdb=" CA  GLY E 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.22   21.78     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 6593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1668
       0.063 -    0.126: 252
       0.126 -    0.189: 24
       0.189 -    0.252: 3
       0.252 -    0.315: 1
  Chirality restraints: 1948
  Sorted by residual:
  chirality pdb=" CA  TYR E 110 "
            pdb=" N   TYR E 110 "
            pdb=" C   TYR E 110 "
            pdb=" CB  TYR E 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  ARG E  80 "
            pdb=" N   ARG E  80 "
            pdb=" C   ARG E  80 "
            pdb=" CB  ARG E  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.85e-01
  ... (remaining 1945 not shown)

  Planarity restraints: 1307
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I   5 "    0.029 2.00e-02 2.50e+03   1.40e-02 4.92e+00
        pdb=" N1   DT I   5 "   -0.031 2.00e-02 2.50e+03
        pdb=" C2   DT I   5 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2   DT I   5 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DT I   5 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT I   5 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT I   5 "    0.010 2.00e-02 2.50e+03
        pdb=" C5   DT I   5 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I   5 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT I   5 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  57 "   -0.029 2.00e-02 2.50e+03   1.27e-02 4.45e+00
        pdb=" N9   DA I  57 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA I  57 "    0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I  57 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  57 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I  57 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DA I  57 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 118 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   ARG E 118 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ARG E 118 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL E 119 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1304 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2013
        2.76 -     3.30: 10136
        3.30 -     3.83: 22576
        3.83 -     4.37: 27405
        4.37 -     4.90: 37724
  Nonbonded interactions: 99854
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   SER C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG1 THR L 514 "
            pdb=" N   SER L 515 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" NH2 ARG E  69 "
            pdb=" OP2  DA I  17 "
     model   vdw
     2.277 3.120
  ... (remaining 99849 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 46 through 139)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 24 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 15 through 111)
  selection = (chain 'G' and resid 15 through 111)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = (chain 'L' and resid 515 through 535)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.620
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.600
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3661
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      :  0.010   0.054  11895  Z= 0.464
  Angle     :  0.776   8.174  17116  Z= 0.492
  Chirality :  0.047   0.315   1948
  Planarity :  0.004   0.038   1307
  Dihedral  : 28.133 176.257   5146
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 13.53 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.27), residues: 759
  helix:  0.24 (0.20), residues: 541
  sheet:  None (None), residues: 0
  loop : -2.63 (0.31), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  35 
 TYR   0.014   0.002   TYR F  51 
 PHE   0.011   0.002   PHE A  67 
 TRP   0.007   0.001   TRP K 531 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00970 (11895)
  covalent geometry    : angle       0.77623 (17116)
  hydrogen bonds       : bond        0.13500 (  690)
  hydrogen bonds       : angle       4.69526 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 171
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  107 GLU cc_start: 0.4059 (mt-10) cc_final: 0.3831 (mt-10)
REVERT: A  137 GLU cc_start: 0.4620 (tt0) cc_final: 0.4236 (tt0)
REVERT: B   44 LYS cc_start: 0.5387 (mtmt) cc_final: 0.4830 (tttt)
REVERT: B   78 ARG cc_start: 0.5414 (mtm-85) cc_final: 0.5186 (mtm110)
REVERT: C   20 ARG cc_start: 0.4966 (ttm110) cc_final: 0.4624 (mtm180)
REVERT: D   71 GLU cc_start: 0.4649 (tm-30) cc_final: 0.4446 (tp30)
REVERT: E   57 SER cc_start: 0.5724 (t) cc_final: 0.5509 (p)
REVERT: E   82 VAL cc_start: 0.4382 (OUTLIER) cc_final: 0.4164 (p)
REVERT: E   83 ASP cc_start: 0.6312 (p0) cc_final: 0.6030 (t70)
REVERT: F   31 LYS cc_start: 0.5009 (mttp) cc_final: 0.4705 (mtpt)
REVERT: F   44 LYS cc_start: 0.5327 (tttt) cc_final: 0.4232 (mttt)
REVERT: F   63 GLU cc_start: 0.5441 (mt-10) cc_final: 0.5168 (mt-10)
REVERT: F   91 LYS cc_start: 0.5476 (tttm) cc_final: 0.5205 (ttpp)
REVERT: G   36 LYS cc_start: 0.5899 (mptt) cc_final: 0.5657 (pttt)
REVERT: G  104 GLN cc_start: 0.5425 (mm-40) cc_final: 0.5119 (mm110)
REVERT: L  525 ARG cc_start: 0.5300 (mtm-85) cc_final: 0.5074 (mtt-85)
  outliers start: 2
  outliers final: 0
  residues processed: 173
  average time/residue: 0.9603
  time to fit residues: 173.5576
Evaluate side-chains
  119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  24 GLN
C  94 ASN
C 104 GLN
D  47 GLN
D  84 ASN
E  87 GLN
E 115 HIS
F  27 GLN
F  75 HIS
F  93 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  94 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.163311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.116724 restraints weight = 13030.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 0.98
r_work: 0.3122 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11895  Z= 0.180
  Angle     :  0.625   7.654  17116  Z= 0.370
  Chirality :  0.036   0.134   1948
  Planarity :  0.004   0.040   1307
  Dihedral  : 30.965 177.887   3648
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.66 %
    Favored  : 78.38 %
  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:  1.01 (0.28), residues: 759
  helix:  1.58 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.75 (0.35), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 526 
 TYR   0.010   0.002   TYR E 110 
 PHE   0.012   0.002   PHE A  67 
 TRP   0.004   0.001   TRP A  47 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (11895)
  covalent geometry    : angle       0.62477 (17116)
  hydrogen bonds       : bond        0.04821 (  690)
  hydrogen bonds       : angle       3.29353 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.292 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8181 (mttt) cc_final: 0.7904 (tttt)
REVERT: D   46 LYS cc_start: 0.8365 (mmpt) cc_final: 0.7917 (mppt)
REVERT: F   44 LYS cc_start: 0.8770 (tttt) cc_final: 0.7901 (mttt)
REVERT: G   73 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7793 (t0)
REVERT: H   57 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7980 (mtpt)
REVERT: H   68 ASP cc_start: 0.9163 (t0) cc_final: 0.8928 (t70)
REVERT: L  525 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7398 (mtt-85)
  outliers start: 19
  outliers final: 5
  residues processed: 139
  average time/residue: 0.9277
  time to fit residues: 135.2095
Evaluate side-chains
  126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   57 LYS
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0970
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
C  24 GLN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.163393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.115256 restraints weight = 13069.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.03
r_work: 0.3113 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.182
  Angle     :  0.615   7.899  17116  Z= 0.364
  Chirality :  0.036   0.137   1948
  Planarity :  0.004   0.045   1307
  Dihedral  : 30.850 173.490   3647
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.28 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.29), residues: 759
  helix:  1.97 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.20 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 133 
 TYR   0.011   0.002   TYR E 110 
 PHE   0.013   0.002   PHE A  67 
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (11895)
  covalent geometry    : angle       0.61483 (17116)
  hydrogen bonds       : bond        0.04931 (  690)
  hydrogen bonds       : angle       3.24732 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8008 (mtp85)
REVERT: B   31 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8295 (mtpt)
REVERT: B   44 LYS cc_start: 0.8197 (mttt) cc_final: 0.7902 (tttt)
REVERT: C   38 ASN cc_start: 0.7807 (p0) cc_final: 0.7531 (p0)
REVERT: C   77 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.5314 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5657 (pt) cc_final: 0.5066 (pp)
REVERT: D   46 LYS cc_start: 0.8306 (mmpt) cc_final: 0.7861 (mppt)
REVERT: E   49 LYS cc_start: 0.8126 (tttp) cc_final: 0.7873 (tmtp)
REVERT: F   44 LYS cc_start: 0.8816 (tttt) cc_final: 0.7913 (mttt)
REVERT: H   68 ASP cc_start: 0.9171 (t0) cc_final: 0.8946 (t70)
REVERT: K  525 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6895 (mpt180)
REVERT: L  525 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7403 (mtt-85)
  outliers start: 21
  outliers final: 6
  residues processed: 136
  average time/residue: 0.9583
  time to fit residues: 136.4164
Evaluate side-chains
  127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain F residue   79 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.163228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.116024 restraints weight = 13098.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 0.98
r_work: 0.3112 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.186
  Angle     :  0.617   7.719  17116  Z= 0.364
  Chirality :  0.036   0.140   1948
  Planarity :  0.004   0.051   1307
  Dihedral  : 30.753 172.481   3647
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.44 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.29), residues: 759
  helix:  2.05 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.00 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  52 
 TYR   0.012   0.002   TYR B  51 
 PHE   0.012   0.002   PHE A  67 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (11895)
  covalent geometry    : angle       0.61695 (17116)
  hydrogen bonds       : bond        0.04911 (  690)
  hydrogen bonds       : angle       3.23413 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8122 (mtp85)
REVERT: B   44 LYS cc_start: 0.8192 (mttt) cc_final: 0.7928 (tttt)
REVERT: C   77 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.5387 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5517 (pt) cc_final: 0.4989 (pp)
REVERT: E   49 LYS cc_start: 0.8180 (tttp) cc_final: 0.7906 (tmtp)
REVERT: F   44 LYS cc_start: 0.8819 (tttt) cc_final: 0.7923 (mttt)
REVERT: G   73 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7791 (t0)
REVERT: H   47 GLN cc_start: 0.8342 (mt0) cc_final: 0.8120 (mt0)
REVERT: H   57 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8018 (mtpt)
REVERT: H   68 ASP cc_start: 0.9144 (t0) cc_final: 0.8938 (t70)
REVERT: L  525 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7520 (mtt-85)
  outliers start: 19
  outliers final: 7
  residues processed: 129
  average time/residue: 0.9606
  time to fit residues: 129.5435
Evaluate side-chains
  125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   57 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.163733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.116544 restraints weight = 13060.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 0.99
r_work: 0.3110 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.174
  Angle     :  0.606   7.468  17116  Z= 0.359
  Chirality :  0.036   0.140   1948
  Planarity :  0.004   0.042   1307
  Dihedral  : 30.727 172.063   3647
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.75 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.29), residues: 759
  helix:  2.16 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.85 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 525 
 TYR   0.012   0.002   TYR B  51 
 PHE   0.012   0.002   PHE A  78 
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (11895)
  covalent geometry    : angle       0.60596 (17116)
  hydrogen bonds       : bond        0.04782 (  690)
  hydrogen bonds       : angle       3.20720 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8064 (mtp85)
REVERT: B   44 LYS cc_start: 0.8189 (mttt) cc_final: 0.7964 (tttt)
REVERT: C   38 ASN cc_start: 0.7647 (p0) cc_final: 0.7405 (p0)
REVERT: C   77 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.5418 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5711 (pt) cc_final: 0.5235 (pp)
REVERT: D   46 LYS cc_start: 0.8397 (mmpt) cc_final: 0.8066 (mppt)
REVERT: E   49 LYS cc_start: 0.8223 (tttp) cc_final: 0.7992 (tmtp)
REVERT: F   44 LYS cc_start: 0.8820 (tttt) cc_final: 0.7995 (mttt)
REVERT: G   73 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7828 (t0)
REVERT: H   47 GLN cc_start: 0.8360 (mt0) cc_final: 0.8148 (mt0)
REVERT: H   68 ASP cc_start: 0.9124 (t0) cc_final: 0.8907 (t70)
REVERT: K  525 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7199 (mtt180)
REVERT: K  526 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7318 (mpt-90)
REVERT: L  525 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7502 (mtt-85)
  outliers start: 18
  outliers final: 7
  residues processed: 130
  average time/residue: 0.9374
  time to fit residues: 127.6726
Evaluate side-chains
  129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain K residue  526 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0670
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    1.3324

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  47 GLN
F  64 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.161337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.113728 restraints weight = 13025.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 0.99
r_work: 0.3070 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11895  Z= 0.231
  Angle     :  0.662   8.377  17116  Z= 0.387
  Chirality :  0.039   0.142   1948
  Planarity :  0.005   0.050   1307
  Dihedral  : 31.037 176.499   3647
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.91 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.29), residues: 759
  helix:  1.90 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.90 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 525 
 TYR   0.014   0.002   TYR B  51 
 PHE   0.017   0.002   PHE A  78 
 TRP   0.004   0.001   TRP E  47 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (11895)
  covalent geometry    : angle       0.66178 (17116)
  hydrogen bonds       : bond        0.05644 (  690)
  hydrogen bonds       : angle       3.35286 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8079 (mtp85)
REVERT: B   44 LYS cc_start: 0.8143 (mttt) cc_final: 0.7871 (tttt)
REVERT: C   77 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.5473 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5696 (pt) cc_final: 0.5271 (pp)
REVERT: D   46 LYS cc_start: 0.8441 (mmpt) cc_final: 0.7914 (mppt)
REVERT: E   49 LYS cc_start: 0.8120 (tttp) cc_final: 0.7829 (tmtp)
REVERT: F   44 LYS cc_start: 0.8881 (tttt) cc_final: 0.7901 (mttt)
REVERT: G   73 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7771 (t0)
REVERT: K  523 ILE cc_start: 0.8210 (mp) cc_final: 0.7940 (mt)
REVERT: K  525 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7115 (mtt180)
REVERT: K  526 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7210 (mpt-90)
REVERT: L  525 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7485 (mtt-85)
  outliers start: 18
  outliers final: 7
  residues processed: 131
  average time/residue: 0.9155
  time to fit residues: 125.7268
Evaluate side-chains
  130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain K residue  526 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  47 GLN
F  64 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN
H  82 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.162712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.115190 restraints weight = 12965.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 0.94
r_work: 0.3101 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11895  Z= 0.176
  Angle     :  0.623   7.945  17116  Z= 0.368
  Chirality :  0.036   0.135   1948
  Planarity :  0.004   0.066   1307
  Dihedral  : 30.942 177.188   3647
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.22 %
    Favored  : 76.83 %
  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:  1.88 (0.29), residues: 759
  helix:  2.02 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.77 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  52 
 TYR   0.012   0.002   TYR B  51 
 PHE   0.011   0.002   PHE E  67 
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (11895)
  covalent geometry    : angle       0.62295 (17116)
  hydrogen bonds       : bond        0.05025 (  690)
  hydrogen bonds       : angle       3.30231 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8040 (mtp85)
REVERT: B   44 LYS cc_start: 0.8114 (mttt) cc_final: 0.7882 (tttt)
REVERT: B   49 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8311 (mt)
REVERT: C   77 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.5399 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5732 (pt) cc_final: 0.5356 (pp)
REVERT: D   46 LYS cc_start: 0.8436 (mmpt) cc_final: 0.7966 (mppt)
REVERT: E   49 LYS cc_start: 0.8171 (tttp) cc_final: 0.7907 (tmtp)
REVERT: E   77 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7734 (mtpt)
REVERT: F   44 LYS cc_start: 0.8839 (tttt) cc_final: 0.7920 (mttt)
REVERT: G   73 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7797 (t0)
REVERT: K  523 ILE cc_start: 0.8183 (mp) cc_final: 0.7904 (mt)
REVERT: K  525 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7126 (mtt180)
REVERT: K  526 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7232 (mpt-90)
REVERT: L  525 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7479 (mtt-85)
  outliers start: 19
  outliers final: 6
  residues processed: 131
  average time/residue: 0.9071
  time to fit residues: 124.4537
Evaluate side-chains
  131 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain K residue  526 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0070
   chunk 4 optimal weight:    0.3980
   chunk 72 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C  38 ASN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.163714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.116279 restraints weight = 13047.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.00
r_work: 0.3113 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11895  Z= 0.164
  Angle     :  0.608   7.382  17116  Z= 0.361
  Chirality :  0.035   0.136   1948
  Planarity :  0.004   0.082   1307
  Dihedral  : 30.807 177.960   3647
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.68 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.29), residues: 759
  helix:  2.21 (0.21), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.70 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  52 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.010   0.002   PHE E  67 
 TRP   0.004   0.001   TRP K 530 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (11895)
  covalent geometry    : angle       0.60827 (17116)
  hydrogen bonds       : bond        0.04704 (  690)
  hydrogen bonds       : angle       3.23708 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8117 (mttt) cc_final: 0.7856 (tttt)
REVERT: B   92 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8159 (ptm160)
REVERT: C   77 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5282 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5634 (pt) cc_final: 0.5274 (pp)
REVERT: D   46 LYS cc_start: 0.8443 (mmpt) cc_final: 0.7929 (mppt)
REVERT: E   49 LYS cc_start: 0.8111 (tttp) cc_final: 0.7830 (tmtp)
REVERT: E   77 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7660 (mtpt)
REVERT: F   44 LYS cc_start: 0.8837 (tttt) cc_final: 0.7895 (mttt)
REVERT: G   73 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7782 (t0)
REVERT: G   91 GLU cc_start: 0.8140 (pt0) cc_final: 0.7930 (tt0)
REVERT: H   47 GLN cc_start: 0.8550 (mt0) cc_final: 0.8330 (mt0)
REVERT: K  523 ILE cc_start: 0.8069 (mp) cc_final: 0.7775 (mt)
REVERT: K  525 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7102 (mtt180)
REVERT: K  526 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7192 (mpt-90)
REVERT: L  525 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7497 (mtt-85)
  outliers start: 19
  outliers final: 7
  residues processed: 133
  average time/residue: 0.9570
  time to fit residues: 133.2571
Evaluate side-chains
  133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue  116 LYS
Chi-restraints excluded: chain K residue  526 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0970
   chunk 2 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0010
   chunk 53 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C  38 ASN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.164397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.116432 restraints weight = 12963.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.00
r_work: 0.3136 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11895  Z= 0.153
  Angle     :  0.601   7.431  17116  Z= 0.357
  Chirality :  0.035   0.134   1948
  Planarity :  0.004   0.088   1307
  Dihedral  : 30.743 178.255   3647
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.53 %
    Favored  : 76.83 %
  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:  2.22 (0.29), residues: 759
  helix:  2.27 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.62 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A  52 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.004   0.001   TRP K 530 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11895)
  covalent geometry    : angle       0.60129 (17116)
  hydrogen bonds       : bond        0.04532 (  690)
  hydrogen bonds       : angle       3.21236 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.191 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8087 (mttt) cc_final: 0.7850 (tttt)
REVERT: B   92 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8166 (ptm160)
REVERT: C   77 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.5229 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5652 (pt) cc_final: 0.5288 (pp)
REVERT: D   46 LYS cc_start: 0.8414 (mmpt) cc_final: 0.7912 (mppt)
REVERT: E   49 LYS cc_start: 0.8153 (tttp) cc_final: 0.7876 (tmtp)
REVERT: E   77 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7587 (mtpt)
REVERT: F   44 LYS cc_start: 0.8822 (tttt) cc_final: 0.7891 (mttt)
REVERT: G   73 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7764 (t0)
REVERT: G   91 GLU cc_start: 0.8079 (pt0) cc_final: 0.7878 (tt0)
REVERT: K  523 ILE cc_start: 0.8102 (mp) cc_final: 0.7790 (mt)
REVERT: K  525 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7105 (mtt180)
REVERT: K  526 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7199 (mpt-90)
REVERT: L  525 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7463 (mtt-85)
  outliers start: 17
  outliers final: 7
  residues processed: 130
  average time/residue: 0.9427
  time to fit residues: 128.4217
Evaluate side-chains
  132 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue  116 LYS
Chi-restraints excluded: chain K residue  526 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0770
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C  38 ASN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.164022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.115664 restraints weight = 13081.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.01
r_work: 0.3127 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.171
  Angle     :  0.609   7.632  17116  Z= 0.360
  Chirality :  0.036   0.173   1948
  Planarity :  0.004   0.044   1307
  Dihedral  : 30.644 179.468   3647
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.46 %
    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:  2.26 (0.29), residues: 759
  helix:  2.26 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.51 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  52 
 TYR   0.012   0.002   TYR B  51 
 PHE   0.011   0.002   PHE A  67 
 TRP   0.004   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (11895)
  covalent geometry    : angle       0.60912 (17116)
  hydrogen bonds       : bond        0.04793 (  690)
  hydrogen bonds       : angle       3.18021 ( 1785)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.346 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8118 (mttt) cc_final: 0.7869 (tttt)
REVERT: B   92 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8167 (ptm160)
REVERT: C   77 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5392 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5677 (pt) cc_final: 0.5308 (pp)
REVERT: D   46 LYS cc_start: 0.8405 (mmpt) cc_final: 0.7926 (mppt)
REVERT: E   49 LYS cc_start: 0.8166 (tttp) cc_final: 0.7891 (tmtp)
REVERT: E   77 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7641 (mtpt)
REVERT: F   44 LYS cc_start: 0.8827 (tttt) cc_final: 0.7909 (mttt)
REVERT: G   73 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7787 (t0)
REVERT: G   91 GLU cc_start: 0.8114 (pt0) cc_final: 0.7912 (tt0)
REVERT: K  525 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7116 (mtt180)
REVERT: K  526 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7239 (mpt-90)
REVERT: L  525 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7501 (mtt-85)
  outliers start: 15
  outliers final: 6
  residues processed: 129
  average time/residue: 0.9752
  time to fit residues: 131.4908
Evaluate side-chains
  127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue  116 LYS
Chi-restraints excluded: chain K residue  526 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0030
   chunk 65 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0570
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4508

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 104 GLN
D  47 GLN
F  64 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.164516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.116284 restraints weight = 13136.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.01
r_work: 0.3135 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11895  Z= 0.157
  Angle     :  0.604   7.626  17116  Z= 0.358
  Chirality :  0.035   0.144   1948
  Planarity :  0.004   0.077   1307
  Dihedral  : 30.639 179.566   3647
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.93 %
    Favored  : 75.89 %
  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:  2.33 (0.29), residues: 759
  helix:  2.31 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.48 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A  52 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11895)
  covalent geometry    : angle       0.60361 (17116)
  hydrogen bonds       : bond        0.04615 (  690)
  hydrogen bonds       : angle       3.18933 ( 1785)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4548.54 seconds
wall clock time: 77 minutes 45.16 seconds (4665.16 seconds total)