Starting phenix.real_space_refine
on Sat Jul 26 13:46:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i7p_52658/07_2025/9i7p_52658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i7p_52658/07_2025/9i7p_52658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i7p_52658/07_2025/9i7p_52658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i7p_52658/07_2025/9i7p_52658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i7p_52658/07_2025/9i7p_52658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i7p_52658/07_2025/9i7p_52658.cif"
  }
  resolution = 3.2
  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=   0.004 sd=   0.068
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     S      24      5.16       5
     C    5646      2.51       5
     N    1339      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8644
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "C"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 451
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "E"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 326
          Classifications: {'peptide': 43}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 39}
    Chain: "G"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 298
          Classifications: {'peptide': 41}
          Link IDs: {'TRANS': 40}
    Chain: "I"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 410
          Classifications: {'peptide': 51}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46}
    Chain: "A"
      Number of atoms: 2466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2466
          Classifications: {'peptide': 318}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 451
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "C"
      Number of atoms: 124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 124
          Unusual residues: {'DU0': 1, 'PC1': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
    Chain: "G"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'DU0': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 47
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
    Chain: "A"
      Number of atoms: 142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 142
          Unusual residues: {'DU0': 2, 'PC1': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 40
    Chain: "D"
      Number of atoms: 166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 166
          Unusual residues: {'DU0': 1, 'PC1': 2, 'PLC': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
  Restraints were copied for chains:
    B, F, H, J
  Time building chain proxies: 6.40, per 1000 atoms: 0.74
  Number of scatterers: 8644
  At special positions: 0
  Unit cell: (112.995, 149.823, 92.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      11     15.00
     O    1624      8.00
     N    1339      7.00
     C    5646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 870.8 milliseconds
  

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 2 sheets defined
      38.8% alpha, 33.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'C' and resid 62 through 117
      Proline residue:  C 100  - end of helix
    Processing helix  chain 'E' and resid 11 through 50
      removed outlier: 3.545A  pdb=" N   ARG E  16 " --> pdb=" O   PRO E  12 " (cutoff:3.500A)
      Proline residue:  E  40  - end of helix
    Processing helix  chain 'G' and resid 17 through 26
      removed outlier: 3.877A  pdb=" N   ALA G  23 " --> pdb=" O   GLY G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 48
    Processing helix  chain 'G' and resid 49 through 56
    Processing helix  chain 'I' and resid 23 through 57
      removed outlier: 5.536A  pdb=" N   LEU I  46 " --> pdb=" O   HIS I  42 " (cutoff:3.500A)
      Proline residue:  I  47  - end of helix
    Processing helix  chain 'I' and resid 64 through 68
    Processing helix  chain 'A' and resid 22 through 34
      removed outlier: 3.754A  pdb=" N   ALA A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'D' and resid 62 through 117
      Proline residue:  D 100  - end of helix
    Processing helix  chain 'F' and resid 11 through 50
      removed outlier: 3.545A  pdb=" N   ARG F  16 " --> pdb=" O   PRO F  12 " (cutoff:3.500A)
      Proline residue:  F  40  - end of helix
    Processing helix  chain 'H' and resid 17 through 26
      removed outlier: 3.877A  pdb=" N   ALA H  23 " --> pdb=" O   GLY H  19 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 48
    Processing helix  chain 'H' and resid 49 through 56
    Processing helix  chain 'J' and resid 23 through 57
      removed outlier: 5.536A  pdb=" N   LEU J  46 " --> pdb=" O   HIS J  42 " (cutoff:3.500A)
      Proline residue:  J  47  - end of helix
    Processing helix  chain 'J' and resid 64 through 68
    Processing helix  chain 'B' and resid 22 through 34
      removed outlier: 3.754A  pdb=" N   ALA B  27 " --> pdb=" O   ASP B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 47 through 52
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73
      removed outlier: 6.466A  pdb=" N   PHE A  78 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ALA A 146 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   THR A 174 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS A 293 " --> pdb=" O   ASP A 289 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73
      removed outlier: 6.466A  pdb=" N   PHE B  78 " --> pdb=" O   PHE B  72 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ALA B 146 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   THR B 174 " --> pdb=" O   PRO B 166 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS B 293 " --> pdb=" O   ASP B 289 " (cutoff:3.500A)

    594 hydrogen bonds defined for protein.
    1704 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: 2.36

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1342
        1.32 -     1.44: 2320
        1.44 -     1.56: 5107
        1.56 -     1.68: 24
        1.68 -     1.80: 46
  Bond restraints: 8839
  Sorted by residual:
  bond pdb=" CG  LEU A 336 "
       pdb=" CD1 LEU A 336 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  bond pdb=" CG  LEU B 336 "
       pdb=" CD1 LEU B 336 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  bond pdb=" C09 DU0 B 402 "
       pdb=" O16 DU0 B 402 "
    ideal  model  delta    sigma   weight residual
    1.404  1.431 -0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C09 DU0 A 402 "
       pdb=" O16 DU0 A 402 "
    ideal  model  delta    sigma   weight residual
    1.404  1.431 -0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C09 DU0 D 204 "
       pdb=" O16 DU0 D 204 "
    ideal  model  delta    sigma   weight residual
    1.404  1.431 -0.027 2.00e-02 2.50e+03 1.86e+00
  ... (remaining 8834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 11280
        1.57 -     3.13: 565
        3.13 -     4.70: 114
        4.70 -     6.27: 18
        6.27 -     7.84: 14
  Bond angle restraints: 11991
  Sorted by residual:
  angle pdb=" C   PRO A 343 "
        pdb=" N   ASN A 344 "
        pdb=" CA  ASN A 344 "
      ideal   model   delta    sigma   weight residual
     122.46  126.82   -4.36 1.41e+00 5.03e-01 9.57e+00
  angle pdb=" C   PRO B 343 "
        pdb=" N   ASN B 344 "
        pdb=" CA  ASN B 344 "
      ideal   model   delta    sigma   weight residual
     122.46  126.82   -4.36 1.41e+00 5.03e-01 9.57e+00
  angle pdb=" CD  ARG I  29 "
        pdb=" NE  ARG I  29 "
        pdb=" CZ  ARG I  29 "
      ideal   model   delta    sigma   weight residual
     124.40  127.91   -3.51 1.40e+00 5.10e-01 6.29e+00
  angle pdb=" CD  ARG J  29 "
        pdb=" NE  ARG J  29 "
        pdb=" CZ  ARG J  29 "
      ideal   model   delta    sigma   weight residual
     124.40  127.91   -3.51 1.40e+00 5.10e-01 6.29e+00
  angle pdb=" C   LYS A 103 "
        pdb=" N   MET A 104 "
        pdb=" CA  MET A 104 "
      ideal   model   delta    sigma   weight residual
     121.75  117.48    4.27 1.73e+00 3.34e-01 6.10e+00
  ... (remaining 11986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.39: 5418
       27.39 -    54.77: 337
       54.77 -    82.16: 104
       82.16 -   109.55: 38
      109.55 -   136.93: 16
  Dihedral angle restraints: 5913
    sinusoidal: 2975
      harmonic: 2938
  Sorted by residual:
  dihedral pdb=" CD  ARG J  29 "
           pdb=" NE  ARG J  29 "
           pdb=" CZ  ARG J  29 "
           pdb=" NH1 ARG J  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.47  -80.47     1      1.00e+01 1.00e-02 8.01e+01
  dihedral pdb=" CD  ARG I  29 "
           pdb=" NE  ARG I  29 "
           pdb=" CZ  ARG I  29 "
           pdb=" NH1 ARG I  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.47  -80.47     1      1.00e+01 1.00e-02 8.01e+01
  dihedral pdb=" C26 DU0 B 403 "
           pdb=" C24 DU0 B 403 "
           pdb=" C25 DU0 B 403 "
           pdb=" O23 DU0 B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     189.32   52.39  136.93     1      3.00e+01 1.11e-03 1.85e+01
  ... (remaining 5910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 865
       0.041 -    0.081: 312
       0.081 -    0.122: 108
       0.122 -    0.163: 36
       0.163 -    0.203: 8
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" CA  ASN B 344 "
            pdb=" N   ASN B 344 "
            pdb=" C   ASN B 344 "
            pdb=" CB  ASN B 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ASN A 344 "
            pdb=" N   ASN A 344 "
            pdb=" C   ASN A 344 "
            pdb=" CB  ASN A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ILE A 345 "
            pdb=" N   ILE A 345 "
            pdb=" C   ILE A 345 "
            pdb=" CB  ILE A 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.38e-01
  ... (remaining 1326 not shown)

  Planarity restraints: 1428
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG J  29 "    0.931 9.50e-02 1.11e+02   4.18e-01 1.17e+02
        pdb=" NE  ARG J  29 "   -0.077 2.00e-02 2.50e+03
        pdb=" CZ  ARG J  29 "    0.046 2.00e-02 2.50e+03
        pdb=" NH1 ARG J  29 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG J  29 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG I  29 "   -0.931 9.50e-02 1.11e+02   4.18e-01 1.17e+02
        pdb=" NE  ARG I  29 "    0.077 2.00e-02 2.50e+03
        pdb=" CZ  ARG I  29 "   -0.046 2.00e-02 2.50e+03
        pdb=" NH1 ARG I  29 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG I  29 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 301 "    0.196 9.50e-02 1.11e+02   8.84e-02 5.97e+00
        pdb=" NE  ARG A 301 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 301 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 301 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 301 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1425 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 181
        2.68 -     3.24: 7779
        3.24 -     3.79: 12611
        3.79 -     4.35: 17347
        4.35 -     4.90: 30199
  Nonbonded interactions: 68117
  Sorted by model distance:
  nonbonded pdb=" NE  ARG J  38 "
            pdb=" OD2 ASP B 144 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" NE  ARG I  38 "
            pdb=" OD2 ASP A 144 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" O   TYR E  37 "
            pdb=" NH1 ARG A  32 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" O   TYR F  37 "
            pdb=" NH1 ARG B  32 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" NH2 ARG A 301 "
            pdb=" O   ALA A 304 "
     model   vdw
     2.295 3.120
  ... (remaining 68112 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 62 through 118 or (resid 201 and (name N or name C1 or nam \ 
e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or  \ 
name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ 
 or name C29 or name C2A or name C2B or name C3 or name C31 or name C32 or name  \ 
C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ 
ame C3A or name O11 or name O12 or name O13 or name O14 or name O21 or name O22  \ 
or name O31 or name O32 or name P )) or resid 203))
  selection = (chain 'D' and (resid 62 through 118 or resid 201 or (resid 203 and (name N or n \ 
ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or \ 
 name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 
7 or name C28 or name C29 or name C2A or name C2B or name C3 or name C31 or name \ 
 C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or  \ 
name C39 or name C3A or name O11 or name O12 or name O13 or name O14 or name O21 \ 
 or name O22 or name O31 or name O32 or name P ))))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

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:             2.060
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.530
  Find NCS groups from input model:        0.310
  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:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
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      :  0.007   0.063   8839  Z= 0.287
  Angle     :  0.836   7.836  11991  Z= 0.405
  Chirality :  0.051   0.203   1329
  Planarity :  0.018   0.418   1428
  Dihedral  : 21.096 136.931   4025
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.46 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.26), residues: 996
  helix:  0.13 (0.24), residues: 362
  sheet:  1.04 (0.25), residues: 408
  loop : -0.06 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP G  50 
 HIS   0.004   0.001   HIS J  42 
 PHE   0.018   0.002   PHE A 128 
 TYR   0.014   0.003   TYR D 111 
 ARG   0.057   0.004   ARG J  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18627 (  594)
  hydrogen bonds       : angle       7.65136 ( 1704)
  covalent geometry    : bond        0.00680 ( 8839)
  covalent geometry    : angle       0.83598 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.946 
Fit side-chains
REVERT: C   85 ARG cc_start: 0.8503 (tpt-90) cc_final: 0.8233 (tpt90)
REVERT: I   43 TYR cc_start: 0.8615 (m-80) cc_final: 0.8220 (m-80)
REVERT: A   33 GLN cc_start: 0.8063 (mt0) cc_final: 0.7684 (mp10)
REVERT: A  104 MET cc_start: 0.8658 (ptm) cc_final: 0.8450 (ptp)
REVERT: A  168 PHE cc_start: 0.6377 (t80) cc_final: 0.6164 (t80)
REVERT: A  207 ASP cc_start: 0.6757 (t0) cc_final: 0.6261 (p0)
REVERT: A  244 LYS cc_start: 0.8694 (mttm) cc_final: 0.8368 (mtmt)
REVERT: A  307 MET cc_start: 0.8287 (ttp) cc_final: 0.8002 (ttm)
REVERT: A  308 MET cc_start: 0.8529 (mmm) cc_final: 0.7806 (ttp)
REVERT: A  315 ASP cc_start: 0.7834 (t0) cc_final: 0.7623 (t0)
REVERT: D   85 ARG cc_start: 0.8503 (tpt-90) cc_final: 0.8233 (tpt90)
REVERT: J   43 TYR cc_start: 0.8612 (m-80) cc_final: 0.8219 (m-80)
REVERT: B   33 GLN cc_start: 0.8065 (mt0) cc_final: 0.7684 (mp10)
REVERT: B  104 MET cc_start: 0.8657 (ptm) cc_final: 0.8447 (ptp)
REVERT: B  168 PHE cc_start: 0.6370 (t80) cc_final: 0.6161 (t80)
REVERT: B  207 ASP cc_start: 0.6761 (t0) cc_final: 0.6266 (p0)
REVERT: B  244 LYS cc_start: 0.8692 (mttm) cc_final: 0.8362 (mtmt)
REVERT: B  307 MET cc_start: 0.8291 (ttp) cc_final: 0.8004 (ttm)
REVERT: B  308 MET cc_start: 0.8542 (mmm) cc_final: 0.7777 (ttp)
REVERT: B  315 ASP cc_start: 0.7833 (t0) cc_final: 0.7623 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1930
  time to fit residues: 51.0019
Evaluate side-chains
  156 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
I  27 GLN
A  29 GLN
A 344 ASN
B  29 GLN
B 344 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.165439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.123181 restraints weight = 10577.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.38
r_work: 0.3319 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8839  Z= 0.177
  Angle     :  0.664   6.987  11991  Z= 0.332
  Chirality :  0.044   0.206   1329
  Planarity :  0.005   0.036   1428
  Dihedral  : 17.838 123.488   2227
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  6.31 %
    Favored  : 92.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.27), residues: 996
  helix:  2.12 (0.26), residues: 362
  sheet:  1.14 (0.26), residues: 408
  loop :  0.12 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 221 
 HIS   0.002   0.001   HIS J  42 
 PHE   0.013   0.001   PHE B 347 
 TYR   0.016   0.002   TYR C  66 
 ARG   0.004   0.001   ARG B 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  594)
  hydrogen bonds       : angle       5.14491 ( 1704)
  covalent geometry    : bond        0.00406 ( 8839)
  covalent geometry    : angle       0.66408 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.942 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7795 (mt) cc_final: 0.7562 (mm)
REVERT: A   33 GLN cc_start: 0.8133 (mt0) cc_final: 0.7817 (mp10)
REVERT: A  207 ASP cc_start: 0.7092 (t0) cc_final: 0.6858 (p0)
REVERT: A  244 LYS cc_start: 0.8803 (mttm) cc_final: 0.8554 (mtmt)
REVERT: A  308 MET cc_start: 0.8519 (mmm) cc_final: 0.8174 (ttp)
REVERT: F   42 ILE cc_start: 0.7797 (mt) cc_final: 0.7564 (mm)
REVERT: B   33 GLN cc_start: 0.8135 (mt0) cc_final: 0.7817 (mp10)
REVERT: B  207 ASP cc_start: 0.7107 (t0) cc_final: 0.6869 (p0)
REVERT: B  244 LYS cc_start: 0.8791 (mttm) cc_final: 0.8541 (mtmt)
REVERT: B  308 MET cc_start: 0.8530 (mmm) cc_final: 0.8138 (ttp)
  outliers start: 10
  outliers final: 6
  residues processed: 142
  average time/residue: 0.1527
  time to fit residues: 32.6580
Evaluate side-chains
  145 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 13 optimal weight:    0.0370
   chunk 74 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.1662

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
B 150 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.164593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.122081 restraints weight = 10806.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.41
r_work: 0.3306 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8839  Z= 0.183
  Angle     :  0.600   5.725  11991  Z= 0.309
  Chirality :  0.043   0.222   1329
  Planarity :  0.004   0.038   1428
  Dihedral  : 16.116 115.976   2227
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  8.50 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.27), residues: 996
  helix:  2.37 (0.27), residues: 362
  sheet:  1.06 (0.26), residues: 408
  loop : -0.01 (0.43), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 197 
 HIS   0.002   0.001   HIS B  82 
 PHE   0.016   0.001   PHE B 168 
 TYR   0.010   0.001   TYR I  43 
 ARG   0.002   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03583 (  594)
  hydrogen bonds       : angle       4.86231 ( 1704)
  covalent geometry    : bond        0.00425 ( 8839)
  covalent geometry    : angle       0.60018 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.853 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7862 (mt) cc_final: 0.7552 (mm)
REVERT: A   33 GLN cc_start: 0.8124 (mt0) cc_final: 0.7826 (mp10)
REVERT: A  207 ASP cc_start: 0.7033 (t0) cc_final: 0.6818 (p0)
REVERT: A  244 LYS cc_start: 0.8822 (mttm) cc_final: 0.8585 (mtmt)
REVERT: A  308 MET cc_start: 0.8539 (mmm) cc_final: 0.8194 (ttp)
REVERT: F   42 ILE cc_start: 0.7863 (mt) cc_final: 0.7552 (mm)
REVERT: B   33 GLN cc_start: 0.8115 (mt0) cc_final: 0.7820 (mp10)
REVERT: B  207 ASP cc_start: 0.7043 (t0) cc_final: 0.6836 (p0)
REVERT: B  244 LYS cc_start: 0.8815 (mttm) cc_final: 0.8574 (mtmt)
REVERT: B  308 MET cc_start: 0.8540 (mmm) cc_final: 0.8133 (ttp)
  outliers start: 18
  outliers final: 16
  residues processed: 154
  average time/residue: 0.1526
  time to fit residues: 35.6386
Evaluate side-chains
  152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 88 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
J  27 GLN
B 344 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.166235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.124115 restraints weight = 10662.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.37
r_work: 0.3328 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8839  Z= 0.135
  Angle     :  0.554   6.061  11991  Z= 0.283
  Chirality :  0.041   0.240   1329
  Planarity :  0.004   0.042   1428
  Dihedral  : 14.818 104.255   2227
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.95 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.27), residues: 996
  helix:  2.57 (0.27), residues: 362
  sheet:  1.07 (0.26), residues: 406
  loop : -0.03 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 197 
 HIS   0.001   0.000   HIS A  82 
 PHE   0.015   0.001   PHE B 168 
 TYR   0.010   0.001   TYR D 105 
 ARG   0.003   0.000   ARG I  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03071 (  594)
  hydrogen bonds       : angle       4.56551 ( 1704)
  covalent geometry    : bond        0.00315 ( 8839)
  covalent geometry    : angle       0.55397 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.915 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7853 (mt) cc_final: 0.7529 (mm)
REVERT: A   33 GLN cc_start: 0.8111 (mt0) cc_final: 0.7823 (mp10)
REVERT: A  207 ASP cc_start: 0.7048 (t0) cc_final: 0.6822 (p0)
REVERT: A  244 LYS cc_start: 0.8857 (mttm) cc_final: 0.8475 (mtmm)
REVERT: A  268 GLU cc_start: 0.8151 (tt0) cc_final: 0.7784 (tp30)
REVERT: A  308 MET cc_start: 0.8503 (mmm) cc_final: 0.8182 (ttp)
REVERT: F   42 ILE cc_start: 0.7852 (mt) cc_final: 0.7529 (mm)
REVERT: B   33 GLN cc_start: 0.8105 (mt0) cc_final: 0.7820 (mp10)
REVERT: B  207 ASP cc_start: 0.7048 (t0) cc_final: 0.6831 (p0)
REVERT: B  244 LYS cc_start: 0.8859 (mttm) cc_final: 0.8477 (mtmm)
REVERT: B  268 GLU cc_start: 0.8150 (tt0) cc_final: 0.7792 (tp30)
REVERT: B  308 MET cc_start: 0.8505 (mmm) cc_final: 0.8158 (ttp)
  outliers start: 18
  outliers final: 14
  residues processed: 160
  average time/residue: 0.1515
  time to fit residues: 36.9330
Evaluate side-chains
  156 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain G residue   21 TYR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain H residue   21 TYR
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0770
   chunk 63 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.166977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.124908 restraints weight = 10598.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.37
r_work: 0.3334 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8839  Z= 0.126
  Angle     :  0.541   7.888  11991  Z= 0.277
  Chirality :  0.041   0.246   1329
  Planarity :  0.004   0.042   1428
  Dihedral  : 13.927  94.229   2227
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.29 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.27), residues: 996
  helix:  2.75 (0.26), residues: 362
  sheet:  1.08 (0.26), residues: 406
  loop : -0.06 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 197 
 HIS   0.002   0.001   HIS B 316 
 PHE   0.012   0.001   PHE H  45 
 TYR   0.007   0.001   TYR E  37 
 ARG   0.003   0.000   ARG I  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02901 (  594)
  hydrogen bonds       : angle       4.38443 ( 1704)
  covalent geometry    : bond        0.00289 ( 8839)
  covalent geometry    : angle       0.54132 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.859 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7879 (mt) cc_final: 0.7562 (mm)
REVERT: I   32 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7610 (pttt)
REVERT: A   33 GLN cc_start: 0.8176 (mt0) cc_final: 0.7855 (mp10)
REVERT: A   51 GLN cc_start: 0.8728 (mt0) cc_final: 0.8316 (mp10)
REVERT: A  207 ASP cc_start: 0.7016 (t0) cc_final: 0.6782 (p0)
REVERT: A  244 LYS cc_start: 0.8878 (mttm) cc_final: 0.8541 (mtmm)
REVERT: A  268 GLU cc_start: 0.8134 (tt0) cc_final: 0.7787 (tp30)
REVERT: A  308 MET cc_start: 0.8474 (mmm) cc_final: 0.8179 (ttp)
REVERT: F   42 ILE cc_start: 0.7874 (mt) cc_final: 0.7558 (mm)
REVERT: J   32 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7616 (pttt)
REVERT: B   33 GLN cc_start: 0.8163 (mt0) cc_final: 0.7845 (mp10)
REVERT: B   51 GLN cc_start: 0.8732 (mt0) cc_final: 0.8320 (mp10)
REVERT: B  207 ASP cc_start: 0.7016 (t0) cc_final: 0.6796 (p0)
REVERT: B  244 LYS cc_start: 0.8876 (mttm) cc_final: 0.8536 (mtmm)
REVERT: B  268 GLU cc_start: 0.8134 (tt0) cc_final: 0.7787 (tp30)
REVERT: B  308 MET cc_start: 0.8493 (mmm) cc_final: 0.8133 (ttp)
  outliers start: 14
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1666
  time to fit residues: 38.3708
Evaluate side-chains
  151 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   21 TYR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain H residue   21 TYR
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 86 optimal weight:    0.3980
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN
A 344 ASN
B 147 GLN
B 344 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.165469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.123450 restraints weight = 10540.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.37
r_work: 0.3327 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8839  Z= 0.134
  Angle     :  0.530   5.698  11991  Z= 0.274
  Chirality :  0.040   0.225   1329
  Planarity :  0.004   0.042   1428
  Dihedral  : 13.410  88.547   2227
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.53 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.27), residues: 996
  helix:  2.82 (0.26), residues: 362
  sheet:  1.05 (0.26), residues: 406
  loop : -0.10 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 197 
 HIS   0.002   0.001   HIS A 150 
 PHE   0.010   0.001   PHE A 168 
 TYR   0.007   0.001   TYR A 181 
 ARG   0.002   0.000   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02864 (  594)
  hydrogen bonds       : angle       4.37441 ( 1704)
  covalent geometry    : bond        0.00311 ( 8839)
  covalent geometry    : angle       0.53015 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.821 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7890 (mt) cc_final: 0.7592 (mm)
REVERT: I   32 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7610 (pttt)
REVERT: A   33 GLN cc_start: 0.8182 (mt0) cc_final: 0.7815 (mp10)
REVERT: A   51 GLN cc_start: 0.8735 (mt0) cc_final: 0.8316 (mp10)
REVERT: A  207 ASP cc_start: 0.6956 (t0) cc_final: 0.6751 (p0)
REVERT: A  244 LYS cc_start: 0.8880 (mttm) cc_final: 0.8519 (mtmm)
REVERT: A  268 GLU cc_start: 0.8114 (tt0) cc_final: 0.7771 (tp30)
REVERT: A  294 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8666 (tp)
REVERT: A  308 MET cc_start: 0.8414 (mmm) cc_final: 0.8130 (ttp)
REVERT: F   42 ILE cc_start: 0.7886 (mt) cc_final: 0.7589 (mm)
REVERT: J   32 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7612 (pttt)
REVERT: B   33 GLN cc_start: 0.8174 (mt0) cc_final: 0.7807 (mp10)
REVERT: B   51 GLN cc_start: 0.8735 (mt0) cc_final: 0.8318 (mp10)
REVERT: B  244 LYS cc_start: 0.8886 (mttm) cc_final: 0.8522 (mtmm)
REVERT: B  268 GLU cc_start: 0.8121 (tt0) cc_final: 0.7777 (tp30)
REVERT: B  294 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8661 (tp)
REVERT: B  308 MET cc_start: 0.8500 (mmm) cc_final: 0.8123 (ttp)
  outliers start: 20
  outliers final: 14
  residues processed: 150
  average time/residue: 0.1541
  time to fit residues: 34.3758
Evaluate side-chains
  148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain G residue   21 TYR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain H residue   21 TYR
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0570
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 71 optimal weight:    0.3980
   chunk 23 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.167519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125494 restraints weight = 10687.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.38
r_work: 0.3344 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8839  Z= 0.115
  Angle     :  0.517   8.349  11991  Z= 0.266
  Chirality :  0.039   0.163   1329
  Planarity :  0.004   0.043   1428
  Dihedral  : 12.947  83.568   2227
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.74 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.27), residues: 996
  helix:  2.93 (0.26), residues: 362
  sheet:  1.03 (0.26), residues: 406
  loop :  0.02 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 197 
 HIS   0.001   0.000   HIS B  82 
 PHE   0.010   0.001   PHE G  45 
 TYR   0.006   0.001   TYR A 181 
 ARG   0.001   0.000   ARG J  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02725 (  594)
  hydrogen bonds       : angle       4.27602 ( 1704)
  covalent geometry    : bond        0.00264 ( 8839)
  covalent geometry    : angle       0.51730 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.844 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7936 (mt) cc_final: 0.7634 (mm)
REVERT: I   32 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7602 (pttt)
REVERT: A   33 GLN cc_start: 0.8158 (mt0) cc_final: 0.7818 (mp10)
REVERT: A   51 GLN cc_start: 0.8724 (mt0) cc_final: 0.8340 (mp10)
REVERT: A  244 LYS cc_start: 0.8863 (mttm) cc_final: 0.8534 (mtmm)
REVERT: A  268 GLU cc_start: 0.8074 (tt0) cc_final: 0.7770 (tp30)
REVERT: A  294 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8668 (tp)
REVERT: A  308 MET cc_start: 0.8351 (mmm) cc_final: 0.8115 (ttp)
REVERT: F   42 ILE cc_start: 0.7937 (mt) cc_final: 0.7633 (mm)
REVERT: J   32 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7615 (pttt)
REVERT: B   33 GLN cc_start: 0.8143 (mt0) cc_final: 0.7807 (mp10)
REVERT: B   51 GLN cc_start: 0.8720 (mt0) cc_final: 0.8339 (mp10)
REVERT: B  244 LYS cc_start: 0.8869 (mttm) cc_final: 0.8538 (mtmm)
REVERT: B  268 GLU cc_start: 0.8079 (tt0) cc_final: 0.7755 (tp30)
REVERT: B  294 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8657 (tp)
REVERT: B  308 MET cc_start: 0.8461 (mmm) cc_final: 0.8127 (ttp)
  outliers start: 12
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1621
  time to fit residues: 34.7625
Evaluate side-chains
  142 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    0.3980
   chunk 35 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.165821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.123608 restraints weight = 10738.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.39
r_work: 0.3318 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8839  Z= 0.156
  Angle     :  0.535   6.252  11991  Z= 0.276
  Chirality :  0.040   0.154   1329
  Planarity :  0.004   0.042   1428
  Dihedral  : 12.956  83.951   2227
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.86 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.27), residues: 996
  helix:  2.75 (0.26), residues: 374
  sheet:  0.96 (0.26), residues: 406
  loop : -0.19 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 197 
 HIS   0.002   0.001   HIS A 150 
 PHE   0.010   0.001   PHE D 101 
 TYR   0.010   0.001   TYR A 277 
 ARG   0.001   0.000   ARG B 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02899 (  594)
  hydrogen bonds       : angle       4.33934 ( 1704)
  covalent geometry    : bond        0.00368 ( 8839)
  covalent geometry    : angle       0.53524 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.915 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7916 (mt) cc_final: 0.7626 (mm)
REVERT: I   32 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7602 (pttt)
REVERT: A   33 GLN cc_start: 0.8208 (mt0) cc_final: 0.7816 (mp10)
REVERT: A   51 GLN cc_start: 0.8756 (mt0) cc_final: 0.8346 (mp10)
REVERT: A  244 LYS cc_start: 0.8848 (mttm) cc_final: 0.8522 (mtmm)
REVERT: A  268 GLU cc_start: 0.8077 (tt0) cc_final: 0.7755 (tp30)
REVERT: A  294 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8696 (tp)
REVERT: A  308 MET cc_start: 0.8307 (mmm) cc_final: 0.8098 (ttp)
REVERT: F   42 ILE cc_start: 0.7913 (mt) cc_final: 0.7622 (mm)
REVERT: J   32 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7603 (pttt)
REVERT: B   33 GLN cc_start: 0.8197 (mt0) cc_final: 0.7808 (mp10)
REVERT: B   51 GLN cc_start: 0.8755 (mt0) cc_final: 0.8344 (mp10)
REVERT: B  244 LYS cc_start: 0.8857 (mttm) cc_final: 0.8524 (mtmm)
REVERT: B  268 GLU cc_start: 0.8128 (tt0) cc_final: 0.7789 (tp30)
REVERT: B  294 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8666 (tp)
REVERT: B  308 MET cc_start: 0.8469 (mmm) cc_final: 0.8121 (ttp)
  outliers start: 14
  outliers final: 12
  residues processed: 135
  average time/residue: 0.1650
  time to fit residues: 33.6268
Evaluate side-chains
  141 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0870
   chunk 81 optimal weight:    0.0980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.167768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.125825 restraints weight = 10679.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.39
r_work: 0.3344 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8839  Z= 0.108
  Angle     :  0.513   9.398  11991  Z= 0.264
  Chirality :  0.039   0.150   1329
  Planarity :  0.004   0.043   1428
  Dihedral  : 12.561  82.754   2227
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.71 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.27), residues: 996
  helix:  2.86 (0.26), residues: 374
  sheet:  0.98 (0.26), residues: 406
  loop : -0.17 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 197 
 HIS   0.001   0.000   HIS B  82 
 PHE   0.009   0.001   PHE G  45 
 TYR   0.006   0.001   TYR J  45 
 ARG   0.001   0.000   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02646 (  594)
  hydrogen bonds       : angle       4.21983 ( 1704)
  covalent geometry    : bond        0.00250 ( 8839)
  covalent geometry    : angle       0.51331 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 1.022 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7899 (mt) cc_final: 0.7611 (mm)
REVERT: I   32 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7587 (pttt)
REVERT: A   33 GLN cc_start: 0.8177 (mt0) cc_final: 0.7832 (mp10)
REVERT: A   51 GLN cc_start: 0.8717 (mt0) cc_final: 0.8347 (mp10)
REVERT: A  244 LYS cc_start: 0.8860 (mttm) cc_final: 0.8545 (mtmm)
REVERT: A  268 GLU cc_start: 0.8073 (tt0) cc_final: 0.7770 (tp30)
REVERT: F   42 ILE cc_start: 0.7898 (mt) cc_final: 0.7610 (mm)
REVERT: J   32 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7587 (pttt)
REVERT: B   33 GLN cc_start: 0.8163 (mt0) cc_final: 0.7823 (mp10)
REVERT: B   51 GLN cc_start: 0.8724 (mt0) cc_final: 0.8351 (mp10)
REVERT: B  244 LYS cc_start: 0.8864 (mttm) cc_final: 0.8546 (mtmm)
REVERT: B  268 GLU cc_start: 0.8114 (tt0) cc_final: 0.7796 (tp30)
REVERT: B  308 MET cc_start: 0.8465 (mmm) cc_final: 0.8104 (ttp)
  outliers start: 11
  outliers final: 11
  residues processed: 140
  average time/residue: 0.1672
  time to fit residues: 34.8699
Evaluate side-chains
  138 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
B 230 GLN
B 344 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.166061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.123801 restraints weight = 10660.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.39
r_work: 0.3323 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8839  Z= 0.152
  Angle     :  0.536   7.088  11991  Z= 0.277
  Chirality :  0.040   0.156   1329
  Planarity :  0.004   0.043   1428
  Dihedral  : 12.638  83.209   2227
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.56 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.27), residues: 996
  helix:  2.82 (0.26), residues: 374
  sheet:  0.96 (0.26), residues: 406
  loop : -0.25 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 150 
 PHE   0.010   0.001   PHE C 101 
 TYR   0.010   0.001   TYR A 277 
 ARG   0.003   0.000   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02825 (  594)
  hydrogen bonds       : angle       4.25300 ( 1704)
  covalent geometry    : bond        0.00358 ( 8839)
  covalent geometry    : angle       0.53617 (11991)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.903 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7938 (mt) cc_final: 0.7655 (mm)
REVERT: I   32 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7598 (pttt)
REVERT: A   33 GLN cc_start: 0.8192 (mt0) cc_final: 0.7816 (mp10)
REVERT: A   51 GLN cc_start: 0.8780 (mt0) cc_final: 0.8394 (mp10)
REVERT: A  244 LYS cc_start: 0.8819 (mttm) cc_final: 0.8491 (mtmm)
REVERT: A  268 GLU cc_start: 0.8055 (tt0) cc_final: 0.7754 (tp30)
REVERT: A  294 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8678 (tp)
REVERT: F   42 ILE cc_start: 0.7947 (mt) cc_final: 0.7660 (mm)
REVERT: J   32 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7599 (pttt)
REVERT: B   33 GLN cc_start: 0.8188 (mt0) cc_final: 0.7811 (mp10)
REVERT: B   51 GLN cc_start: 0.8767 (mt0) cc_final: 0.8388 (mp10)
REVERT: B  244 LYS cc_start: 0.8810 (mttm) cc_final: 0.8481 (mtmm)
REVERT: B  268 GLU cc_start: 0.8072 (tt0) cc_final: 0.7772 (tp30)
REVERT: B  294 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8683 (tp)
REVERT: B  308 MET cc_start: 0.8416 (mmm) cc_final: 0.8104 (ttp)
  outliers start: 12
  outliers final: 10
  residues processed: 140
  average time/residue: 0.1678
  time to fit residues: 34.9998
Evaluate side-chains
  142 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0000
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.8586

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.165895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.123970 restraints weight = 10639.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.37
r_work: 0.3324 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8839  Z= 0.141
  Angle     :  0.540   9.965  11991  Z= 0.277
  Chirality :  0.040   0.154   1329
  Planarity :  0.004   0.044   1428
  Dihedral  : 12.495  82.943   2227
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.56 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.27), residues: 996
  helix:  2.86 (0.26), residues: 374
  sheet:  0.93 (0.26), residues: 406
  loop : -0.19 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 197 
 HIS   0.002   0.001   HIS B 150 
 PHE   0.010   0.001   PHE H  45 
 TYR   0.007   0.001   TYR J  51 
 ARG   0.002   0.000   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02795 (  594)
  hydrogen bonds       : angle       4.21378 ( 1704)
  covalent geometry    : bond        0.00329 ( 8839)
  covalent geometry    : angle       0.54007 (11991)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4530.07 seconds
wall clock time: 78 minutes 23.84 seconds (4703.84 seconds total)