Starting phenix.real_space_refine
on Wed Jul 30 02:31:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y7i_33666/07_2025/7y7i_33666.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y7i_33666/07_2025/7y7i_33666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y7i_33666/07_2025/7y7i_33666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y7i_33666/07_2025/7y7i_33666.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y7i_33666/07_2025/7y7i_33666.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y7i_33666/07_2025/7y7i_33666.cif"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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     286      5.49       5
     S      14      5.16       5
     C    6943      2.51       5
     N    2341      2.21       5
     O    2861      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12445
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 845
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 811
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 2915
          Classifications: {'DNA': 143}
          Link IDs: {'rna3p': 142}
    Chain: "J"
      Number of atoms: 2948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 2948
          Classifications: {'DNA': 143}
          Link IDs: {'rna3p': 142}
    Chain: "K"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 281
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 2, 'TRANS': 31}
    Chain: "L"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 281
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 2, 'TRANS': 31}
  Time building chain proxies: 7.43, per 1000 atoms: 0.60
  Number of scatterers: 12445
  At special positions: 0
  Unit cell: (117.6, 111.72, 116.62, 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     286     15.00
     O    2861      8.00
     N    2341      7.00
     C    6943      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.23
  Conformation dependent library (CDL) restraints added in 967.8 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1528

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 12 sheets defined
      67.8% alpha, 3.6% beta
      136 base pairs and 228 stacking pairs defined.
    Time for finding SS restraints: 6.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
      removed outlier: 4.057A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 80
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.684A  pdb=" N   LEU A  91 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 133
      removed outlier: 3.629A  pdb=" N   LEU A 126 " --> pdb=" O   TYR A 122 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 3.901A  pdb=" N   GLY A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.684A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.058A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.694A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 28 through 38
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 90
      removed outlier: 3.607A  pdb=" N   ASN C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 98
      removed outlier: 3.987A  pdb=" N   LYS C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.707A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.558A  pdb=" N   MET D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.553A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.691A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.978A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 80
      removed outlier: 3.546A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.694A  pdb=" N   LEU E  91 " --> pdb=" O   GLN E  87 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 133
      removed outlier: 3.794A  pdb=" N   LEU E 126 " --> pdb=" O   TYR E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.615A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.812A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.504A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
      removed outlier: 3.836A  pdb=" N   ALA G  22 " --> pdb=" O   ARG G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 38
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.410A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 89
    Processing helix  chain 'G' and resid 91 through 98
      removed outlier: 4.103A  pdb=" N   LEU G  97 " --> pdb=" O   GLU G  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 38 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.605A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.793A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 123
    Processing helix  chain 'K' and resid 534 through 538
    Processing helix  chain 'L' and resid 534 through 538
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.594A  pdb=" N   ARG 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 98
      removed outlier: 6.559A  pdb=" N   THR B  96 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.636A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
      removed outlier: 3.560A  pdb=" N   ILE C  79 " --> pdb=" O   GLY D  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86
      removed outlier: 6.818A  pdb=" N   ARG E  85 " --> 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 120 through 121
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.584A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79
    Processing sheet with id=AB2, first strand: chain 'K' and resid 541 through 543
    Processing sheet with id=AB3, first strand: chain 'L' and resid 540 through 542

    393 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      351 hydrogen bonds
      702 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      228 stacking parallelities
  Total time for adding SS restraints: 5.17

  Time building geometry restraints manager: 3.63 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: 2513
        1.33 -     1.45: 4151
        1.45 -     1.57: 6002
        1.57 -     1.69: 570
        1.69 -     1.81: 22
  Bond restraints: 13258
  Sorted by residual:
  bond pdb=" CB  MET H  59 "
       pdb=" CG  MET H  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.62e+00
  bond pdb=" C3'  DC J 192 "
       pdb=" O3'  DC J 192 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.59e+00
  bond pdb=" C3'  DC J 178 "
       pdb=" O3'  DC J 178 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.50e+00
  bond pdb=" C1'  DT I 103 "
       pdb=" N1   DT I 103 "
    ideal  model  delta    sigma   weight residual
    1.490  1.525 -0.035 3.00e-02 1.11e+03 1.37e+00
  bond pdb=" C3'  DC J 242 "
       pdb=" C2'  DC J 242 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.09e+00
  ... (remaining 13253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 18584
        1.58 -     3.15: 510
        3.15 -     4.73: 32
        4.73 -     6.30: 7
        6.30 -     7.88: 2
  Bond angle restraints: 19135
  Sorted by residual:
  angle pdb=" C3'  DC J 190 "
        pdb=" C2'  DC J 190 "
        pdb=" C1'  DC J 190 "
      ideal   model   delta    sigma   weight residual
     101.60   96.94    4.66 1.50e+00 4.44e-01 9.65e+00
  angle pdb=" CB  MET H  59 "
        pdb=" CG  MET H  59 "
        pdb=" SD  MET H  59 "
      ideal   model   delta    sigma   weight residual
     112.70  104.82    7.88 3.00e+00 1.11e-01 6.90e+00
  angle pdb=" C   ASN G 111 "
        pdb=" CA  ASN G 111 "
        pdb=" CB  ASN G 111 "
      ideal   model   delta    sigma   weight residual
     109.68  114.86   -5.18 1.98e+00 2.55e-01 6.84e+00
  angle pdb=" C3'  DC J 192 "
        pdb=" O3'  DC J 192 "
        pdb=" P    DC J 193 "
      ideal   model   delta    sigma   weight residual
     120.20  123.84   -3.64 1.50e+00 4.44e-01 5.89e+00
  angle pdb=" C4'  DG I  66 "
        pdb=" C3'  DG I  66 "
        pdb=" C2'  DG I  66 "
      ideal   model   delta    sigma   weight residual
     102.40   98.79    3.61 1.50e+00 4.44e-01 5.81e+00
  ... (remaining 19130 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.68: 5122
       25.68 -    51.37: 1590
       51.37 -    77.05: 472
       77.05 -   102.73: 26
      102.73 -   128.41: 2
  Dihedral angle restraints: 7212
    sinusoidal: 4834
      harmonic: 2378
  Sorted by residual:
  dihedral pdb=" C4'  DC J 178 "
           pdb=" C3'  DC J 178 "
           pdb=" O3'  DC J 178 "
           pdb=" P    DT J 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -11.59 -128.41     1      3.50e+01 8.16e-04 1.27e+01
  dihedral pdb=" C4'  DC J 192 "
           pdb=" C3'  DC J 192 "
           pdb=" O3'  DC J 192 "
           pdb=" P    DC J 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -13.98 -126.02     1      3.50e+01 8.16e-04 1.24e+01
  dihedral pdb=" CA  ARG E  80 "
           pdb=" C   ARG E  80 "
           pdb=" N   GLY E  81 "
           pdb=" CA  GLY E  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.25   16.75     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 7209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1519
       0.032 -    0.064: 478
       0.064 -    0.095: 117
       0.095 -    0.127: 46
       0.127 -    0.159: 5
  Chirality restraints: 2165
  Sorted by residual:
  chirality pdb=" C3'  DC J 191 "
            pdb=" C4'  DC J 191 "
            pdb=" O3'  DC J 191 "
            pdb=" C2'  DC J 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" C3'  DC J 190 "
            pdb=" C4'  DC J 190 "
            pdb=" O3'  DC J 190 "
            pdb=" C2'  DC J 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  ILE G 112 "
            pdb=" N   ILE G 112 "
            pdb=" C   ILE G 112 "
            pdb=" CB  ILE G 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 2162 not shown)

  Planarity restraints: 1429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 162 "   -0.016 2.00e-02 2.50e+03   1.52e-02 6.92e+00
        pdb=" N9   DG J 162 "    0.022 2.00e-02 2.50e+03
        pdb=" C8   DG J 162 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DG J 162 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG J 162 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG J 162 "   -0.013 2.00e-02 2.50e+03
        pdb=" O6   DG J 162 "    0.004 2.00e-02 2.50e+03
        pdb=" N1   DG J 162 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG J 162 "   -0.034 2.00e-02 2.50e+03
        pdb=" N2   DG J 162 "    0.026 2.00e-02 2.50e+03
        pdb=" N3   DG J 162 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DG J 162 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K 530 "   -0.039 5.00e-02 4.00e+02   5.95e-02 5.67e+00
        pdb=" N   PRO K 531 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO K 531 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO K 531 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  63 "   -0.006 2.00e-02 2.50e+03   1.30e-02 3.80e+00
        pdb=" N1   DC I  63 "    0.008 2.00e-02 2.50e+03
        pdb=" C2   DC I  63 "   -0.031 2.00e-02 2.50e+03
        pdb=" O2   DC I  63 "    0.021 2.00e-02 2.50e+03
        pdb=" N3   DC I  63 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I  63 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DC I  63 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DC I  63 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1426 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1936
        2.77 -     3.30: 11063
        3.30 -     3.83: 23605
        3.83 -     4.37: 26505
        4.37 -     4.90: 40152
  Nonbonded interactions: 103261
  Sorted by model distance:
  nonbonded pdb=" OG1 THR L 523 "
            pdb=" OG  SER L 525 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" NH2 ARG A  40 "
            pdb=" O2   DT J 227 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   TYR C  40 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR C  40 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" N2   DG I 127 "
            pdb=" N3   DC J 164 "
     model   vdw
     2.305 3.200
  ... (remaining 103256 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 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 31 through 123)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

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:             0.460
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     35.110
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13258  Z= 0.161
  Angle     :  0.571   7.878  19135  Z= 0.342
  Chirality :  0.036   0.159   2165
  Planarity :  0.004   0.060   1429
  Dihedral  : 28.764 128.413   5684
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 14.85 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.30), residues: 804
  helix:  2.59 (0.23), residues: 511
  sheet: -2.85 (0.88), residues: 26
  loop : -0.40 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K 536 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.006   0.001   PHE E  78 
 TYR   0.031   0.001   TYR B  88 
 ARG   0.006   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10507 (  744)
  hydrogen bonds       : angle       3.77518 ( 1854)
  covalent geometry    : bond        0.00351 (13258)
  covalent geometry    : angle       0.57069 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.995 
Fit side-chains
REVERT: B   91 LYS cc_start: 0.8317 (tttt) cc_final: 0.7880 (tmtt)
REVERT: C   21 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7973 (mmm-85)
REVERT: C   96 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7839 (mtmm)
REVERT: D   99 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8070 (mtm-85)
REVERT: D  119 THR cc_start: 0.8233 (m) cc_final: 0.7866 (p)
REVERT: E   42 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7364 (mtp180)
REVERT: E   77 LEU cc_start: 0.8318 (tt) cc_final: 0.8055 (tp)
REVERT: E   89 MET cc_start: 0.7559 (mmm) cc_final: 0.7159 (mmt)
REVERT: F   29 ILE cc_start: 0.8516 (mp) cc_final: 0.8231 (mm)
REVERT: F   79 LYS cc_start: 0.8403 (mttp) cc_final: 0.8168 (mmtp)
REVERT: H   34 LYS cc_start: 0.7799 (tptt) cc_final: 0.6514 (mttt)
REVERT: L  544 ASP cc_start: 0.7010 (p0) cc_final: 0.6723 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.4560
  time to fit residues: 89.3858
Evaluate side-chains
  98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  25 GLN
D  82 HIS
H  49 HIS
K 548 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.178304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.142664 restraints weight = 14973.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 0.89
r_work: 0.3165 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13258  Z= 0.192
  Angle     :  0.611   7.947  19135  Z= 0.361
  Chirality :  0.038   0.164   2165
  Planarity :  0.005   0.055   1429
  Dihedral  : 31.457 128.119   4056
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.99 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.29), residues: 804
  helix:  2.56 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.46 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K 536 
 HIS   0.006   0.001   HIS D  82 
 PHE   0.010   0.002   PHE A 101 
 TYR   0.037   0.002   TYR B  88 
 ARG   0.007   0.000   ARG E  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05785 (  744)
  hydrogen bonds       : angle       3.01684 ( 1854)
  covalent geometry    : bond        0.00433 (13258)
  covalent geometry    : angle       0.61074 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8314 (mp)
REVERT: B   91 LYS cc_start: 0.8376 (tttt) cc_final: 0.7914 (tmtt)
REVERT: C   65 GLU cc_start: 0.8611 (tt0) cc_final: 0.8301 (tt0)
REVERT: D   99 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8206 (mtm-85)
REVERT: D  119 THR cc_start: 0.8567 (m) cc_final: 0.8294 (p)
REVERT: E   48 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8850 (mm)
REVERT: E   89 MET cc_start: 0.7869 (mmm) cc_final: 0.7455 (mmt)
REVERT: E  108 ASP cc_start: 0.8164 (m-30) cc_final: 0.7963 (m-30)
REVERT: F   79 LYS cc_start: 0.8570 (mttp) cc_final: 0.8365 (mmtp)
REVERT: F   95 ARG cc_start: 0.8305 (mtt90) cc_final: 0.8078 (ptp90)
REVERT: G   65 GLU cc_start: 0.8239 (tp30) cc_final: 0.7812 (tt0)
REVERT: G   93 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7895 (mm-30)
REVERT: H   34 LYS cc_start: 0.7626 (tptt) cc_final: 0.6635 (mttt)
  outliers start: 10
  outliers final: 4
  residues processed: 103
  average time/residue: 0.3695
  time to fit residues: 49.5101
Evaluate side-chains
  86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain F residue   81 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
C  25 GLN
D  47 GLN
F  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.176014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.138875 restraints weight = 15074.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 0.88
r_work: 0.3163 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13258  Z= 0.185
  Angle     :  0.591   6.616  19135  Z= 0.352
  Chirality :  0.038   0.169   2165
  Planarity :  0.005   0.053   1429
  Dihedral  : 31.351 124.496   4056
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.41 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.30), residues: 804
  helix:  2.70 (0.22), residues: 522
  sheet: -2.34 (1.32), residues: 20
  loop : -0.53 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K 536 
 HIS   0.002   0.001   HIS E 115 
 PHE   0.010   0.002   PHE A 101 
 TYR   0.023   0.001   TYR B  88 
 ARG   0.007   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05479 (  744)
  hydrogen bonds       : angle       2.88521 ( 1854)
  covalent geometry    : bond        0.00417 (13258)
  covalent geometry    : angle       0.59115 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 1.008 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8318 (mp)
REVERT: B   91 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7821 (tmtt)
REVERT: C   65 GLU cc_start: 0.8629 (tt0) cc_final: 0.8300 (tt0)
REVERT: D  119 THR cc_start: 0.8582 (m) cc_final: 0.8265 (p)
REVERT: E   48 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8791 (mm)
REVERT: E   89 MET cc_start: 0.7862 (mmm) cc_final: 0.7343 (mmt)
REVERT: E  108 ASP cc_start: 0.8117 (m-30) cc_final: 0.7884 (m-30)
REVERT: E  117 ARG cc_start: 0.7342 (mtm110) cc_final: 0.7078 (mtm110)
REVERT: F   79 LYS cc_start: 0.8584 (mttp) cc_final: 0.8341 (mmtp)
REVERT: F   95 ARG cc_start: 0.8289 (mtt90) cc_final: 0.8063 (ptp90)
REVERT: G   93 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8021 (mm-30)
REVERT: H   34 LYS cc_start: 0.7635 (tptt) cc_final: 0.6625 (mttt)
REVERT: K  521 ILE cc_start: 0.3236 (OUTLIER) cc_final: 0.2811 (mm)
  outliers start: 15
  outliers final: 8
  residues processed: 100
  average time/residue: 0.3835
  time to fit residues: 49.7602
Evaluate side-chains
  92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain K residue  521 ILE
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0970
   chunk 48 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 90 optimal weight:    9.9990
   chunk 81 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
D  49 HIS
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.180357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.144286 restraints weight = 15033.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 0.95
r_work: 0.3192 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13258  Z= 0.147
  Angle     :  0.535   6.426  19135  Z= 0.324
  Chirality :  0.035   0.167   2165
  Planarity :  0.004   0.049   1429
  Dihedral  : 31.098 127.924   4056
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.01 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.29), residues: 804
  helix:  2.97 (0.22), residues: 523
  sheet:  None (None), residues: 0
  loop : -0.44 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 536 
 HIS   0.002   0.000   HIS D  49 
 PHE   0.009   0.001   PHE L 535 
 TYR   0.018   0.001   TYR B  88 
 ARG   0.012   0.000   ARG E  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  744)
  hydrogen bonds       : angle       2.69021 ( 1854)
  covalent geometry    : bond        0.00314 (13258)
  covalent geometry    : angle       0.53533 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8157 (mp)
REVERT: B   91 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7832 (tmtt)
REVERT: C   65 GLU cc_start: 0.8596 (tt0) cc_final: 0.8264 (tt0)
REVERT: C   93 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7797 (mt-10)
REVERT: D  119 THR cc_start: 0.8560 (m) cc_final: 0.8239 (p)
REVERT: E   48 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8752 (mm)
REVERT: E   49 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7995 (ttp-110)
REVERT: E   89 MET cc_start: 0.7738 (mmm) cc_final: 0.7264 (mmt)
REVERT: E  108 ASP cc_start: 0.7988 (m-30) cc_final: 0.7729 (m-30)
REVERT: E  133 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7149 (ptt180)
REVERT: F   79 LYS cc_start: 0.8505 (mttp) cc_final: 0.8203 (mmtp)
REVERT: G   72 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7218 (ttm170)
REVERT: H   34 LYS cc_start: 0.7548 (tptt) cc_final: 0.6494 (mttt)
  outliers start: 9
  outliers final: 4
  residues processed: 91
  average time/residue: 0.4726
  time to fit residues: 55.0121
Evaluate side-chains
  85 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain C residue   93 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain K residue  534 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 38 optimal weight:    0.4980
   chunk 20 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0970
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.179221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.142306 restraints weight = 15030.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 0.89
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13258  Z= 0.150
  Angle     :  0.534   6.209  19135  Z= 0.323
  Chirality :  0.035   0.161   2165
  Planarity :  0.004   0.048   1429
  Dihedral  : 31.106 128.914   4056
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.87 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.29), residues: 804
  helix:  2.99 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.41 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 536 
 HIS   0.002   0.000   HIS A 115 
 PHE   0.007   0.001   PHE A 101 
 TYR   0.014   0.001   TYR B  88 
 ARG   0.007   0.000   ARG E  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04415 (  744)
  hydrogen bonds       : angle       2.67235 ( 1854)
  covalent geometry    : bond        0.00324 (13258)
  covalent geometry    : angle       0.53433 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 1.519 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8234 (mp)
REVERT: B   91 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7643 (tmtt)
REVERT: C   65 GLU cc_start: 0.7750 (tt0) cc_final: 0.7488 (tt0)
REVERT: C   93 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7178 (mt-10)
REVERT: E   89 MET cc_start: 0.7066 (mmm) cc_final: 0.6478 (mmt)
REVERT: F   79 LYS cc_start: 0.8364 (mttp) cc_final: 0.8141 (mmtp)
REVERT: G   65 GLU cc_start: 0.7918 (tp30) cc_final: 0.7437 (tp30)
REVERT: G   93 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7396 (mm-30)
REVERT: H   34 LYS cc_start: 0.7487 (tptt) cc_final: 0.6718 (mtpt)
  outliers start: 13
  outliers final: 7
  residues processed: 94
  average time/residue: 0.3732
  time to fit residues: 45.8453
Evaluate side-chains
  90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   93 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.176531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.139735 restraints weight = 15224.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 0.93
r_work: 0.3129 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13258  Z= 0.168
  Angle     :  0.562   6.123  19135  Z= 0.337
  Chirality :  0.037   0.160   2165
  Planarity :  0.004   0.048   1429
  Dihedral  : 31.205 126.724   4056
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.43 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.30), residues: 804
  helix:  2.87 (0.22), residues: 521
  sheet: -2.32 (1.33), residues: 20
  loop : -0.32 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  86 
 HIS   0.003   0.001   HIS E 115 
 PHE   0.010   0.001   PHE C  26 
 TYR   0.011   0.001   TYR B  88 
 ARG   0.006   0.000   ARG G  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05174 (  744)
  hydrogen bonds       : angle       2.82310 ( 1854)
  covalent geometry    : bond        0.00374 (13258)
  covalent geometry    : angle       0.56172 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8307 (mp)
REVERT: B   91 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7796 (tmtt)
REVERT: C   65 GLU cc_start: 0.8617 (tt0) cc_final: 0.8292 (tt0)
REVERT: C   93 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7822 (mt-10)
REVERT: E   53 ARG cc_start: 0.8252 (ttp80) cc_final: 0.8023 (ttp-110)
REVERT: E   59 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (pm20)
REVERT: E   89 MET cc_start: 0.7889 (mmm) cc_final: 0.7301 (mmt)
REVERT: E  133 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7221 (ptt180)
REVERT: F   79 LYS cc_start: 0.8664 (mttp) cc_final: 0.8391 (mmtp)
REVERT: G   65 GLU cc_start: 0.8400 (tp30) cc_final: 0.8105 (tt0)
REVERT: H   34 LYS cc_start: 0.7535 (tptt) cc_final: 0.6462 (mtpt)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.3768
  time to fit residues: 47.7407
Evaluate side-chains
  94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   93 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
H  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.169939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.132695 restraints weight = 14982.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 0.90
r_work: 0.3044 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  13258  Z= 0.255
  Angle     :  0.669   6.638  19135  Z= 0.395
  Chirality :  0.043   0.203   2165
  Planarity :  0.005   0.075   1429
  Dihedral  : 31.602 122.977   4056
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.57 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.29), residues: 804
  helix:  2.47 (0.22), residues: 519
  sheet: -2.43 (1.24), residues: 20
  loop : -0.49 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L 536 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.002   PHE A 101 
 TYR   0.016   0.002   TYR B  51 
 ARG   0.008   0.001   ARG G  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07047 (  744)
  hydrogen bonds       : angle       3.09108 ( 1854)
  covalent geometry    : bond        0.00598 (13258)
  covalent geometry    : angle       0.66931 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8350 (mp)
REVERT: B   91 LYS cc_start: 0.8366 (ttpt) cc_final: 0.7886 (ttpp)
REVERT: C   65 GLU cc_start: 0.8617 (tt0) cc_final: 0.8289 (tt0)
REVERT: C   93 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7708 (mt-10)
REVERT: E   45 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8423 (m)
REVERT: E   53 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8028 (ttp-110)
REVERT: E   89 MET cc_start: 0.7954 (mmm) cc_final: 0.7350 (mmt)
REVERT: E  133 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7466 (ptt180)
REVERT: F   79 LYS cc_start: 0.8559 (mttp) cc_final: 0.8310 (mmtp)
REVERT: G   65 GLU cc_start: 0.8485 (tp30) cc_final: 0.7912 (tp30)
REVERT: H   34 LYS cc_start: 0.7589 (tptt) cc_final: 0.6531 (mtpt)
  outliers start: 23
  outliers final: 15
  residues processed: 98
  average time/residue: 0.3758
  time to fit residues: 47.2998
Evaluate side-chains
  96 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   93 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  523 THR
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 103 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 99 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 94 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.174825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.139586 restraints weight = 15214.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 0.80
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13258  Z= 0.245
  Angle     :  0.662   6.070  19135  Z= 0.393
  Chirality :  0.043   0.179   2165
  Planarity :  0.006   0.071   1429
  Dihedral  : 31.656 121.851   4056
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.16 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.29), residues: 804
  helix:  2.36 (0.22), residues: 521
  sheet: -2.36 (1.26), residues: 20
  loop : -0.61 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 536 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.012   0.002   PHE A 101 
 TYR   0.014   0.002   TYR B  51 
 ARG   0.009   0.001   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06818 (  744)
  hydrogen bonds       : angle       3.08533 ( 1854)
  covalent geometry    : bond        0.00576 (13258)
  covalent geometry    : angle       0.66160 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8414 (mp)
REVERT: B   91 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7663 (ttpp)
REVERT: C   65 GLU cc_start: 0.7748 (tt0) cc_final: 0.7459 (tt0)
REVERT: C   93 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7103 (mt-10)
REVERT: E   89 MET cc_start: 0.7168 (mmm) cc_final: 0.6560 (mmt)
REVERT: E  133 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7238 (ptt180)
REVERT: G   65 GLU cc_start: 0.7965 (tp30) cc_final: 0.7402 (tp30)
REVERT: H   34 LYS cc_start: 0.7535 (tptt) cc_final: 0.6734 (mtpt)
  outliers start: 19
  outliers final: 15
  residues processed: 91
  average time/residue: 0.3772
  time to fit residues: 44.3045
Evaluate side-chains
  90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   93 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.175376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.141233 restraints weight = 15067.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 0.80
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13258  Z= 0.180
  Angle     :  0.595   6.009  19135  Z= 0.358
  Chirality :  0.038   0.181   2165
  Planarity :  0.004   0.046   1429
  Dihedral  : 31.436 124.270   4056
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.30 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.30), residues: 804
  helix:  2.62 (0.22), residues: 523
  sheet: -2.24 (1.26), residues: 20
  loop : -0.52 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  86 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.002   PHE A 101 
 TYR   0.011   0.001   TYR B  51 
 ARG   0.008   0.000   ARG G  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05589 (  744)
  hydrogen bonds       : angle       2.90531 ( 1854)
  covalent geometry    : bond        0.00405 (13258)
  covalent geometry    : angle       0.59501 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8346 (mp)
REVERT: B   91 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7651 (ttpp)
REVERT: C   65 GLU cc_start: 0.7748 (tt0) cc_final: 0.7451 (tt0)
REVERT: C   93 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7149 (mt-10)
REVERT: E   89 MET cc_start: 0.7104 (mmm) cc_final: 0.6503 (mmt)
REVERT: E  133 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7127 (ptt180)
REVERT: G   65 GLU cc_start: 0.7981 (tp30) cc_final: 0.7426 (tp30)
REVERT: H   34 LYS cc_start: 0.7442 (tptt) cc_final: 0.6705 (mtpt)
  outliers start: 17
  outliers final: 13
  residues processed: 91
  average time/residue: 0.4087
  time to fit residues: 49.0139
Evaluate side-chains
  93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   93 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  523 THR
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 105 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 23 optimal weight:    0.7980
   chunk 76 optimal weight:   10.0000
   overall best weight:    2.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.168827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.130778 restraints weight = 14922.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 0.86
r_work: 0.3109 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  13258  Z= 0.219
  Angle     :  0.630   5.924  19135  Z= 0.375
  Chirality :  0.041   0.173   2165
  Planarity :  0.005   0.065   1429
  Dihedral  : 31.518 123.973   4056
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.30 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.30), residues: 804
  helix:  2.49 (0.22), residues: 521
  sheet: -2.17 (1.26), residues: 20
  loop : -0.60 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L 536 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.012   0.002   PHE A 101 
 TYR   0.013   0.002   TYR B  51 
 ARG   0.008   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06300 (  744)
  hydrogen bonds       : angle       2.98461 ( 1854)
  covalent geometry    : bond        0.00509 (13258)
  covalent geometry    : angle       0.63047 (19135)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8435 (mp)
REVERT: B   91 LYS cc_start: 0.8362 (ttpt) cc_final: 0.7917 (ttpp)
REVERT: C   65 GLU cc_start: 0.8626 (tt0) cc_final: 0.8324 (tt0)
REVERT: C   93 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7786 (mt-10)
REVERT: E   45 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8430 (m)
REVERT: E   89 MET cc_start: 0.8062 (mmm) cc_final: 0.7460 (mmt)
REVERT: E  133 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7476 (ptt180)
REVERT: G   65 GLU cc_start: 0.8643 (tp30) cc_final: 0.8188 (tp30)
REVERT: H   34 LYS cc_start: 0.7561 (tptt) cc_final: 0.6635 (mtpt)
  outliers start: 18
  outliers final: 14
  residues processed: 90
  average time/residue: 0.3797
  time to fit residues: 44.5385
Evaluate side-chains
  90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   93 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  523 THR
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 104 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.9788

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

Flipped N/Q/H residues before XYZ refinement:
H  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.176992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.140661 restraints weight = 14984.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 0.86
r_work: 0.3165 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13258  Z= 0.154
  Angle     :  0.552   6.071  19135  Z= 0.334
  Chirality :  0.036   0.175   2165
  Planarity :  0.004   0.046   1429
  Dihedral  : 31.193 126.578   4056
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.18 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.30), residues: 804
  helix:  2.80 (0.22), residues: 523
  sheet: -2.13 (1.22), residues: 20
  loop : -0.48 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  86 
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE L 535 
 TYR   0.011   0.001   TYR B  88 
 ARG   0.008   0.000   ARG G  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04676 (  744)
  hydrogen bonds       : angle       2.76045 ( 1854)
  covalent geometry    : bond        0.00331 (13258)
  covalent geometry    : angle       0.55162 (19135)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4681.82 seconds
wall clock time: 82 minutes 27.95 seconds (4947.95 seconds total)