Starting phenix.real_space_refine
on Sun Jul 27 19:14:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7v_15903/07_2025/8b7v_15903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7v_15903/07_2025/8b7v_15903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7v_15903/07_2025/8b7v_15903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7v_15903/07_2025/8b7v_15903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7v_15903/07_2025/8b7v_15903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7v_15903/07_2025/8b7v_15903.cif"
  }
  resolution = 3.0
  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=   0.004
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: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6330      2.51       5
     N    1713      2.21       5
     O    1965      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 99 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: 10050
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3350
          Classifications: {'peptide': 421}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412}
    Chain: "B"
      Number of atoms: 3350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3350
          Classifications: {'peptide': 421}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412}
    Chain: "C"
      Number of atoms: 3350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3350
          Classifications: {'peptide': 421}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412}
  Time building chain proxies: 6.60, per 1000 atoms: 0.66
  Number of scatterers: 10050
  At special positions: 0
  Unit cell: (97.11, 96.28, 76.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1965      8.00
     N    1713      7.00
     C    6330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  38 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  38 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  38 " 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: 2.62
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2238

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      4.0% alpha, 57.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 238 through 240
      No H-bonds generated for 'chain 'A' and resid 238 through 240'
    Processing helix  chain 'A' and resid 397 through 401
    Processing helix  chain 'B' and resid 113 through 116
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 238 through 240
      No H-bonds generated for 'chain 'B' and resid 238 through 240'
    Processing helix  chain 'B' and resid 397 through 401
    Processing helix  chain 'C' and resid 113 through 116
    Processing helix  chain 'C' and resid 159 through 163
      removed outlier: 3.566A  pdb=" N   ASP C 162 " --> pdb=" O   ASN C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 240
      No H-bonds generated for 'chain 'C' and resid 238 through 240'
    Processing helix  chain 'C' and resid 397 through 401
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 14
      removed outlier: 4.015A  pdb=" N   LEU A  46 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR A  62 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   PHE A  58 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   LYS A  52 " --> pdb=" O   LYS A  56 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LYS A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ALA A  65 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   PHE A  81 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   LEU A 139 " --> pdb=" O   ASN A 131 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA A 142 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLY A 150 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   ASN A 165 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA A 168 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN A 178 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   LEU A 187 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   GLU A 180 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   GLY A 185 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TRP A 213 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112
      removed outlier: 3.516A  pdb=" N   TRP A 120 " --> pdb=" O   HIS A 110 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   VAL A 112 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   TYR A 118 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254
    Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378
    Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 14
      removed outlier: 3.968A  pdb=" N   LEU B  46 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR B  62 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   PHE B  58 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LYS B  52 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   LYS B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA B  65 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   PHE B  81 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 11.618A  pdb=" N   GLY B 124 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 10.464A  pdb=" N   SER B 147 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   GLY B 126 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ARG B 145 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   GLY B 128 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   ALA B 143 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   GLU B 130 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU B 141 " --> pdb=" O   GLU B 130 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA B 142 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLY B 150 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   ASN B 165 " --> pdb=" O   GLY B 150 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA B 168 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   LEU B 187 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TRP B 213 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   MET B 320 " --> pdb=" O   TRP B 316 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 112
      removed outlier: 6.898A  pdb=" N   HIS B 110 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254
    Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 378
    Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 204
      removed outlier: 4.081A  pdb=" N   ALA C 142 " --> pdb=" O   ASP C 173 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY C 150 " --> pdb=" O   ASN C 165 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   ASN C 165 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA C 168 " --> pdb=" O   ASN C 197 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   LEU C 187 " --> pdb=" O   GLN C 178 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   GLU C 180 " --> pdb=" O   GLY C 185 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   GLY C 185 " --> pdb=" O   GLU C 180 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TRP C 213 " --> pdb=" O   THR C 236 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TRP C 284 " --> pdb=" O   MET C 280 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   MET C 320 " --> pdb=" O   TRP C 316 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU C  46 " --> pdb=" O   THR C  62 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   THR C  62 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   PHE C  58 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LYS C  52 " --> pdb=" O   LYS C  56 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LYS C  56 " --> pdb=" O   LYS C  52 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   SER C  57 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   GLY C  88 " --> pdb=" O   SER C  57 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TYR C  59 " --> pdb=" O   VAL C  86 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL C  86 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ASP C  61 " --> pdb=" O   ALA C  84 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA C  84 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   ASN C  63 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   LEU C 139 " --> pdb=" O   ASN C 131 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112
      removed outlier: 6.659A  pdb=" N   VAL C 112 " --> pdb=" O   TYR C 118 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   TYR C 118 " --> pdb=" O   VAL C 112 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 252 through 254
    Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379
      removed outlier: 4.020A  pdb=" N   LYS C 392 " --> pdb=" O   ASP C 379 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1551 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: 4.23

  Time building geometry restraints manager: 3.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2204
        1.34 -     1.46: 3960
        1.46 -     1.58: 4087
        1.58 -     1.71: 0
        1.71 -     1.83: 78
  Bond restraints: 10329
  Sorted by residual:
  bond pdb=" CD  ARG B 335 "
       pdb=" NE  ARG B 335 "
    ideal  model  delta    sigma   weight residual
    1.458  1.510 -0.052 1.40e-02 5.10e+03 1.39e+01
  bond pdb=" CD  ARG C 335 "
       pdb=" NE  ARG C 335 "
    ideal  model  delta    sigma   weight residual
    1.458  1.510 -0.052 1.40e-02 5.10e+03 1.36e+01
  bond pdb=" CD  ARG A 335 "
       pdb=" NE  ARG A 335 "
    ideal  model  delta    sigma   weight residual
    1.458  1.509 -0.051 1.40e-02 5.10e+03 1.31e+01
  bond pdb=" CE1 HIS B 275 "
       pdb=" NE2 HIS B 275 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.30e+01
  bond pdb=" CE1 HIS C 275 "
       pdb=" NE2 HIS C 275 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.27e+01
  ... (remaining 10324 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10932
        2.09 -     4.18: 2642
        4.18 -     6.28: 391
        6.28 -     8.37: 43
        8.37 -    10.46: 2
  Bond angle restraints: 14010
  Sorted by residual:
  angle pdb=" CA  ARG C 360 "
        pdb=" C   ARG C 360 "
        pdb=" N   PRO C 361 "
      ideal   model   delta    sigma   weight residual
     117.68  126.03   -8.35 7.10e-01 1.98e+00 1.38e+02
  angle pdb=" CA  THR B 317 "
        pdb=" C   THR B 317 "
        pdb=" N   PRO B 318 "
      ideal   model   delta    sigma   weight residual
     117.96  125.95   -7.99 8.10e-01 1.52e+00 9.72e+01
  angle pdb=" CA  THR C 317 "
        pdb=" C   THR C 317 "
        pdb=" N   PRO C 318 "
      ideal   model   delta    sigma   weight residual
     117.96  125.52   -7.56 8.10e-01 1.52e+00 8.71e+01
  angle pdb=" CA  ARG B 360 "
        pdb=" C   ARG B 360 "
        pdb=" N   PRO B 361 "
      ideal   model   delta    sigma   weight residual
     117.95  125.05   -7.10 7.70e-01 1.69e+00 8.50e+01
  angle pdb=" CA  ASP A 211 "
        pdb=" CB  ASP A 211 "
        pdb=" CG  ASP A 211 "
      ideal   model   delta    sigma   weight residual
     112.60  119.94   -7.34 1.00e+00 1.00e+00 5.39e+01
  ... (remaining 14005 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.77: 5385
       18.77 -    37.54: 313
       37.54 -    56.32: 60
       56.32 -    75.09: 58
       75.09 -    93.86: 22
  Dihedral angle restraints: 5838
    sinusoidal: 2274
      harmonic: 3564
  Sorted by residual:
  dihedral pdb=" N   GLN B  70 "
           pdb=" C   GLN B  70 "
           pdb=" CA  GLN B  70 "
           pdb=" CB  GLN B  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.61  -14.81     0      2.50e+00 1.60e-01 3.51e+01
  dihedral pdb=" CA  TYR B  32 "
           pdb=" C   TYR B  32 "
           pdb=" N   ARG B  33 "
           pdb=" CA  ARG B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.66  -29.34     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" C   GLN B  70 "
           pdb=" N   GLN B  70 "
           pdb=" CA  GLN B  70 "
           pdb=" CB  GLN B  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.11   14.51     0      2.50e+00 1.60e-01 3.37e+01
  ... (remaining 5835 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 1021
       0.116 -    0.232: 284
       0.232 -    0.348: 53
       0.348 -    0.464: 7
       0.464 -    0.580: 3
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" CA  GLN B  70 "
            pdb=" N   GLN B  70 "
            pdb=" C   GLN B  70 "
            pdb=" CB  GLN B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.40e+00
  chirality pdb=" CA  GLN A  70 "
            pdb=" N   GLN A  70 "
            pdb=" C   GLN A  70 "
            pdb=" CB  GLN A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.63e+00
  chirality pdb=" CA  GLN C  70 "
            pdb=" N   GLN C  70 "
            pdb=" C   GLN C  70 "
            pdb=" CB  GLN C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.84e+00
  ... (remaining 1365 not shown)

  Planarity restraints: 1854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 118 "   -0.202 2.00e-02 2.50e+03   1.21e-01 2.91e+02
        pdb=" CG  TYR C 118 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 118 "    0.078 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 118 "    0.087 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 118 "    0.075 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 118 "    0.089 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 118 "    0.043 2.00e-02 2.50e+03
        pdb=" OH  TYR C 118 "   -0.211 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 118 "   -0.164 2.00e-02 2.50e+03   9.65e-02 1.86e+02
        pdb=" CG  TYR A 118 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 118 "    0.073 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 118 "    0.059 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 118 "    0.066 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 118 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 118 "    0.036 2.00e-02 2.50e+03
        pdb=" OH  TYR A 118 "   -0.168 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  32 "    0.125 2.00e-02 2.50e+03   7.29e-02 1.06e+02
        pdb=" CG  TYR A  32 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  32 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  32 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  32 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  32 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  32 "   -0.018 2.00e-02 2.50e+03
        pdb=" OH  TYR A  32 "    0.124 2.00e-02 2.50e+03
  ... (remaining 1851 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 3752
        2.91 -     3.41: 8290
        3.41 -     3.90: 17791
        3.90 -     4.40: 19949
        4.40 -     4.90: 35305
  Nonbonded interactions: 85087
  Sorted by model distance:
  nonbonded pdb=" N   THR B 317 "
            pdb=" O   THR B 317 "
     model   vdw
     2.409 2.496
  nonbonded pdb=" N   THR C 317 "
            pdb=" O   THR C 317 "
     model   vdw
     2.425 2.496
  nonbonded pdb=" N   ARG C 360 "
            pdb=" O   ARG C 360 "
     model   vdw
     2.449 2.496
  nonbonded pdb=" N   THR A 317 "
            pdb=" O   THR A 317 "
     model   vdw
     2.465 2.496
  nonbonded pdb=" N   ARG B 360 "
            pdb=" O   ARG B 360 "
     model   vdw
     2.488 2.496
  ... (remaining 85082 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             0.160
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.810
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
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   0.052  10332  Z= 0.848
  Angle     :  1.804  10.461  14016  Z= 1.245
  Chirality :  0.114   0.580   1368
  Planarity :  0.019   0.276   1854
  Dihedral  : 15.921  93.858   3591
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 0.05
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  2.63 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  5.29 %
    Favored  : 92.94 %
  Cbeta Deviations :  0.71 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.16 (0.21), residues: 1257
  helix: -4.93 (0.16), residues: 18
  sheet:  1.57 (0.19), residues: 612
  loop : -1.85 (0.20), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.100   0.015   TRP A  51 
 HIS   0.012   0.003   HIS A   4 
 PHE   0.076   0.011   PHE C 254 
 TYR   0.211   0.022   TYR C 118 
 ARG   0.042   0.005   ARG B  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14269 (  560)
  hydrogen bonds       : angle       7.62839 ( 1551)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       1.38489 (    6)
  covalent geometry    : bond        0.01474 (10329)
  covalent geometry    : angle       1.80416 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 2
  residues processed: 146
  average time/residue: 1.5194
  time to fit residues: 235.0059
Evaluate side-chains
  76 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain B residue  420 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 95 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 114 optimal weight:    7.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A   4 HIS
A  70 GLN
A 349 GLN
B   4 HIS
B  70 GLN
B  90 ASN
C   4 HIS
C  70 GLN
C 159 ASN
C 165 ASN
C 341 ASN
C 386 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.070927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.057926 restraints weight = 20019.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 3.08
r_work: 0.2614 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10332  Z= 0.185
  Angle     :  0.638   5.616  14016  Z= 0.363
  Chirality :  0.046   0.148   1368
  Planarity :  0.004   0.064   1854
  Dihedral  :  6.309  61.099   1381
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.27 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  8.53 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.24 (0.21), residues: 1257
  helix: -4.98 (0.13), residues: 18
  sheet:  1.24 (0.19), residues: 600
  loop : -1.50 (0.20), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 120 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.009   0.001   PHE B  58 
 TYR   0.012   0.001   TYR A 343 
 ARG   0.008   0.001   ARG C 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  560)
  hydrogen bonds       : angle       5.69643 ( 1551)
  SS BOND              : bond        0.01542 (    3)
  SS BOND              : angle       3.34439 (    6)
  covalent geometry    : bond        0.00403 (10329)
  covalent geometry    : angle       0.63392 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7726 (mt-10)
REVERT: A   53 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: B   39 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8315 (pm20)
REVERT: B   49 GLU cc_start: 0.8986 (tt0) cc_final: 0.8676 (tm-30)
REVERT: B   53 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: B  148 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7827 (mt-10)
REVERT: B  179 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8531 (mtm)
REVERT: B  188 GLU cc_start: 0.9091 (tt0) cc_final: 0.8888 (tt0)
  outliers start: 27
  outliers final: 0
  residues processed: 89
  average time/residue: 1.4938
  time to fit residues: 142.2835
Evaluate side-chains
  57 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  179 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 50 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 106 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 159 ASN
C 416 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.068373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.055402 restraints weight = 20554.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 3.08
r_work: 0.2564 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10332  Z= 0.222
  Angle     :  0.605   8.277  14016  Z= 0.339
  Chirality :  0.045   0.150   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.617  24.494   1377
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.99 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.61 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.43 (0.21), residues: 1257
  helix: -5.05 (0.12), residues: 18
  sheet:  0.94 (0.20), residues: 606
  loop : -1.46 (0.20), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 120 
 HIS   0.004   0.001   HIS B 113 
 PHE   0.008   0.001   PHE A  58 
 TYR   0.016   0.001   TYR A 343 
 ARG   0.004   0.001   ARG C 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03326 (  560)
  hydrogen bonds       : angle       5.47140 ( 1551)
  SS BOND              : bond        0.01293 (    3)
  SS BOND              : angle       2.31908 (    6)
  covalent geometry    : bond        0.00494 (10329)
  covalent geometry    : angle       0.60320 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7891 (mt-10)
REVERT: A   53 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: B   39 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8580 (pm20)
REVERT: B   49 GLU cc_start: 0.9005 (tt0) cc_final: 0.8636 (tm-30)
REVERT: B   53 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7962 (tm-30)
REVERT: B  179 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8658 (mpp)
REVERT: B  188 GLU cc_start: 0.9066 (tt0) cc_final: 0.8841 (tt0)
REVERT: C   53 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8000 (mp0)
  outliers start: 18
  outliers final: 1
  residues processed: 80
  average time/residue: 1.5776
  time to fit residues: 134.4017
Evaluate side-chains
  65 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue   53 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:   30.0000
   chunk 38 optimal weight:   30.0000
   chunk 2 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   chunk 50 optimal weight:    7.9990
   chunk 60 optimal weight:   30.0000
   chunk 20 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    9.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
B 296 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.065178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.052623 restraints weight = 20991.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.2658 rms_B_bonded: 3.08
r_work: 0.2507 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  10332  Z= 0.261
  Angle     :  0.604   7.221  14016  Z= 0.338
  Chirality :  0.045   0.146   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.479  19.610   1377
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.07 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.69 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.58 (0.21), residues: 1257
  helix: -5.08 (0.11), residues: 18
  sheet:  0.79 (0.20), residues: 606
  loop : -1.49 (0.20), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 420 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.008   0.001   PHE C 398 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.006   0.001   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03272 (  560)
  hydrogen bonds       : angle       5.43741 ( 1551)
  SS BOND              : bond        0.00730 (    3)
  SS BOND              : angle       2.33061 (    6)
  covalent geometry    : bond        0.00584 (10329)
  covalent geometry    : angle       0.60264 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A   37 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: A   53 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8070 (tm-30)
REVERT: A   78 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8927 (m-30)
REVERT: B   39 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8665 (pm20)
REVERT: B   49 GLU cc_start: 0.9010 (tt0) cc_final: 0.8638 (tm-30)
REVERT: B   53 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: B   75 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8041 (mt-10)
REVERT: B  188 GLU cc_start: 0.9074 (tt0) cc_final: 0.8836 (tt0)
REVERT: C  100 ILE cc_start: 0.9063 (tp) cc_final: 0.8700 (pp)
REVERT: C  148 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7636 (mt-10)
  outliers start: 13
  outliers final: 1
  residues processed: 73
  average time/residue: 1.6148
  time to fit residues: 125.4528
Evaluate side-chains
  62 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain B residue   39 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 91 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 120 optimal weight:    9.9990
   chunk 106 optimal weight:    0.0970
   chunk 35 optimal weight:   20.0000
   chunk 111 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    5.8186

-------------------------------------------------------------------------------
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 = 0.2973 r_free = 0.2973 target = 0.068370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.055440 restraints weight = 20276.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 3.07
r_work: 0.2566 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10332  Z= 0.171
  Angle     :  0.566   7.751  14016  Z= 0.317
  Chirality :  0.043   0.140   1368
  Planarity :  0.004   0.063   1854
  Dihedral  :  5.357  24.756   1377
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.91 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.27 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.60 (0.22), residues: 1257
  helix: -5.06 (0.11), residues: 18
  sheet:  0.67 (0.20), residues: 588
  loop : -1.32 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 420 
 HIS   0.002   0.001   HIS B 113 
 PHE   0.006   0.001   PHE A  58 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.005   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02890 (  560)
  hydrogen bonds       : angle       5.29586 ( 1551)
  SS BOND              : bond        0.00466 (    3)
  SS BOND              : angle       4.26967 (    6)
  covalent geometry    : bond        0.00380 (10329)
  covalent geometry    : angle       0.55924 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: A  130 GLU cc_start: 0.9014 (tt0) cc_final: 0.8746 (pt0)
REVERT: A  195 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8070 (ptm-80)
REVERT: A  417 MET cc_start: 0.9006 (ttp) cc_final: 0.8637 (ppp)
REVERT: B   39 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8491 (pm20)
REVERT: B   49 GLU cc_start: 0.8998 (tt0) cc_final: 0.8625 (tm-30)
REVERT: B   53 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: B   75 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8093 (mt-10)
REVERT: B  148 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7866 (mt-10)
REVERT: B  179 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8593 (mtm)
REVERT: B  188 GLU cc_start: 0.9073 (tt0) cc_final: 0.8831 (tt0)
REVERT: C   37 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8284 (mt-10)
REVERT: C   53 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8007 (mp0)
REVERT: C  100 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8787 (pp)
REVERT: C  130 GLU cc_start: 0.8961 (tt0) cc_final: 0.8554 (pt0)
REVERT: C  148 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7549 (mt-10)
  outliers start: 12
  outliers final: 3
  residues processed: 77
  average time/residue: 1.6663
  time to fit residues: 136.0671
Evaluate side-chains
  71 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue   53 GLU
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0170
   chunk 43 optimal weight:    5.9990
   chunk 30 optimal weight:   30.0000
   chunk 65 optimal weight:   20.0000
   chunk 110 optimal weight:   30.0000
   chunk 56 optimal weight:    9.9990
   chunk 99 optimal weight:   40.0000
   chunk 55 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    3.9224

-------------------------------------------------------------------------------
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 = 0.2991 r_free = 0.2991 target = 0.069344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.056384 restraints weight = 20334.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 3.08
r_work: 0.2580 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10332  Z= 0.130
  Angle     :  0.538   6.483  14016  Z= 0.301
  Chirality :  0.043   0.138   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.090  21.180   1377
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.59 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.37 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.52 (0.22), residues: 1257
  helix: -5.04 (0.11), residues: 18
  sheet:  0.71 (0.20), residues: 588
  loop : -1.24 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 420 
 HIS   0.002   0.001   HIS A 113 
 PHE   0.005   0.001   PHE B  23 
 TYR   0.012   0.001   TYR C 343 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02603 (  560)
  hydrogen bonds       : angle       5.12586 ( 1551)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       3.21937 (    6)
  covalent geometry    : bond        0.00284 (10329)
  covalent geometry    : angle       0.53390 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.193 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: A   78 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8966 (m-30)
REVERT: A  130 GLU cc_start: 0.8952 (tt0) cc_final: 0.8724 (pt0)
REVERT: A  195 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8027 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9012 (tt0) cc_final: 0.8670 (tm-30)
REVERT: B   53 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7970 (tm-30)
REVERT: B   75 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8124 (mt-10)
REVERT: B   93 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7410 (pm20)
REVERT: B  148 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7693 (mt-10)
REVERT: B  188 GLU cc_start: 0.9043 (tt0) cc_final: 0.8793 (tt0)
REVERT: B  417 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8483 (ppp)
REVERT: C  100 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8767 (pp)
REVERT: C  130 GLU cc_start: 0.8954 (tt0) cc_final: 0.8493 (pt0)
REVERT: C  148 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7574 (mt-10)
  outliers start: 16
  outliers final: 3
  residues processed: 83
  average time/residue: 1.5706
  time to fit residues: 138.8204
Evaluate side-chains
  72 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 35 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 106 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 60 optimal weight:    0.7980
   chunk 80 optimal weight:   30.0000
   chunk 83 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 97 optimal weight:   20.0000
   overall best weight:    9.3590

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.064983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.052435 restraints weight = 21184.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2652 rms_B_bonded: 3.11
r_work: 0.2500 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  10332  Z= 0.258
  Angle     :  0.601   6.939  14016  Z= 0.333
  Chirality :  0.044   0.135   1368
  Planarity :  0.004   0.059   1854
  Dihedral  :  5.271  24.685   1377
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.15 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 11.67 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.62 (0.22), residues: 1257
  helix: -5.06 (0.11), residues: 18
  sheet:  0.64 (0.20), residues: 588
  loop : -1.30 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  51 
 HIS   0.003   0.001   HIS C 113 
 PHE   0.007   0.001   PHE A 254 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.004   0.001   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03079 (  560)
  hydrogen bonds       : angle       5.29632 ( 1551)
  SS BOND              : bond        0.00500 (    3)
  SS BOND              : angle       3.61369 (    6)
  covalent geometry    : bond        0.00580 (10329)
  covalent geometry    : angle       0.59661 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 1.073 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: A   78 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8944 (m-30)
REVERT: A  130 GLU cc_start: 0.9000 (tt0) cc_final: 0.8747 (pt0)
REVERT: A  195 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8009 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9056 (tt0) cc_final: 0.8658 (tm-30)
REVERT: B   53 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: B   75 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: B   93 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7411 (pm20)
REVERT: B  148 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7898 (mt-10)
REVERT: B  188 GLU cc_start: 0.9072 (tt0) cc_final: 0.8821 (tt0)
REVERT: C  100 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8671 (pp)
REVERT: C  130 GLU cc_start: 0.8995 (tt0) cc_final: 0.8576 (pt0)
REVERT: C  148 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7551 (mt-10)
  outliers start: 15
  outliers final: 4
  residues processed: 75
  average time/residue: 1.5520
  time to fit residues: 124.1756
Evaluate side-chains
  69 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 112 optimal weight:   10.0000
   chunk 119 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 118 optimal weight:    7.9990
   chunk 28 optimal weight:    8.9990
   chunk 90 optimal weight:    4.9990
   chunk 82 optimal weight:   30.0000
   chunk 10 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.2918 r_free = 0.2918 target = 0.066250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.053542 restraints weight = 20994.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.2683 rms_B_bonded: 3.15
r_work: 0.2530 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10332  Z= 0.178
  Angle     :  0.568   8.092  14016  Z= 0.316
  Chirality :  0.043   0.137   1368
  Planarity :  0.004   0.057   1854
  Dihedral  :  5.200  28.572   1377
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.99 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.16 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.59 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.64 (0.20), residues: 588
  loop : -1.27 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  51 
 HIS   0.002   0.001   HIS C 113 
 PHE   0.006   0.001   PHE B  23 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02803 (  560)
  hydrogen bonds       : angle       5.20753 ( 1551)
  SS BOND              : bond        0.00423 (    3)
  SS BOND              : angle       4.05512 (    6)
  covalent geometry    : bond        0.00399 (10329)
  covalent geometry    : angle       0.56153 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.190 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: A   78 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8874 (m-30)
REVERT: A  130 GLU cc_start: 0.8989 (tt0) cc_final: 0.8739 (pt0)
REVERT: A  148 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7792 (mt-10)
REVERT: A  195 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7979 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9059 (tt0) cc_final: 0.8620 (tm-30)
REVERT: B   53 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8009 (tm-30)
REVERT: B   75 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8075 (mt-10)
REVERT: B   93 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7331 (pm20)
REVERT: B  148 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: B  179 MET cc_start: 0.9139 (mpp) cc_final: 0.8386 (mpt)
REVERT: B  188 GLU cc_start: 0.9057 (tt0) cc_final: 0.8796 (tt0)
REVERT: C  100 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8684 (pp)
REVERT: C  130 GLU cc_start: 0.8965 (tt0) cc_final: 0.8528 (pt0)
REVERT: C  148 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7527 (mt-10)
  outliers start: 13
  outliers final: 4
  residues processed: 75
  average time/residue: 1.6052
  time to fit residues: 128.3830
Evaluate side-chains
  72 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 82 optimal weight:   30.0000
   chunk 35 optimal weight:   20.0000
   chunk 69 optimal weight:    6.9990
   chunk 118 optimal weight:   20.0000
   chunk 28 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:   20.0000
   chunk 96 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    5.7788

-------------------------------------------------------------------------------
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 = 0.2967 r_free = 0.2967 target = 0.068309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.055290 restraints weight = 20395.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 3.09
r_work: 0.2554 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8847
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10332  Z= 0.172
  Angle     :  0.573   9.548  14016  Z= 0.316
  Chirality :  0.043   0.136   1368
  Planarity :  0.004   0.058   1854
  Dihedral  :  5.124  27.280   1377
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.07 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.16 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.59 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.62 (0.20), residues: 591
  loop : -1.26 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  51 
 HIS   0.002   0.001   HIS B 113 
 PHE   0.006   0.001   PHE B  23 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02730 (  560)
  hydrogen bonds       : angle       5.16510 ( 1551)
  SS BOND              : bond        0.00414 (    3)
  SS BOND              : angle       3.71476 (    6)
  covalent geometry    : bond        0.00387 (10329)
  covalent geometry    : angle       0.56779 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.174 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: A  130 GLU cc_start: 0.8995 (tt0) cc_final: 0.8764 (pt0)
REVERT: A  148 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7839 (mt-10)
REVERT: A  195 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8093 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9029 (tt0) cc_final: 0.8677 (tm-30)
REVERT: B   53 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: B   75 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8076 (mt-10)
REVERT: B   93 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7344 (pm20)
REVERT: B  148 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7871 (mt-10)
REVERT: B  179 MET cc_start: 0.9173 (mpp) cc_final: 0.8456 (mpt)
REVERT: B  188 GLU cc_start: 0.9069 (tt0) cc_final: 0.8817 (tt0)
REVERT: C  100 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8770 (pp)
REVERT: C  130 GLU cc_start: 0.8976 (tt0) cc_final: 0.8580 (pt0)
REVERT: C  148 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7567 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 72
  average time/residue: 1.5623
  time to fit residues: 119.9172
Evaluate side-chains
  70 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  166 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 120 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 75 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 91 optimal weight:    0.0040
   chunk 24 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    4.6000

-------------------------------------------------------------------------------
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 = 0.2974 r_free = 0.2974 target = 0.068737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.055799 restraints weight = 20342.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.2721 rms_B_bonded: 3.09
r_work: 0.2566 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10332  Z= 0.146
  Angle     :  0.567   8.809  14016  Z= 0.312
  Chirality :  0.043   0.140   1368
  Planarity :  0.004   0.061   1854
  Dihedral  :  5.083  26.845   1377
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.99 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.06 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.56 (0.22), residues: 1257
  helix: -5.04 (0.11), residues: 18
  sheet:  0.63 (0.20), residues: 591
  loop : -1.23 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 420 
 HIS   0.002   0.001   HIS C 113 
 PHE   0.005   0.001   PHE B  23 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02642 (  560)
  hydrogen bonds       : angle       5.13691 ( 1551)
  SS BOND              : bond        0.00371 (    3)
  SS BOND              : angle       3.30986 (    6)
  covalent geometry    : bond        0.00327 (10329)
  covalent geometry    : angle       0.56267 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8112 (tm-30)
REVERT: A  130 GLU cc_start: 0.8976 (tt0) cc_final: 0.8755 (pt0)
REVERT: A  148 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: A  195 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9024 (tt0) cc_final: 0.8673 (tm-30)
REVERT: B   53 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: B   75 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8080 (mt-10)
REVERT: B   93 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7336 (pm20)
REVERT: B  148 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7848 (mt-10)
REVERT: B  179 MET cc_start: 0.9156 (mpp) cc_final: 0.8439 (mpt)
REVERT: B  188 GLU cc_start: 0.9069 (tt0) cc_final: 0.8817 (tt0)
REVERT: C  100 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8761 (pp)
REVERT: C  130 GLU cc_start: 0.8952 (tt0) cc_final: 0.8564 (pt0)
REVERT: C  148 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7482 (mt-10)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 1.5338
  time to fit residues: 118.0065
Evaluate side-chains
  72 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9990
   chunk 92 optimal weight:   20.0000
   chunk 85 optimal weight:   20.0000
   chunk 32 optimal weight:   20.0000
   chunk 56 optimal weight:    6.9990
   chunk 102 optimal weight:   20.0000
   chunk 72 optimal weight:   30.0000
   chunk 114 optimal weight:    6.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.2912 r_free = 0.2912 target = 0.066016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.053346 restraints weight = 20923.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.2672 rms_B_bonded: 3.14
r_work: 0.2520 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10332  Z= 0.195
  Angle     :  0.576   8.674  14016  Z= 0.317
  Chirality :  0.043   0.138   1368
  Planarity :  0.004   0.063   1854
  Dihedral  :  5.118  27.142   1377
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.23 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.16 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.56 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.62 (0.20), residues: 591
  loop : -1.22 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  51 
 HIS   0.003   0.001   HIS B 113 
 PHE   0.006   0.001   PHE B  23 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.003   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02802 (  560)
  hydrogen bonds       : angle       5.16502 ( 1551)
  SS BOND              : bond        0.00397 (    3)
  SS BOND              : angle       3.39813 (    6)
  covalent geometry    : bond        0.00436 (10329)
  covalent geometry    : angle       0.57212 (14010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4562.52 seconds
wall clock time: 79 minutes 14.00 seconds (4754.00 seconds total)