Starting phenix.real_space_refine
on Fri Jul 25 07:55:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t04_40934/07_2025/8t04_40934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t04_40934/07_2025/8t04_40934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2025/8t04_40934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2025/8t04_40934.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2025/8t04_40934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2025/8t04_40934.cif"
  }
  resolution = 2.98
  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=   0.003 sd=   0.088
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     S      44      5.16       5
     C    4492      2.51       5
     N    1092      2.21       5
     O    1242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6874
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1593
          Classifications: {'peptide': 199}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190}
    Chain: "B"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1593
          Classifications: {'peptide': 199}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "E"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 76
          Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "B"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 76
          Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
  Time building chain proxies: 6.23, per 1000 atoms: 0.91
  Number of scatterers: 6874
  At special positions: 0
  Unit cell: (72.21, 108.73, 103.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      44     16.00
     P       2     15.00
     O    1242      8.00
     N    1092      7.00
     C    4492      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  59 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  59 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  97 " distance=2.03

  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: 1.78
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 180 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 184 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A  48 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 184 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 180 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B  48 "


  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 12 sheets defined
      43.1% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 14
      removed outlier: 3.745A  pdb=" N   LEU A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      Proline residue:  A  11  - end of helix
    Processing helix  chain 'A' and resid 17 through 28
      removed outlier: 4.144A  pdb=" N   THR A  21 " --> pdb=" O   ALA A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 52
    Processing helix  chain 'A' and resid 55 through 59
    Processing helix  chain 'A' and resid 62 through 87
    Processing helix  chain 'A' and resid 91 through 111
    Processing helix  chain 'A' and resid 118 through 141
    Processing helix  chain 'A' and resid 146 through 153
    Processing helix  chain 'A' and resid 153 through 170
    Processing helix  chain 'A' and resid 171 through 174
    Processing helix  chain 'A' and resid 175 through 195
      removed outlier: 3.898A  pdb=" N   SER A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   CYS A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 14
      Proline residue:  B  11  - end of helix
    Processing helix  chain 'B' and resid 17 through 28
      removed outlier: 4.142A  pdb=" N   THR B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 52
    Processing helix  chain 'B' and resid 55 through 59
    Processing helix  chain 'B' and resid 62 through 87
    Processing helix  chain 'B' and resid 91 through 111
      removed outlier: 3.501A  pdb=" N   THR B  95 " --> pdb=" O   PRO B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 141
    Processing helix  chain 'B' and resid 146 through 153
    Processing helix  chain 'B' and resid 153 through 170
    Processing helix  chain 'B' and resid 171 through 174
    Processing helix  chain 'B' and resid 175 through 195
      removed outlier: 3.899A  pdb=" N   SER B 181 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   CYS B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 67
      No H-bonds generated for 'chain 'C' and resid 65 through 67'
    Processing helix  chain 'C' and resid 88 through 91
    Processing helix  chain 'D' and resid 79 through 83
    Processing helix  chain 'E' and resid 65 through 67
      No H-bonds generated for 'chain 'E' and resid 65 through 67'
    Processing helix  chain 'E' and resid 88 through 91
    Processing helix  chain 'F' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 7.054A  pdb=" N   VAL C  36 " --> pdb=" O   HIS C  52 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   HIS C  52 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   TRP C  38 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.816A  pdb=" N   TYR C 109 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6
    Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.426A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ILE D  33 " --> pdb=" O   HIS D  49 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   HIS D  49 " --> pdb=" O   ILE D  33 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.426A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12
      removed outlier: 7.050A  pdb=" N   VAL E  36 " --> pdb=" O   HIS E  52 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   HIS E  52 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   TRP E  38 " --> pdb=" O   LEU E  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.813A  pdb=" N   TYR E 109 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.423A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE F  33 " --> pdb=" O   HIS F  49 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   HIS F  49 " --> pdb=" O   ILE F  33 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.423A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)

    393 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.10

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1024
        1.31 -     1.44: 2033
        1.44 -     1.56: 3921
        1.56 -     1.69: 8
        1.69 -     1.82: 72
  Bond restraints: 7058
  Sorted by residual:
  bond pdb=" C   ARG B  93 "
       pdb=" N   SER B  94 "
    ideal  model  delta    sigma   weight residual
    1.335  1.446 -0.111 1.31e-02 5.83e+03 7.19e+01
  bond pdb=" C25 LBN B 303 "
       pdb=" O5  LBN B 303 "
    ideal  model  delta    sigma   weight residual
    1.326  1.433 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" C25 LBN A 303 "
       pdb=" O5  LBN A 303 "
    ideal  model  delta    sigma   weight residual
    1.326  1.432 -0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" C34 LBN A 303 "
       pdb=" O7  LBN A 303 "
    ideal  model  delta    sigma   weight residual
    1.331  1.423 -0.092 2.00e-02 2.50e+03 2.12e+01
  bond pdb=" C34 LBN B 303 "
       pdb=" O7  LBN B 303 "
    ideal  model  delta    sigma   weight residual
    1.331  1.422 -0.091 2.00e-02 2.50e+03 2.08e+01
  ... (remaining 7053 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.36: 8955
        3.36 -     6.73: 584
        6.73 -    10.09: 22
       10.09 -    13.45: 1
       13.45 -    16.82: 2
  Bond angle restraints: 9564
  Sorted by residual:
  angle pdb=" O   ARG A  93 "
        pdb=" C   ARG A  93 "
        pdb=" N   SER A  94 "
      ideal   model   delta    sigma   weight residual
     122.09  129.02   -6.93 1.04e+00 9.25e-01 4.45e+01
  angle pdb=" O1  LBN A 303 "
        pdb=" P1  LBN A 303 "
        pdb=" O2  LBN A 303 "
      ideal   model   delta    sigma   weight residual
      93.45  110.27  -16.82 3.00e+00 1.11e-01 3.14e+01
  angle pdb=" O1  LBN B 303 "
        pdb=" P1  LBN B 303 "
        pdb=" O2  LBN B 303 "
      ideal   model   delta    sigma   weight residual
      93.45  110.19  -16.74 3.00e+00 1.11e-01 3.12e+01
  angle pdb=" N   GLU B  90 "
        pdb=" CA  GLU B  90 "
        pdb=" C   GLU B  90 "
      ideal   model   delta    sigma   weight residual
     110.07  103.09    6.98 1.26e+00 6.30e-01 3.07e+01
  angle pdb=" N   GLU A  90 "
        pdb=" CA  GLU A  90 "
        pdb=" C   GLU A  90 "
      ideal   model   delta    sigma   weight residual
     110.07  103.11    6.96 1.26e+00 6.30e-01 3.06e+01
  ... (remaining 9559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.41: 4126
       34.41 -    68.82: 103
       68.82 -   103.23: 17
      103.23 -   137.64: 2
      137.64 -   172.05: 2
  Dihedral angle restraints: 4250
    sinusoidal: 1788
      harmonic: 2462
  Sorted by residual:
  dihedral pdb=" CA  HIS F  49 "
           pdb=" C   HIS F  49 "
           pdb=" N   TYR F  50 "
           pdb=" CA  TYR F  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.96  -29.04     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  HIS D  49 "
           pdb=" C   HIS D  49 "
           pdb=" N   TYR D  50 "
           pdb=" CA  TYR D  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.08  -28.92     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CA  GLU A  90 "
           pdb=" C   GLU A  90 "
           pdb=" N   PRO A  91 "
           pdb=" CA  PRO A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   26.21  -26.21     0      5.00e+00 4.00e-02 2.75e+01
  ... (remaining 4247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.983: 1052
       0.983 -    1.966: 0
       1.966 -    2.949: 0
       2.949 -    3.932: 0
       3.932 -    4.915: 2
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" C2  LBN B 303 "
            pdb=" C1  LBN B 303 "
            pdb=" C3  LBN B 303 "
            pdb=" O7  LBN B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.55   -4.91 2.00e-01 2.50e+01 6.04e+02
  chirality pdb=" C2  LBN A 303 "
            pdb=" C1  LBN A 303 "
            pdb=" C3  LBN A 303 "
            pdb=" O7  LBN A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.55   -4.91 2.00e-01 2.50e+01 6.03e+02
  chirality pdb=" CA  ILE D  21 "
            pdb=" N   ILE D  21 "
            pdb=" C   ILE D  21 "
            pdb=" CB  ILE D  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1051 not shown)

  Planarity restraints: 1156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 110 "    0.021 2.00e-02 2.50e+03   1.19e-02 3.55e+00
        pdb=" CG  TRP C 110 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 110 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 110 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 110 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 110 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 110 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 110 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 110 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 110 "   -0.021 2.00e-02 2.50e+03   1.18e-02 3.46e+00
        pdb=" CG  TRP E 110 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 110 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 110 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 110 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 110 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 110 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 110 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  93 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.74e+00
        pdb=" C   ARG B  93 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ARG B  93 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER B  94 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1153 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1240
        2.84 -     3.35: 6694
        3.35 -     3.87: 10820
        3.87 -     4.38: 14301
        4.38 -     4.90: 23575
  Nonbonded interactions: 56630
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG D  61 "
            pdb=" OD2 ASP D  82 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NH1 ARG F  61 "
            pdb=" OD2 ASP F  82 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NH2 ARG D  61 "
            pdb=" OE2 GLU D  81 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" NH2 ARG F  61 "
            pdb=" OE2 GLU F  81 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" N   GLY B 116 "
            pdb=" O4  LBN B 303 "
     model   vdw
     2.483 3.120
  ... (remaining 56625 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             2.140
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.040
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:13.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6556
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      :  0.015   0.220   7068  Z= 1.078
  Angle     :  1.828  16.817   9572  Z= 1.300
  Chirality :  0.230   4.915   1054
  Planarity :  0.004   0.027   1156
  Dihedral  : 16.387 172.049   2666
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.81 %
    Favored  : 92.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.07 (0.29), residues: 840
  helix: -1.11 (0.26), residues: 278
  sheet:  0.01 (0.40), residues: 166
  loop : -0.57 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP C 110 
 HIS   0.007   0.002   HIS C  52 
 PHE   0.021   0.002   PHE B  69 
 TYR   0.028   0.003   TYR D  91 
 ARG   0.006   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18540 (  379)
  hydrogen bonds       : angle       8.76850 ( 1047)
  metal coordination   : bond        0.11773 (    6)
  SS BOND              : bond        0.00684 (    4)
  SS BOND              : angle       1.17853 (    8)
  covalent geometry    : bond        0.01440 ( 7058)
  covalent geometry    : angle       1.82850 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.6311 (mt) cc_final: 0.6099 (mp)
REVERT: A   29 ARG cc_start: 0.6564 (mmm160) cc_final: 0.6358 (mtp180)
REVERT: A   61 MET cc_start: 0.6262 (mtm) cc_final: 0.6026 (mtp)
REVERT: A   87 ASP cc_start: 0.6284 (t70) cc_final: 0.6065 (t70)
REVERT: A   94 SER cc_start: 0.6510 (m) cc_final: 0.6075 (p)
REVERT: A  137 MET cc_start: 0.5787 (mtm) cc_final: 0.5572 (mtm)
REVERT: A  170 PHE cc_start: 0.6461 (t80) cc_final: 0.6152 (t80)
REVERT: B    9 LEU cc_start: 0.7564 (mt) cc_final: 0.7242 (mp)
REVERT: B   83 MET cc_start: 0.8086 (mmp) cc_final: 0.7550 (mmp)
REVERT: B  137 MET cc_start: 0.7561 (mtm) cc_final: 0.7157 (mtm)
REVERT: B  170 PHE cc_start: 0.7342 (t80) cc_final: 0.7119 (t80)
REVERT: B  189 MET cc_start: 0.7518 (tpt) cc_final: 0.7299 (mmm)
REVERT: C   61 TYR cc_start: 0.7574 (m-80) cc_final: 0.7330 (m-80)
REVERT: C   83 MET cc_start: 0.5581 (mmt) cc_final: 0.5237 (mmt)
REVERT: C  112 GLN cc_start: 0.7255 (mt0) cc_final: 0.6928 (mm110)
REVERT: D   63 SER cc_start: 0.6740 (m) cc_final: 0.6539 (p)
REVERT: E   83 MET cc_start: 0.6846 (mmt) cc_final: 0.6255 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 1.1642
  time to fit residues: 144.0497
Evaluate side-chains
  84 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.174925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.123969 restraints weight = 6983.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.35
r_work: 0.3295 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7068  Z= 0.164
  Angle     :  0.607   6.250   9572  Z= 0.318
  Chirality :  0.045   0.161   1054
  Planarity :  0.005   0.035   1156
  Dihedral  : 12.411 138.993   1136
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 11.17 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.47 (0.30), residues: 840
  helix:  1.16 (0.28), residues: 288
  sheet:  0.05 (0.36), residues: 230
  loop : -0.10 (0.40), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 110 
 HIS   0.006   0.002   HIS E  52 
 PHE   0.021   0.002   PHE A  42 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.002   0.000   ARG B  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (  379)
  hydrogen bonds       : angle       5.30403 ( 1047)
  metal coordination   : bond        0.00578 (    6)
  SS BOND              : bond        0.00080 (    4)
  SS BOND              : angle       0.63773 (    8)
  covalent geometry    : bond        0.00383 ( 7058)
  covalent geometry    : angle       0.60661 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7607 (ttmt) cc_final: 0.6704 (mptt)
REVERT: A   61 MET cc_start: 0.7767 (mtm) cc_final: 0.7563 (mtp)
REVERT: A  138 LYS cc_start: 0.6577 (mttt) cc_final: 0.6144 (mppt)
REVERT: B   27 LYS cc_start: 0.7614 (ttmt) cc_final: 0.6725 (mptt)
REVERT: B  138 LYS cc_start: 0.6595 (mttt) cc_final: 0.6127 (mppt)
REVERT: C   83 MET cc_start: 0.7289 (mmt) cc_final: 0.6748 (mmt)
REVERT: C  107 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8730 (pmm)
REVERT: D   63 SER cc_start: 0.8468 (m) cc_final: 0.8160 (p)
REVERT: D   65 SER cc_start: 0.8308 (m) cc_final: 0.8018 (p)
REVERT: E   83 MET cc_start: 0.7317 (mmt) cc_final: 0.6775 (mmt)
REVERT: F    4 MET cc_start: 0.7381 (mmm) cc_final: 0.6902 (mmm)
REVERT: F   65 SER cc_start: 0.8277 (m) cc_final: 0.8059 (p)
  outliers start: 23
  outliers final: 9
  residues processed: 117
  average time/residue: 2.0484
  time to fit residues: 254.7100
Evaluate side-chains
  101 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.177818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127539 restraints weight = 7033.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.32
r_work: 0.3339 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7068  Z= 0.114
  Angle     :  0.518   6.093   9572  Z= 0.271
  Chirality :  0.042   0.145   1054
  Planarity :  0.004   0.035   1156
  Dihedral  : 11.066 134.250   1136
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.44 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.07 (0.31), residues: 840
  helix:  1.80 (0.28), residues: 296
  sheet:  0.37 (0.37), residues: 230
  loop :  0.05 (0.40), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 110 
 HIS   0.005   0.001   HIS E  52 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.008   0.001   TYR D  91 
 ARG   0.003   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  379)
  hydrogen bonds       : angle       4.81848 ( 1047)
  metal coordination   : bond        0.00184 (    6)
  SS BOND              : bond        0.00082 (    4)
  SS BOND              : angle       0.43967 (    8)
  covalent geometry    : bond        0.00255 ( 7058)
  covalent geometry    : angle       0.51818 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 1.154 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.7988 (mt) cc_final: 0.7735 (mp)
REVERT: A   27 LYS cc_start: 0.7608 (ttmt) cc_final: 0.6788 (mptt)
REVERT: A  138 LYS cc_start: 0.6757 (mttt) cc_final: 0.6328 (tppt)
REVERT: B   27 LYS cc_start: 0.7638 (ttmt) cc_final: 0.6809 (mptt)
REVERT: B  138 LYS cc_start: 0.6714 (mttt) cc_final: 0.6299 (tppt)
REVERT: C   83 MET cc_start: 0.7357 (mmt) cc_final: 0.7094 (mmm)
REVERT: D   61 ARG cc_start: 0.7142 (ptp-170) cc_final: 0.6936 (ptp-170)
REVERT: D   65 SER cc_start: 0.8079 (m) cc_final: 0.7793 (p)
REVERT: E   83 MET cc_start: 0.7344 (mmt) cc_final: 0.7066 (mmm)
REVERT: F   61 ARG cc_start: 0.7197 (ptp-170) cc_final: 0.6978 (ptp-170)
  outliers start: 17
  outliers final: 5
  residues processed: 112
  average time/residue: 1.8480
  time to fit residues: 221.1649
Evaluate side-chains
  99 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 46 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4041 r_free = 0.4041 target = 0.175440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124451 restraints weight = 7112.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.37
r_work: 0.3306 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7068  Z= 0.128
  Angle     :  0.517   6.124   9572  Z= 0.269
  Chirality :  0.042   0.142   1054
  Planarity :  0.004   0.033   1156
  Dihedral  : 10.973 134.096   1136
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.03 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.15 (0.31), residues: 840
  helix:  2.01 (0.28), residues: 296
  sheet:  0.54 (0.38), residues: 220
  loop : -0.16 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 110 
 HIS   0.004   0.001   HIS C  52 
 PHE   0.016   0.002   PHE A  39 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.003   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  379)
  hydrogen bonds       : angle       4.72262 ( 1047)
  metal coordination   : bond        0.00208 (    6)
  SS BOND              : bond        0.00084 (    4)
  SS BOND              : angle       0.37337 (    8)
  covalent geometry    : bond        0.00294 ( 7058)
  covalent geometry    : angle       0.51678 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 1.326 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7742 (ttmt) cc_final: 0.6822 (mptt)
REVERT: A   29 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7885 (mtp85)
REVERT: A  138 LYS cc_start: 0.6733 (mttt) cc_final: 0.6320 (tppt)
REVERT: A  200 LYS cc_start: 0.8152 (mttt) cc_final: 0.7943 (mttt)
REVERT: B   27 LYS cc_start: 0.7714 (ttmt) cc_final: 0.6805 (mptt)
REVERT: B   29 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7857 (mtp85)
REVERT: B  138 LYS cc_start: 0.6732 (mttt) cc_final: 0.6320 (tppt)
REVERT: C   83 MET cc_start: 0.7362 (mmt) cc_final: 0.7117 (mmm)
REVERT: D   61 ARG cc_start: 0.7261 (ptp-170) cc_final: 0.7035 (ptp-170)
REVERT: E   83 MET cc_start: 0.7357 (mmt) cc_final: 0.7108 (mmm)
REVERT: F   61 ARG cc_start: 0.7377 (ptp-170) cc_final: 0.7163 (ptp-170)
  outliers start: 17
  outliers final: 6
  residues processed: 103
  average time/residue: 1.5628
  time to fit residues: 170.6384
Evaluate side-chains
  95 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 3.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 20 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4063 r_free = 0.4063 target = 0.177183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.126797 restraints weight = 6985.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.34
r_work: 0.3317 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7068  Z= 0.123
  Angle     :  0.508   6.068   9572  Z= 0.264
  Chirality :  0.041   0.139   1054
  Planarity :  0.004   0.032   1156
  Dihedral  : 10.501 136.178   1136
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.44 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.21 (0.30), residues: 840
  helix:  2.13 (0.28), residues: 296
  sheet:  0.63 (0.38), residues: 220
  loop : -0.27 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  55 
 HIS   0.004   0.001   HIS E  52 
 PHE   0.025   0.002   PHE B  42 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  379)
  hydrogen bonds       : angle       4.62273 ( 1047)
  metal coordination   : bond        0.00187 (    6)
  SS BOND              : bond        0.00062 (    4)
  SS BOND              : angle       0.41199 (    8)
  covalent geometry    : bond        0.00280 ( 7058)
  covalent geometry    : angle       0.50811 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7928 (mtp85)
REVERT: A  138 LYS cc_start: 0.6737 (mttt) cc_final: 0.6334 (tppt)
REVERT: A  200 LYS cc_start: 0.8156 (mttt) cc_final: 0.7925 (mtpt)
REVERT: B   29 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7872 (mtp85)
REVERT: B  138 LYS cc_start: 0.6733 (mttt) cc_final: 0.6335 (tppt)
REVERT: C   83 MET cc_start: 0.7460 (mmt) cc_final: 0.7148 (mmm)
REVERT: C  107 MET cc_start: 0.8975 (ptp) cc_final: 0.8596 (pmm)
REVERT: D   61 ARG cc_start: 0.7351 (ptp-170) cc_final: 0.7147 (ptp-170)
REVERT: E   83 MET cc_start: 0.7465 (mmt) cc_final: 0.7141 (mmm)
  outliers start: 18
  outliers final: 10
  residues processed: 107
  average time/residue: 1.8630
  time to fit residues: 211.4670
Evaluate side-chains
  102 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 1.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.177180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126980 restraints weight = 7010.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.33
r_work: 0.3318 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7068  Z= 0.121
  Angle     :  0.505   6.060   9572  Z= 0.262
  Chirality :  0.041   0.139   1054
  Planarity :  0.004   0.031   1156
  Dihedral  : 10.214 132.573   1136
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.99 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.24 (0.30), residues: 840
  helix:  2.22 (0.28), residues: 296
  sheet:  0.67 (0.37), residues: 220
  loop : -0.35 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  55 
 HIS   0.004   0.001   HIS E  52 
 PHE   0.018   0.002   PHE B  42 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.003   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03727 (  379)
  hydrogen bonds       : angle       4.58768 ( 1047)
  metal coordination   : bond        0.00181 (    6)
  SS BOND              : bond        0.00065 (    4)
  SS BOND              : angle       0.44311 (    8)
  covalent geometry    : bond        0.00277 ( 7058)
  covalent geometry    : angle       0.50495 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7669 (mtpt) cc_final: 0.6690 (mptt)
REVERT: A   29 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7937 (mtp85)
REVERT: A  138 LYS cc_start: 0.6717 (mttt) cc_final: 0.6307 (tppt)
REVERT: A  200 LYS cc_start: 0.8201 (mttt) cc_final: 0.7997 (mtpt)
REVERT: B   27 LYS cc_start: 0.7686 (mtpt) cc_final: 0.6700 (mptt)
REVERT: B   29 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7922 (mtp85)
REVERT: B  138 LYS cc_start: 0.6746 (mttt) cc_final: 0.6366 (tppt)
REVERT: C   83 MET cc_start: 0.7424 (mmt) cc_final: 0.7119 (mmm)
REVERT: C  107 MET cc_start: 0.9009 (ptp) cc_final: 0.8775 (pmm)
REVERT: E   83 MET cc_start: 0.7433 (mmt) cc_final: 0.7120 (mmm)
REVERT: F   61 ARG cc_start: 0.7222 (ptp-170) cc_final: 0.6806 (ttp-170)
  outliers start: 19
  outliers final: 15
  residues processed: 110
  average time/residue: 1.0784
  time to fit residues: 126.0064
Evaluate side-chains
  106 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 70 optimal weight:    0.2980
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.177801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127707 restraints weight = 6979.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.31
r_work: 0.3328 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7068  Z= 0.117
  Angle     :  0.497   6.010   9572  Z= 0.259
  Chirality :  0.041   0.140   1054
  Planarity :  0.004   0.031   1156
  Dihedral  :  9.975 128.044   1136
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.26 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.29 (0.30), residues: 840
  helix:  2.30 (0.28), residues: 296
  sheet:  0.73 (0.37), residues: 220
  loop : -0.39 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  55 
 HIS   0.003   0.001   HIS E  52 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.009   0.001   TYR D  71 
 ARG   0.002   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  379)
  hydrogen bonds       : angle       4.53586 ( 1047)
  metal coordination   : bond        0.00159 (    6)
  SS BOND              : bond        0.00103 (    4)
  SS BOND              : angle       0.47742 (    8)
  covalent geometry    : bond        0.00266 ( 7058)
  covalent geometry    : angle       0.49746 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7714 (mtpt) cc_final: 0.6709 (mptt)
REVERT: A   29 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7930 (mtp85)
REVERT: A  138 LYS cc_start: 0.6733 (mttt) cc_final: 0.6353 (tppt)
REVERT: B   27 LYS cc_start: 0.7655 (mtpt) cc_final: 0.6669 (mptt)
REVERT: B   29 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7911 (mtp85)
REVERT: B  138 LYS cc_start: 0.6723 (mttt) cc_final: 0.6346 (tppt)
REVERT: C   83 MET cc_start: 0.7440 (mmt) cc_final: 0.7125 (mmm)
REVERT: C  107 MET cc_start: 0.8970 (ptp) cc_final: 0.8709 (pmm)
REVERT: D   61 ARG cc_start: 0.7255 (ptp-170) cc_final: 0.6859 (ttp-170)
REVERT: E   66 LYS cc_start: 0.7064 (ttpt) cc_final: 0.6857 (ttmm)
REVERT: E   83 MET cc_start: 0.7463 (mmt) cc_final: 0.7138 (mmm)
  outliers start: 21
  outliers final: 15
  residues processed: 112
  average time/residue: 1.0752
  time to fit residues: 127.6136
Evaluate side-chains
  107 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    0.1980
   chunk 50 optimal weight:    8.9990
   chunk 77 optimal weight:    0.2980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4052 r_free = 0.4052 target = 0.175922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.125759 restraints weight = 7089.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.34
r_work: 0.3305 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7068  Z= 0.137
  Angle     :  0.518   6.061   9572  Z= 0.269
  Chirality :  0.042   0.143   1054
  Planarity :  0.004   0.030   1156
  Dihedral  :  9.999 125.629   1136
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 15.26 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.22 (0.30), residues: 840
  helix:  2.10 (0.28), residues: 308
  sheet:  0.81 (0.37), residues: 220
  loop : -0.47 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E  55 
 HIS   0.003   0.001   HIS D  49 
 PHE   0.021   0.002   PHE B  42 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.002   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  379)
  hydrogen bonds       : angle       4.61206 ( 1047)
  metal coordination   : bond        0.00205 (    6)
  SS BOND              : bond        0.00093 (    4)
  SS BOND              : angle       0.43018 (    8)
  covalent geometry    : bond        0.00321 ( 7058)
  covalent geometry    : angle       0.51838 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7734 (mtpt) cc_final: 0.6774 (mptt)
REVERT: A   29 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7950 (mtp85)
REVERT: A  138 LYS cc_start: 0.6699 (mttt) cc_final: 0.6292 (tppt)
REVERT: B   27 LYS cc_start: 0.7716 (mtpt) cc_final: 0.6750 (mptt)
REVERT: B  138 LYS cc_start: 0.6699 (mttt) cc_final: 0.6302 (tppt)
REVERT: C   66 LYS cc_start: 0.7615 (ttmm) cc_final: 0.6795 (ttmm)
REVERT: C   83 MET cc_start: 0.7460 (mmt) cc_final: 0.7138 (mmm)
REVERT: C  107 MET cc_start: 0.8996 (ptp) cc_final: 0.8748 (pmm)
REVERT: D   61 ARG cc_start: 0.7354 (ptp-170) cc_final: 0.7087 (ttp-170)
REVERT: E   83 MET cc_start: 0.7480 (mmt) cc_final: 0.7151 (mmm)
  outliers start: 27
  outliers final: 19
  residues processed: 116
  average time/residue: 1.0925
  time to fit residues: 134.1303
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.173932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.123566 restraints weight = 7053.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.37
r_work: 0.3313 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7068  Z= 0.130
  Angle     :  0.517   6.025   9572  Z= 0.269
  Chirality :  0.042   0.142   1054
  Planarity :  0.004   0.030   1156
  Dihedral  :  9.900 124.133   1136
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.62 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.25 (0.30), residues: 840
  helix:  2.13 (0.28), residues: 308
  sheet:  0.87 (0.37), residues: 220
  loop : -0.52 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E  55 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.018   0.001   PHE B  46 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.002   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03794 (  379)
  hydrogen bonds       : angle       4.58316 ( 1047)
  metal coordination   : bond        0.00182 (    6)
  SS BOND              : bond        0.00107 (    4)
  SS BOND              : angle       0.43952 (    8)
  covalent geometry    : bond        0.00303 ( 7058)
  covalent geometry    : angle       0.51657 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7743 (mtpt) cc_final: 0.6778 (mptt)
REVERT: A   29 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7939 (mtp85)
REVERT: A  138 LYS cc_start: 0.6685 (mttt) cc_final: 0.6277 (tppt)
REVERT: B   27 LYS cc_start: 0.7757 (mtpt) cc_final: 0.6754 (mptt)
REVERT: B   29 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7880 (mtp85)
REVERT: B  138 LYS cc_start: 0.6685 (mttt) cc_final: 0.6286 (tppt)
REVERT: C   83 MET cc_start: 0.7469 (mmt) cc_final: 0.7164 (mmm)
REVERT: C  107 MET cc_start: 0.8979 (ptp) cc_final: 0.8716 (pmm)
REVERT: D   61 ARG cc_start: 0.7363 (ptp-170) cc_final: 0.7099 (ttp-170)
REVERT: E   66 LYS cc_start: 0.7636 (ttmm) cc_final: 0.6854 (ttmm)
REVERT: E   83 MET cc_start: 0.7492 (mmt) cc_final: 0.7177 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 111
  average time/residue: 1.1099
  time to fit residues: 130.4957
Evaluate side-chains
  105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0570
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.175894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125295 restraints weight = 7096.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.40
r_work: 0.3339 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7068  Z= 0.110
  Angle     :  0.501   5.950   9572  Z= 0.260
  Chirality :  0.041   0.144   1054
  Planarity :  0.004   0.030   1156
  Dihedral  :  9.648 120.916   1136
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.57 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.36 (0.30), residues: 840
  helix:  2.27 (0.28), residues: 308
  sheet:  0.92 (0.37), residues: 220
  loop : -0.49 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E  55 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.023   0.001   PHE B  42 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.002   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  379)
  hydrogen bonds       : angle       4.49097 ( 1047)
  metal coordination   : bond        0.00136 (    6)
  SS BOND              : bond        0.00127 (    4)
  SS BOND              : angle       0.45715 (    8)
  covalent geometry    : bond        0.00249 ( 7058)
  covalent geometry    : angle       0.50066 ( 9564)

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7751 (mtpt) cc_final: 0.6758 (mptt)
REVERT: A   29 ARG cc_start: 0.8165 (mtp180) cc_final: 0.7912 (mtp85)
REVERT: A  138 LYS cc_start: 0.6703 (mttt) cc_final: 0.6318 (tppt)
REVERT: B   27 LYS cc_start: 0.7768 (mtpt) cc_final: 0.6758 (mptt)
REVERT: B   29 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7876 (mtp85)
REVERT: B   83 MET cc_start: 0.8316 (mmp) cc_final: 0.7941 (mmp)
REVERT: B  138 LYS cc_start: 0.6703 (mttt) cc_final: 0.6325 (tppt)
REVERT: C   66 LYS cc_start: 0.7582 (ttmm) cc_final: 0.6845 (ttmm)
REVERT: C   83 MET cc_start: 0.7498 (mmt) cc_final: 0.7187 (mmm)
REVERT: D   61 ARG cc_start: 0.7328 (ptp-170) cc_final: 0.7126 (ttp-170)
REVERT: E   66 LYS cc_start: 0.7616 (ttmm) cc_final: 0.6869 (ttmm)
REVERT: E   83 MET cc_start: 0.7477 (mmt) cc_final: 0.7162 (mmm)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 1.2617
  time to fit residues: 143.2711
Evaluate side-chains
  102 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.176571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125578 restraints weight = 7024.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.37
r_work: 0.3321 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7068  Z= 0.127
  Angle     :  0.518   6.734   9572  Z= 0.268
  Chirality :  0.041   0.150   1054
  Planarity :  0.004   0.031   1156
  Dihedral  :  9.662 119.544   1136
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.85 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.30 (0.30), residues: 840
  helix:  2.19 (0.28), residues: 308
  sheet:  0.97 (0.37), residues: 220
  loop : -0.56 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP E  55 
 HIS   0.003   0.001   HIS D  49 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  379)
  hydrogen bonds       : angle       4.55012 ( 1047)
  metal coordination   : bond        0.00173 (    6)
  SS BOND              : bond        0.00124 (    4)
  SS BOND              : angle       0.42887 (    8)
  covalent geometry    : bond        0.00294 ( 7058)
  covalent geometry    : angle       0.51822 ( 9564)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5413.38 seconds
wall clock time: 98 minutes 23.78 seconds (5903.78 seconds total)