Starting phenix.real_space_refine
on Wed Mar 12 02:44:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gms_34152/03_2025/8gms_34152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gms_34152/03_2025/8gms_34152.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gms_34152/03_2025/8gms_34152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gms_34152/03_2025/8gms_34152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gms_34152/03_2025/8gms_34152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gms_34152/03_2025/8gms_34152.cif"
  }
  resolution = 3.31
  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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      2      5.21       5
     S      32      5.16       5
     C    4380      2.51       5
     N    1218      2.21       5
     O    1378      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7022
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 949
          Classifications: {'peptide': 123}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115}
    Chain: "B"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 873
          Classifications: {'peptide': 113}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2508
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "G"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2508
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "S"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 120
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    Chain: "F"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.65, per 1000 atoms: 0.66
  Number of scatterers: 7022
  At special positions: 0
  Unit cell: (102.34, 116.62, 104.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      32     16.00
     P      12     15.00
     Mg      2     11.99
     O    1378      8.00
     N    1218      7.00
     C    4380      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: 1.57
  Conformation dependent library (CDL) restraints added in 932.8 milliseconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1630

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      37.8% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 105
    Processing helix  chain 'A' and resid 120 through 124
      removed outlier: 3.528A  pdb=" N   ILE A 123 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
    Processing helix  chain 'B' and resid 120 through 124
      removed outlier: 3.747A  pdb=" N   ILE B 123 " --> pdb=" O   MET B 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 22
    Processing helix  chain 'F' and resid 32 through 36
    Processing helix  chain 'F' and resid 44 through 52
    Processing helix  chain 'F' and resid 71 through 85
    Processing helix  chain 'F' and resid 100 through 107
    Processing helix  chain 'F' and resid 110 through 112
      No H-bonds generated for 'chain 'F' and resid 110 through 112'
    Processing helix  chain 'F' and resid 121 through 136
      removed outlier: 3.528A  pdb=" N   GLY F 136 " --> pdb=" O   LEU F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 151 through 157
    Processing helix  chain 'F' and resid 165 through 186
      removed outlier: 4.725A  pdb=" N   GLY F 180 " --> pdb=" O   ARG F 176 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ASN F 181 " --> pdb=" O   LYS F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 213 through 219
    Processing helix  chain 'F' and resid 269 through 281
    Processing helix  chain 'F' and resid 301 through 312
    Processing helix  chain 'F' and resid 312 through 328
      removed outlier: 3.794A  pdb=" N   ALA F 316 " --> pdb=" O   ASN F 312 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 22
    Processing helix  chain 'G' and resid 28 through 36
      removed outlier: 6.237A  pdb=" N   ARG G  33 " --> pdb=" O   GLY G  30 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   SER G  34 " --> pdb=" O   GLU G  31 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET G  35 " --> pdb=" O   ASP G  32 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP G  36 " --> pdb=" O   ARG G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 44 through 52
      removed outlier: 3.506A  pdb=" N   GLY G  52 " --> pdb=" O   ASP G  48 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 71 through 86
      removed outlier: 3.707A  pdb=" N   GLU G  86 " --> pdb=" O   ALA G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 100 through 107
    Processing helix  chain 'G' and resid 110 through 113
    Processing helix  chain 'G' and resid 121 through 136
      removed outlier: 3.596A  pdb=" N   GLY G 136 " --> pdb=" O   LEU G 132 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 145 through 149
    Processing helix  chain 'G' and resid 151 through 157
    Processing helix  chain 'G' and resid 165 through 186
      removed outlier: 4.684A  pdb=" N   GLY G 180 " --> pdb=" O   ARG G 176 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ASN G 181 " --> pdb=" O   LYS G 177 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 213 through 219
    Processing helix  chain 'G' and resid 269 through 281
    Processing helix  chain 'G' and resid 301 through 312
    Processing helix  chain 'G' and resid 312 through 328
      removed outlier: 3.513A  pdb=" N   ALA G 316 " --> pdb=" O   ASN G 312 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU G 328 " --> pdb=" O   ARG G 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84
      removed outlier: 3.892A  pdb=" N   GLY A  96 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 96 through 97
    current: chain 'A' and resid 130 through 134
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 130 through 134
    current: chain 'A' and resid 152 through 161
      removed outlier: 3.585A  pdb=" N   ILE A 177 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 177 through 180
    current: chain 'B' and resid 130 through 135
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 130 through 135
    current: chain 'B' and resid 152 through 161
      removed outlier: 3.750A  pdb=" N   ILE B 177 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 26 through 28
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 26 through 28
    current: chain 'G' and resid 115 through 117
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 115 through 117
    current: chain 'G' and resid 188 through 197
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 207 through 209
    current: chain 'G' and resid 236 through 249
    Processing sheet with id=AA3, first strand: chain 'F' and resid 39 through 40
    Processing sheet with id=AA4, first strand: chain 'F' and resid 114 through 117
      removed outlier: 7.130A  pdb=" N   CYS F  90 " --> pdb=" O   LEU F 115 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   SER F 117 " --> pdb=" O   CYS F  90 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   PHE F  92 " --> pdb=" O   SER F 117 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ILE F 141 " --> pdb=" O   ILE F 190 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   ILE F 192 " --> pdb=" O   ILE F 141 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   VAL F 143 " --> pdb=" O   ILE F 192 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL F  62 " --> pdb=" O   PHE F 191 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   ASN F 193 " --> pdb=" O   VAL F  62 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   ILE F  64 " --> pdb=" O   ASN F 193 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE F  61 " --> pdb=" O   VAL F 221 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   LEU F 223 " --> pdb=" O   ILE F  61 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLU F  63 " --> pdb=" O   LEU F 223 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   ILE F 225 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   TYR F  65 " --> pdb=" O   ILE F 225 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   ARG F 227 " --> pdb=" O   TYR F  65 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ARG F 222 " --> pdb=" O   VAL F 247 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLU F 241 " --> pdb=" O   ILE F 228 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ALA F 230 " --> pdb=" O   GLY F 239 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLY F 239 " --> pdb=" O   ALA F 230 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LYS F 232 " --> pdb=" O   VAL F 237 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL F 237 " --> pdb=" O   LYS F 232 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 195 through 197
    Processing sheet with id=AA6, first strand: chain 'F' and resid 285 through 287
      removed outlier: 6.691A  pdb=" N   TYR F 291 " --> pdb=" O   ILE F 298 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 39 through 40
    Processing sheet with id=AA8, first strand: chain 'G' and resid 285 through 287
      removed outlier: 6.737A  pdb=" N   TYR G 291 " --> pdb=" O   ILE G 298 " (cutoff:3.500A)

    276 hydrogen bonds defined for protein.
    753 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: 1.68

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.36: 2372
        1.36 -     1.51: 1708
        1.51 -     1.65: 2981
        1.65 -     1.80: 36
        1.80 -     1.95: 20
  Bond restraints: 7117
  Sorted by residual:
  bond pdb=" N   LEU F 326 "
       pdb=" CA  LEU F 326 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.033 1.30e-02 5.92e+03 6.27e+00
  bond pdb=" CB  THR G  76 "
       pdb=" CG2 THR G  76 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.10e+00
  bond pdb=" CG1 ILE G 141 "
       pdb=" CD1 ILE G 141 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.50e+00
  bond pdb=" CB  GLN F  16 "
       pdb=" CG  GLN F  16 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.06e+00
  bond pdb=" C   VAL A 193 "
       pdb=" O   VAL A 193 "
    ideal  model  delta    sigma   weight residual
    1.236  1.224  0.012 1.19e-02 7.06e+03 1.04e+00
  ... (remaining 7112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 9423
        1.85 -     3.70: 180
        3.70 -     5.55: 17
        5.55 -     7.41: 3
        7.41 -     9.26: 1
  Bond angle restraints: 9624
  Sorted by residual:
  angle pdb=" N   GLY F 204 "
        pdb=" CA  GLY F 204 "
        pdb=" C   GLY F 204 "
      ideal   model   delta    sigma   weight residual
     110.87  116.28   -5.41 1.54e+00 4.22e-01 1.23e+01
  angle pdb=" CA  GLN F  16 "
        pdb=" CB  GLN F  16 "
        pdb=" CG  GLN F  16 "
      ideal   model   delta    sigma   weight residual
     114.10  120.62   -6.52 2.00e+00 2.50e-01 1.06e+01
  angle pdb=" N   GLN A 183 "
        pdb=" CA  GLN A 183 "
        pdb=" C   GLN A 183 "
      ideal   model   delta    sigma   weight residual
     114.75  110.78    3.97 1.26e+00 6.30e-01 9.93e+00
  angle pdb=" CB  MET F 197 "
        pdb=" CG  MET F 197 "
        pdb=" SD  MET F 197 "
      ideal   model   delta    sigma   weight residual
     112.70  121.96   -9.26 3.00e+00 1.11e-01 9.52e+00
  angle pdb=" N   GLU G 266 "
        pdb=" CA  GLU G 266 "
        pdb=" C   GLU G 266 "
      ideal   model   delta    sigma   weight residual
     114.04  110.46    3.58 1.24e+00 6.50e-01 8.34e+00
  ... (remaining 9619 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.98: 3806
       21.98 -    43.96: 445
       43.96 -    65.93: 83
       65.93 -    87.91: 18
       87.91 -   109.89: 3
  Dihedral angle restraints: 4355
    sinusoidal: 1812
      harmonic: 2543
  Sorted by residual:
  dihedral pdb=" O1A AGS F 402 "
           pdb=" O3A AGS F 402 "
           pdb=" PA  AGS F 402 "
           pdb=" PB  AGS F 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73 -177.62  109.89     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" CA  HIS F 163 "
           pdb=" C   HIS F 163 "
           pdb=" N   MET F 164 "
           pdb=" CA  MET F 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.85  -16.15     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CB  GLU G 154 "
           pdb=" CG  GLU G 154 "
           pdb=" CD  GLU G 154 "
           pdb=" OE1 GLU G 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.25   88.25     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 4352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 718
       0.035 -    0.070: 266
       0.070 -    0.106: 88
       0.106 -    0.141: 39
       0.141 -    0.176: 2
  Chirality restraints: 1113
  Sorted by residual:
  chirality pdb=" CB  ILE B 149 "
            pdb=" CA  ILE B 149 "
            pdb=" CG1 ILE B 149 "
            pdb=" CG2 ILE B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CA  ASN F 205 "
            pdb=" N   ASN F 205 "
            pdb=" C   ASN F 205 "
            pdb=" CB  ASN F 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  ILE F  64 "
            pdb=" N   ILE F  64 "
            pdb=" C   ILE F  64 "
            pdb=" CB  ILE F  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  ... (remaining 1110 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F 308 "    0.018 2.00e-02 2.50e+03   2.18e-02 1.19e+01
        pdb=" CG  TRP F 308 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP F 308 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP F 308 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP F 308 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP F 308 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP F 308 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F 308 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F 308 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP F 308 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 106 "   -0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO A 107 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 107 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 107 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 106 "    0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO B 107 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 56
        2.59 -     3.17: 5592
        3.17 -     3.74: 10686
        3.74 -     4.32: 14997
        4.32 -     4.90: 25267
  Nonbonded interactions: 56598
  Sorted by model distance:
  nonbonded pdb="MG    MG F 401 "
            pdb=" O2G AGS F 402 "
     model   vdw
     2.012 2.170
  nonbonded pdb=" OG1 THR F  73 "
            pdb="MG    MG F 401 "
     model   vdw
     2.022 2.170
  nonbonded pdb=" OG1 THR G  73 "
            pdb="MG    MG G 401 "
     model   vdw
     2.089 2.170
  nonbonded pdb=" OG1 THR G  42 "
            pdb=" OD1 ASP G  48 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG  SER G  44 "
            pdb=" OE2 GLU G 273 "
     model   vdw
     2.248 3.040
  ... (remaining 56593 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 76 through 84 or resid 95 through 198))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

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:             0.590
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.810
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7117  Z= 0.244
  Angle     :  0.617   9.258   9624  Z= 0.351
  Chirality :  0.045   0.176   1113
  Planarity :  0.003   0.038   1225
  Dihedral  : 18.790 109.890   2725
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 19.97 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.05 (0.27), residues: 892
  helix:  1.47 (0.30), residues: 302
  sheet:  0.43 (0.41), residues: 156
  loop : -1.34 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.004   TRP F 308 
 HIS   0.003   0.001   HIS A 134 
 PHE   0.011   0.001   PHE F 260 
 TYR   0.009   0.001   TYR F 218 
 ARG   0.002   0.000   ARG B 140 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.811 
Fit side-chains
REVERT: B   78 LEU cc_start: 0.3521 (tp) cc_final: 0.3320 (tp)
REVERT: F  280 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6742 (mttt)
REVERT: F  308 TRP cc_start: 0.7043 (t60) cc_final: 0.6621 (t60)
  outliers start: 4
  outliers final: 1
  residues processed: 105
  average time/residue: 0.2027
  time to fit residues: 28.6412
Evaluate side-chains
  103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  280 LYS
Chi-restraints excluded: chain G residue  240 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.192595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.145298 restraints weight = 7830.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.61
r_work: 0.3337 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.0692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7117  Z= 0.201
  Angle     :  0.510   6.846   9624  Z= 0.272
  Chirality :  0.044   0.164   1113
  Planarity :  0.003   0.032   1225
  Dihedral  : 11.947 117.378   1057
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.87 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.08 (0.27), residues: 892
  helix:  1.62 (0.30), residues: 304
  sheet:  0.46 (0.41), residues: 161
  loop : -1.32 (0.27), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP F 308 
 HIS   0.004   0.001   HIS A 134 
 PHE   0.011   0.001   PHE F  21 
 TYR   0.014   0.001   TYR F 218 
 ARG   0.003   0.000   ARG G 222 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8201 (tm-30)
REVERT: A  126 MET cc_start: 0.7024 (mmm) cc_final: 0.6752 (mtp)
REVERT: A  140 ARG cc_start: 0.7427 (ptt-90) cc_final: 0.6847 (ptt90)
REVERT: A  157 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.7263 (mtt-85)
REVERT: B   78 LEU cc_start: 0.3445 (tp) cc_final: 0.3241 (tp)
REVERT: B  115 VAL cc_start: 0.5110 (t) cc_final: 0.4685 (p)
REVERT: B  196 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.6996 (pt)
  outliers start: 16
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1991
  time to fit residues: 32.3001
Evaluate side-chains
  114 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
B 108 ASN
F  20 GLN
F 124 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.184150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.136410 restraints weight = 8040.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.03
r_work: 0.3176 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   7117  Z= 0.488
  Angle     :  0.639   7.053   9624  Z= 0.333
  Chirality :  0.050   0.191   1113
  Planarity :  0.004   0.030   1225
  Dihedral  : 12.462 124.622   1053
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 19.56 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.51 (0.26), residues: 892
  helix:  1.15 (0.29), residues: 304
  sheet: -0.27 (0.39), residues: 166
  loop : -1.51 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP F 308 
 HIS   0.004   0.002   HIS G  97 
 PHE   0.015   0.002   PHE F 191 
 TYR   0.023   0.002   TYR F 218 
 ARG   0.004   0.001   ARG F 196 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 106
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8408 (tm-30)
REVERT: A  126 MET cc_start: 0.7001 (mmm) cc_final: 0.6726 (mtp)
REVERT: B  107 PRO cc_start: 0.6609 (Cg_exo) cc_final: 0.6405 (Cg_endo)
REVERT: F   18 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5554 (tt0)
REVERT: F  156 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6058 (mp0)
REVERT: G  159 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8236 (mm)
  outliers start: 36
  outliers final: 25
  residues processed: 125
  average time/residue: 0.1805
  time to fit residues: 31.1146
Evaluate side-chains
  126 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  137 GLN
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  166 LEU
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  279 VAL
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  121 THR
Chi-restraints excluded: chain G residue  159 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  166 LEU
Chi-restraints excluded: chain G residue  184 GLN
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  202 MET
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  242 THR
Chi-restraints excluded: chain G residue  315 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 13 optimal weight:    8.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 171 ASN
B 198 ASN
F 269 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.188319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.141514 restraints weight = 8072.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.97
r_work: 0.3258 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7117  Z= 0.193
  Angle     :  0.493   6.401   9624  Z= 0.266
  Chirality :  0.044   0.148   1113
  Planarity :  0.003   0.028   1225
  Dihedral  : 12.086 124.133   1053
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.90 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.17 (0.27), residues: 892
  helix:  1.52 (0.30), residues: 306
  sheet:  0.01 (0.41), residues: 162
  loop : -1.43 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 308 
 HIS   0.004   0.001   HIS A 134 
 PHE   0.009   0.001   PHE G 260 
 TYR   0.022   0.001   TYR F 218 
 ARG   0.001   0.000   ARG G 222 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8273 (tm-30)
REVERT: A  140 ARG cc_start: 0.7565 (ptt-90) cc_final: 0.7300 (ptt90)
REVERT: F   18 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5520 (tt0)
REVERT: F   31 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7058 (pm20)
REVERT: F  156 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6806 (mm-30)
REVERT: F  308 TRP cc_start: 0.7246 (t60) cc_final: 0.6893 (t60)
REVERT: G   76 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8335 (m)
REVERT: G  141 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8547 (mt)
REVERT: G  271 TYR cc_start: 0.7549 (m-80) cc_final: 0.6931 (m-80)
  outliers start: 31
  outliers final: 19
  residues processed: 128
  average time/residue: 0.1752
  time to fit residues: 30.3261
Evaluate side-chains
  126 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  171 ASN
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  198 ASN
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue   38 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  184 GLN
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  242 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 17 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0970
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.189272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.141935 restraints weight = 7899.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.83
r_work: 0.3277 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7117  Z= 0.188
  Angle     :  0.485   6.272   9624  Z= 0.258
  Chirality :  0.044   0.148   1113
  Planarity :  0.003   0.032   1225
  Dihedral  : 11.963 123.446   1053
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 21.90 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.04 (0.28), residues: 892
  helix:  1.67 (0.30), residues: 306
  sheet:  0.21 (0.43), residues: 156
  loop : -1.43 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 308 
 HIS   0.003   0.001   HIS A 134 
 PHE   0.009   0.001   PHE G 260 
 TYR   0.008   0.001   TYR F 218 
 ARG   0.002   0.000   ARG A 157 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8243 (tm-30)
REVERT: F   18 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5538 (tt0)
REVERT: F   31 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6982 (pm20)
REVERT: F  156 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6927 (mm-30)
REVERT: F  308 TRP cc_start: 0.7206 (t60) cc_final: 0.6871 (t60)
REVERT: G  271 TYR cc_start: 0.7504 (m-80) cc_final: 0.6902 (m-80)
REVERT: G  326 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7701 (mp)
  outliers start: 28
  outliers final: 18
  residues processed: 120
  average time/residue: 0.1781
  time to fit residues: 29.1953
Evaluate side-chains
  124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  171 ASN
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue   38 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  242 THR
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 39 optimal weight:    0.0270
   overall best weight:    2.6046

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.186170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.139446 restraints weight = 8057.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.97
r_work: 0.3238 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7117  Z= 0.342
  Angle     :  0.549   6.954   9624  Z= 0.285
  Chirality :  0.046   0.154   1113
  Planarity :  0.003   0.032   1225
  Dihedral  : 12.152 125.543   1053
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 21.21 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.17 (0.27), residues: 892
  helix:  1.55 (0.30), residues: 306
  sheet:  0.02 (0.43), residues: 158
  loop : -1.44 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 290 
 HIS   0.003   0.001   HIS F  97 
 PHE   0.011   0.002   PHE F 191 
 TYR   0.009   0.001   TYR F  65 
 ARG   0.002   0.000   ARG A 197 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 103
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8305 (tm-30)
REVERT: A  118 MET cc_start: 0.6589 (mmm) cc_final: 0.6004 (mmm)
REVERT: A  121 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6386 (ptpp)
REVERT: B  196 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.6873 (pt)
REVERT: F   18 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5518 (tt0)
REVERT: F   31 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6962 (pm20)
REVERT: F  127 GLU cc_start: 0.6970 (pt0) cc_final: 0.6645 (pt0)
REVERT: F  156 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6138 (mp0)
REVERT: F  308 TRP cc_start: 0.7213 (t60) cc_final: 0.6846 (t60)
REVERT: G   76 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8377 (m)
REVERT: G  141 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8597 (mp)
REVERT: G  271 TYR cc_start: 0.7589 (m-80) cc_final: 0.6989 (m-80)
REVERT: G  326 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7765 (mp)
  outliers start: 39
  outliers final: 26
  residues processed: 125
  average time/residue: 0.1725
  time to fit residues: 29.5980
Evaluate side-chains
  137 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  137 GLN
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  171 ASN
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue   38 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain F residue  209 THR
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   69 SER
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  166 LEU
Chi-restraints excluded: chain G residue  184 GLN
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  242 THR
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0980
   chunk 69 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.189569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143530 restraints weight = 7906.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.90
r_work: 0.3269 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7117  Z= 0.159
  Angle     :  0.484   6.010   9624  Z= 0.255
  Chirality :  0.043   0.137   1113
  Planarity :  0.003   0.034   1225
  Dihedral  : 11.884 124.631   1053
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 21.76 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.06 (0.28), residues: 892
  helix:  1.81 (0.30), residues: 306
  sheet:  0.16 (0.43), residues: 158
  loop : -1.38 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 308 
 HIS   0.005   0.001   HIS A 134 
 PHE   0.008   0.001   PHE G 260 
 TYR   0.007   0.001   TYR F 218 
 ARG   0.002   0.000   ARG B 197 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8191 (tm-30)
REVERT: A  118 MET cc_start: 0.6555 (mmm) cc_final: 0.6141 (mmm)
REVERT: A  121 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6211 (ptpp)
REVERT: A  171 ASN cc_start: 0.6103 (OUTLIER) cc_final: 0.5661 (t0)
REVERT: A  180 ASP cc_start: 0.8097 (t0) cc_final: 0.7895 (t70)
REVERT: F   18 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5659 (tt0)
REVERT: F   31 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6946 (pm20)
REVERT: F  156 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6924 (mm-30)
REVERT: F  178 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8366 (mt)
REVERT: F  308 TRP cc_start: 0.7158 (t60) cc_final: 0.6799 (t60)
REVERT: G   76 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8389 (m)
REVERT: G  141 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8558 (mp)
REVERT: G  271 TYR cc_start: 0.7559 (m-80) cc_final: 0.6971 (m-80)
REVERT: G  326 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7641 (mp)
  outliers start: 35
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1686
  time to fit residues: 29.9927
Evaluate side-chains
  129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  171 ASN
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue   38 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  242 THR
Chi-restraints excluded: chain G residue  247 VAL
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 49 optimal weight:    0.5980
   chunk 15 optimal weight:   30.0000
   chunk 8 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0770
   chunk 44 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0740

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.189571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.143474 restraints weight = 7950.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.91
r_work: 0.3269 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7117  Z= 0.188
  Angle     :  0.490   6.732   9624  Z= 0.256
  Chirality :  0.044   0.136   1113
  Planarity :  0.003   0.034   1225
  Dihedral  : 11.839 123.478   1053
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 21.90 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.15 (0.28), residues: 892
  helix:  1.93 (0.30), residues: 304
  sheet:  0.22 (0.43), residues: 158
  loop : -1.35 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 308 
 HIS   0.002   0.001   HIS A 134 
 PHE   0.009   0.001   PHE G 260 
 TYR   0.007   0.001   TYR F 218 
 ARG   0.001   0.000   ARG B 197 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8212 (tm-30)
REVERT: A  118 MET cc_start: 0.6575 (mmm) cc_final: 0.6284 (mmm)
REVERT: A  121 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6367 (pttm)
REVERT: A  157 ARG cc_start: 0.7320 (mtt-85) cc_final: 0.7025 (mtt-85)
REVERT: A  171 ASN cc_start: 0.6124 (OUTLIER) cc_final: 0.5682 (t0)
REVERT: F   18 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5654 (tt0)
REVERT: F   31 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6948 (pm20)
REVERT: F  156 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6148 (mp0)
REVERT: F  178 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8386 (mt)
REVERT: F  308 TRP cc_start: 0.7145 (t60) cc_final: 0.6818 (t60)
REVERT: G   76 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8396 (m)
REVERT: G  141 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8564 (mp)
REVERT: G  271 TYR cc_start: 0.7558 (m-80) cc_final: 0.6955 (m-80)
REVERT: G  326 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7650 (mp)
  outliers start: 35
  outliers final: 21
  residues processed: 127
  average time/residue: 0.1850
  time to fit residues: 32.4994
Evaluate side-chains
  134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  137 GLN
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  171 ASN
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue   38 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   69 SER
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  184 GLN
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  242 THR
Chi-restraints excluded: chain G residue  247 VAL
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 80 optimal weight:    0.6980
   chunk 12 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.187202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.140729 restraints weight = 8023.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.91
r_work: 0.3252 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7117  Z= 0.244
  Angle     :  0.511   6.781   9624  Z= 0.266
  Chirality :  0.045   0.193   1113
  Planarity :  0.003   0.034   1225
  Dihedral  : 11.912 124.120   1053
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 22.31 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.11 (0.28), residues: 892
  helix:  1.89 (0.30), residues: 304
  sheet:  0.16 (0.43), residues: 158
  loop : -1.36 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 290 
 HIS   0.004   0.001   HIS A 134 
 PHE   0.010   0.001   PHE G 260 
 TYR   0.007   0.001   TYR F  65 
 ARG   0.002   0.000   ARG G  33 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8221 (tm-30)
REVERT: A  118 MET cc_start: 0.6578 (mmm) cc_final: 0.6297 (mmm)
REVERT: A  121 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6356 (pttm)
REVERT: A  171 ASN cc_start: 0.6309 (OUTLIER) cc_final: 0.5827 (t0)
REVERT: F   18 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5644 (tt0)
REVERT: F   31 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6988 (pm20)
REVERT: F  156 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6152 (mp0)
REVERT: F  308 TRP cc_start: 0.7146 (t60) cc_final: 0.6814 (t60)
REVERT: G   76 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8402 (m)
REVERT: G  141 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8562 (mp)
REVERT: G  271 TYR cc_start: 0.7549 (m-80) cc_final: 0.6955 (m-80)
REVERT: G  326 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7641 (mp)
  outliers start: 32
  outliers final: 22
  residues processed: 123
  average time/residue: 0.1663
  time to fit residues: 28.4474
Evaluate side-chains
  134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  171 ASN
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue   38 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   69 SER
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  184 GLN
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  242 THR
Chi-restraints excluded: chain G residue  247 VAL
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0060
   chunk 38 optimal weight:    0.0040
   chunk 79 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    0.4808

-------------------------------------------------------------------------------
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 = 0.4091 r_free = 0.4091 target = 0.189911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.143784 restraints weight = 8052.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.88
r_work: 0.3289 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7117  Z= 0.145
  Angle     :  0.488   6.783   9624  Z= 0.254
  Chirality :  0.043   0.161   1113
  Planarity :  0.003   0.036   1225
  Dihedral  : 11.652 122.316   1053
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.00 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.29 (0.28), residues: 892
  helix:  2.07 (0.30), residues: 304
  sheet:  0.26 (0.44), residues: 160
  loop : -1.28 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 308 
 HIS   0.002   0.001   HIS A 134 
 PHE   0.008   0.001   PHE G 260 
 TYR   0.006   0.001   TYR F  65 
 ARG   0.001   0.000   ARG B 197 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   92 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8198 (tm-30)
REVERT: A  118 MET cc_start: 0.6564 (mmm) cc_final: 0.5953 (mmm)
REVERT: A  121 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6351 (pttm)
REVERT: A  157 ARG cc_start: 0.7326 (mtt-85) cc_final: 0.7063 (mtt-85)
REVERT: F   18 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5555 (tt0)
REVERT: F  156 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6179 (mp0)
REVERT: F  281 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7085 (mm-30)
REVERT: F  308 TRP cc_start: 0.7111 (t60) cc_final: 0.6768 (t60)
REVERT: G   76 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8427 (m)
REVERT: G  141 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8559 (mp)
REVERT: G  271 TYR cc_start: 0.7583 (m-80) cc_final: 0.6977 (m-80)
REVERT: G  326 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7643 (mp)
  outliers start: 27
  outliers final: 18
  residues processed: 125
  average time/residue: 0.1691
  time to fit residues: 29.5567
Evaluate side-chains
  132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   18 GLU
Chi-restraints excluded: chain F residue   38 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  156 GLU
Chi-restraints excluded: chain F residue  215 LEU
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   69 SER
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  162 SER
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain G residue  240 SER
Chi-restraints excluded: chain G residue  247 VAL
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.186928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.140262 restraints weight = 7926.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.96
r_work: 0.3225 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7117  Z= 0.318
  Angle     :  0.546   7.876   9624  Z= 0.282
  Chirality :  0.046   0.160   1113
  Planarity :  0.003   0.035   1225
  Dihedral  : 12.044 125.058   1053
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 22.59 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.03 (0.28), residues: 892
  helix:  1.81 (0.30), residues: 304
  sheet:  0.04 (0.42), residues: 160
  loop : -1.36 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 290 
 HIS   0.003   0.001   HIS F  97 
 PHE   0.011   0.002   PHE F 191 
 TYR   0.009   0.001   TYR F  65 
 ARG   0.003   0.000   ARG F 196 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4423.25 seconds
wall clock time: 76 minutes 17.53 seconds (4577.53 seconds total)