Starting phenix.real_space_refine
on Wed Mar 12 07:23:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ima_60686/03_2025/9ima_60686.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ima_60686/03_2025/9ima_60686.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ima_60686/03_2025/9ima_60686.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ima_60686/03_2025/9ima_60686.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ima_60686/03_2025/9ima_60686.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ima_60686/03_2025/9ima_60686.cif"
  }
  resolution = 2.65
  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=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    4933      2.51       5
     N    1182      2.21       5
     O    1306      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 7472
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1661
          Classifications: {'peptide': 221}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209}
    Chain: "D"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1665
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202}
    Chain: "B"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1989
          Classifications: {'peptide': 249}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 239}
    Chain: "A"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1989
          Classifications: {'peptide': 249}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 239}
    Chain: "B"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 84
          Unusual residues: {'CLR': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 84
          Unusual residues: {'CLR': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.71, per 1000 atoms: 0.76
  Number of scatterers: 7472
  At special positions: 0
  Unit cell: (62.814, 104.139, 146.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1306      8.00
     N    1182      7.00
     C    4933      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 132 " - pdb=" SG  CYS D 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 145 " - pdb=" SG  CYS C 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 134 " - pdb=" SG  CYS D 194 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.82
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1758

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 11 sheets defined
      49.5% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.824A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 65
      removed outlier: 3.741A  pdb=" N   GLN C  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 62 through 65'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.752A  pdb=" N   THR C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.895A  pdb=" N   PHE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 128
    Processing helix  chain 'D' and resid 183 through 187
    Processing helix  chain 'B' and resid 25 through 49
      removed outlier: 3.996A  pdb=" N   ARG B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 58
      No H-bonds generated for 'chain 'B' and resid 56 through 58'
    Processing helix  chain 'B' and resid 59 through 82
      removed outlier: 3.673A  pdb=" N   GLY B  72 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B  78 " --> pdb=" O   PHE B  74 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA B  79 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 117
      removed outlier: 4.730A  pdb=" N   GLY B  97 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 153
      removed outlier: 3.719A  pdb=" N   SER B 137 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LEU B 139 " --> pdb=" O   GLY B 135 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   GLN B 140 " --> pdb=" O   CYS B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 161
      removed outlier: 3.541A  pdb=" N   MET B 161 " --> pdb=" O   PHE B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 173
    Processing helix  chain 'B' and resid 174 through 191
      removed outlier: 3.608A  pdb=" N   THR B 191 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 226
      removed outlier: 3.562A  pdb=" N   GLY B 203 " --> pdb=" O   TRP B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
    Processing helix  chain 'B' and resid 238 through 257
      removed outlier: 3.508A  pdb=" N   TYR B 257 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 268
      removed outlier: 3.625A  pdb=" N   ARG B 267 " --> pdb=" O   CYS B 263 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   SER B 268 " --> pdb=" O   ILE B 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 46
      removed outlier: 3.542A  pdb=" N   LEU A  26 " --> pdb=" O   TRP A  22 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   GLU A  27 " --> pdb=" O   GLY A  23 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A  38 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A  41 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 50
    Processing helix  chain 'A' and resid 56 through 58
      No H-bonds generated for 'chain 'A' and resid 56 through 58'
    Processing helix  chain 'A' and resid 59 through 82
      removed outlier: 4.224A  pdb=" N   PHE A  78 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ALA A  79 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 119
      removed outlier: 4.159A  pdb=" N   VAL A  91 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   GLY A  97 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 136
    Processing helix  chain 'A' and resid 137 through 154
    Processing helix  chain 'A' and resid 162 through 173
    Processing helix  chain 'A' and resid 174 through 190
    Processing helix  chain 'A' and resid 191 through 193
      No H-bonds generated for 'chain 'A' and resid 191 through 193'
    Processing helix  chain 'A' and resid 199 through 226
      removed outlier: 3.661A  pdb=" N   GLY A 203 " --> pdb=" O   TRP A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 237 through 257
      removed outlier: 3.656A  pdb=" N   TYR A 257 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 267
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.835A  pdb=" N   THR C  33 " --> pdb=" O   VAL C  99 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   MET C  34 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LEU C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASP C  57 " --> pdb=" O   ASN C  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12
      removed outlier: 4.139A  pdb=" N   TYR C 107 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 125 through 129
      removed outlier: 4.727A  pdb=" N   ALA C 142 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL C 189 " --> pdb=" O   ALA C 142 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   GLY C 144 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL C 187 " --> pdb=" O   GLY C 144 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   LEU C 146 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER C 185 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   LYS C 148 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   LEU C 183 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 125 through 129
      removed outlier: 4.727A  pdb=" N   ALA C 142 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL C 189 " --> pdb=" O   ALA C 142 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   GLY C 144 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL C 187 " --> pdb=" O   GLY C 144 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   LEU C 146 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER C 185 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   LYS C 148 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   LEU C 183 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER C 182 " --> pdb=" O   VAL C 174 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 157 through 159
      removed outlier: 3.791A  pdb=" N   LYS C 214 " --> pdb=" O   CYS C 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.638A  pdb=" N   VAL D  33 " --> pdb=" O   TYR D  49 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   TYR D  49 " --> pdb=" O   VAL D  33 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.995A  pdb=" N   THR D  97 " --> pdb=" O   GLN D  90 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 118
      removed outlier: 3.767A  pdb=" N   ASN D 138 " --> pdb=" O   TYR D 173 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   TYR D 173 " --> pdb=" O   ASN D 138 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 153 through 154

    445 hydrogen bonds defined for protein.
    1245 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: 2.20

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2184
        1.34 -     1.46: 1473
        1.46 -     1.58: 3941
        1.58 -     1.70: 0
        1.70 -     1.81: 70
  Bond restraints: 7668
  Sorted by residual:
  bond pdb=" CA  LYS C 219 "
       pdb=" CB  LYS C 219 "
    ideal  model  delta    sigma   weight residual
    1.513  1.550 -0.037 2.59e-02 1.49e+03 1.99e+00
  bond pdb=" CA  ILE B  24 "
       pdb=" CB  ILE B  24 "
    ideal  model  delta    sigma   weight residual
    1.540  1.559 -0.019 1.36e-02 5.41e+03 1.94e+00
  bond pdb=" CB  GLU D 187 "
       pdb=" CG  GLU D 187 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.84e+00
  bond pdb=" CA  ILE B  24 "
       pdb=" C   ILE B  24 "
    ideal  model  delta    sigma   weight residual
    1.523  1.540 -0.017 1.27e-02 6.20e+03 1.72e+00
  bond pdb=" C   ALA B  89 "
       pdb=" N   PRO B  90 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.28e-02 6.10e+03 1.61e+00
  ... (remaining 7663 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 10225
        1.87 -     3.75: 207
        3.75 -     5.62: 36
        5.62 -     7.50: 16
        7.50 -     9.37: 4
  Bond angle restraints: 10488
  Sorted by residual:
  angle pdb=" C   GLY B  23 "
        pdb=" N   ILE B  24 "
        pdb=" CA  ILE B  24 "
      ideal   model   delta    sigma   weight residual
     121.97  129.66   -7.69 1.80e+00 3.09e-01 1.82e+01
  angle pdb=" CA  GLN D 199 "
        pdb=" CB  GLN D 199 "
        pdb=" CG  GLN D 199 "
      ideal   model   delta    sigma   weight residual
     114.10  120.78   -6.68 2.00e+00 2.50e-01 1.12e+01
  angle pdb=" C   MET A 157 "
        pdb=" N   PHE A 158 "
        pdb=" CA  PHE A 158 "
      ideal   model   delta    sigma   weight residual
     121.54  127.60   -6.06 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" C   VAL A 219 "
        pdb=" N   TRP A 220 "
        pdb=" CA  TRP A 220 "
      ideal   model   delta    sigma   weight residual
     120.68  115.32    5.36 1.70e+00 3.46e-01 9.94e+00
  angle pdb=" C   ILE A 258 "
        pdb=" N   VAL A 259 "
        pdb=" CA  VAL A 259 "
      ideal   model   delta    sigma   weight residual
     120.33  122.77   -2.44 8.00e-01 1.56e+00 9.33e+00
  ... (remaining 10483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4425
       17.90 -    35.79: 313
       35.79 -    53.69: 42
       53.69 -    71.59: 9
       71.59 -    89.49: 7
  Dihedral angle restraints: 4796
    sinusoidal: 2074
      harmonic: 2722
  Sorted by residual:
  dihedral pdb=" CA  ASN D 137 "
           pdb=" C   ASN D 137 "
           pdb=" N   ASN D 138 "
           pdb=" CA  ASN D 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.94  -20.06     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CB  GLU C 138 "
           pdb=" CG  GLU C 138 "
           pdb=" CD  GLU C 138 "
           pdb=" OE1 GLU C 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.49  -89.49     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  PHE A 158 "
           pdb=" C   PHE A 158 "
           pdb=" N   VAL A 159 "
           pdb=" CA  VAL A 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.91  -16.09     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 4793 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 791
       0.035 -    0.070: 311
       0.070 -    0.105: 114
       0.105 -    0.139: 39
       0.139 -    0.174: 3
  Chirality restraints: 1258
  Sorted by residual:
  chirality pdb=" CB  VAL A 241 "
            pdb=" CA  VAL A 241 "
            pdb=" CG1 VAL A 241 "
            pdb=" CG2 VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CA  LEU B  60 "
            pdb=" N   LEU B  60 "
            pdb=" C   LEU B  60 "
            pdb=" CB  LEU B  60 "
    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 D  21 "
            pdb=" N   ILE D  21 "
            pdb=" C   ILE D  21 "
            pdb=" CB  ILE D  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 1255 not shown)

  Planarity restraints: 1251
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 194 "    0.034 5.00e-02 4.00e+02   5.24e-02 4.39e+00
        pdb=" N   PRO B 195 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 195 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 195 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 162 "   -0.034 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO B 163 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 163 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 163 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D 199 "   -0.008 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   GLN D 199 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLN D 199 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY D 200 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1248 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1957
        2.81 -     3.33: 6779
        3.33 -     3.86: 12273
        3.86 -     4.38: 14656
        4.38 -     4.90: 25006
  Nonbonded interactions: 60671
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  84 "
            pdb=" OG1 THR B  88 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   GLN D 124 "
            pdb=" OG  SER D 127 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   CYS A 136 "
            pdb=" OH  TYR A 176 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   ASP D  82 "
            pdb=" OH  TYR D  86 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" ND1 HIS A 202 "
            pdb=" OE2 GLU A 261 "
     model   vdw
     2.341 3.120
  ... (remaining 60666 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'
}

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:             3.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.790
  Find NCS groups from input model:        0.170
  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:12.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
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      :  0.003   0.041   7668  Z= 0.188
  Angle     :  0.696   9.374  10488  Z= 0.361
  Chirality :  0.044   0.174   1258
  Planarity :  0.006   0.052   1251
  Dihedral  : 12.294  89.486   3023
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.27), residues: 925
  helix:  0.75 (0.24), residues: 419
  sheet:  0.60 (0.36), residues: 209
  loop : -1.17 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 220 
 HIS   0.003   0.001   HIS B 110 
 PHE   0.019   0.002   PHE B 124 
 TYR   0.013   0.001   TYR D 140 
 ARG   0.009   0.001   ARG C  98 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 GLN cc_start: 0.8773 (mm110) cc_final: 0.8464 (mm110)
REVERT: C   46 GLU cc_start: 0.8689 (tt0) cc_final: 0.8261 (tt0)
REVERT: C  214 LYS cc_start: 0.7651 (tppt) cc_final: 0.6677 (tppt)
REVERT: D    3 GLN cc_start: 0.8349 (mm110) cc_final: 0.8117 (mp10)
REVERT: D   42 LYS cc_start: 0.8378 (mppt) cc_final: 0.8057 (mmtp)
REVERT: D   45 LYS cc_start: 0.8421 (mttt) cc_final: 0.8177 (mtpm)
REVERT: D   93 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7708 (mtp85)
REVERT: D  126 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7029 (pttp)
REVERT: D  150 VAL cc_start: 0.7531 (t) cc_final: 0.7241 (p)
REVERT: B  113 ASN cc_start: 0.8272 (t0) cc_final: 0.8042 (t160)
REVERT: B  198 ASN cc_start: 0.8168 (t0) cc_final: 0.7808 (p0)
REVERT: B  232 GLN cc_start: 0.7670 (mt0) cc_final: 0.7099 (mp-120)
REVERT: A   50 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7636 (mptp)
REVERT: A  116 LYS cc_start: 0.7939 (tttp) cc_final: 0.7649 (tttm)
REVERT: A  233 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7798 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 1.3722
  time to fit residues: 193.1248
Evaluate side-chains
  92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  86 GLN
B 230 GLN
B 249 ASN
A  86 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.121528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.083587 restraints weight = 8861.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 1.98
r_work: 0.2806 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7668  Z= 0.310
  Angle     :  0.609   7.470  10488  Z= 0.309
  Chirality :  0.044   0.152   1258
  Planarity :  0.005   0.048   1251
  Dihedral  :  7.388  59.661   1387
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  7.30 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.28), residues: 925
  helix:  1.34 (0.25), residues: 423
  sheet:  0.60 (0.36), residues: 222
  loop : -0.94 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 237 
 HIS   0.005   0.001   HIS D 189 
 PHE   0.017   0.002   PHE D 209 
 TYR   0.012   0.002   TYR C 150 
 ARG   0.004   0.001   ARG C  98 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.762 
Fit side-chains
REVERT: C   43 GLN cc_start: 0.8758 (mm110) cc_final: 0.8460 (mm110)
REVERT: C   46 GLU cc_start: 0.8850 (tt0) cc_final: 0.8473 (tt0)
REVERT: C   57 ASP cc_start: 0.8134 (t70) cc_final: 0.7850 (t0)
REVERT: C   67 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.5666 (ptt90)
REVERT: D    3 GLN cc_start: 0.8421 (mm110) cc_final: 0.8180 (mp-120)
REVERT: D   45 LYS cc_start: 0.8619 (mttt) cc_final: 0.8355 (mtpm)
REVERT: D  126 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7079 (pttp)
REVERT: D  179 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7027 (tp)
REVERT: D  199 GLN cc_start: 0.8019 (pp30) cc_final: 0.7787 (pp30)
REVERT: B  157 MET cc_start: 0.7127 (mtm) cc_final: 0.6819 (mtt)
REVERT: B  198 ASN cc_start: 0.8308 (t0) cc_final: 0.7987 (p0)
REVERT: B  232 GLN cc_start: 0.7566 (mt0) cc_final: 0.7003 (mp-120)
REVERT: A   50 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7862 (mptp)
  outliers start: 16
  outliers final: 6
  residues processed: 105
  average time/residue: 1.3133
  time to fit residues: 145.1335
Evaluate side-chains
  93 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
C  35 ASN
D 155 GLN
** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  86 GLN
B 249 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.085639 restraints weight = 9008.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.99
r_work: 0.2839 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7668  Z= 0.173
  Angle     :  0.520   8.317  10488  Z= 0.265
  Chirality :  0.041   0.138   1258
  Planarity :  0.004   0.040   1251
  Dihedral  :  7.009  58.230   1387
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  9.61 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.28), residues: 925
  helix:  1.76 (0.25), residues: 421
  sheet:  0.67 (0.36), residues: 222
  loop : -0.91 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 220 
 HIS   0.004   0.001   HIS D 189 
 PHE   0.015   0.001   PHE D 209 
 TYR   0.008   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 267 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.874 
Fit side-chains
REVERT: C   43 GLN cc_start: 0.8708 (mm110) cc_final: 0.8407 (mm110)
REVERT: C   46 GLU cc_start: 0.8831 (tt0) cc_final: 0.8456 (tt0)
REVERT: C   57 ASP cc_start: 0.8127 (t70) cc_final: 0.7831 (t0)
REVERT: C   67 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.5437 (ptt90)
REVERT: D    3 GLN cc_start: 0.8394 (mm110) cc_final: 0.8150 (mp-120)
REVERT: D   45 LYS cc_start: 0.8566 (mttt) cc_final: 0.8286 (mtpm)
REVERT: D  126 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7116 (pttp)
REVERT: D  155 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7304 (mp10)
REVERT: D  179 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7064 (tp)
REVERT: B  157 MET cc_start: 0.6995 (mtm) cc_final: 0.6641 (mtt)
REVERT: B  198 ASN cc_start: 0.8275 (t0) cc_final: 0.7947 (p0)
REVERT: B  232 GLN cc_start: 0.7572 (mt0) cc_final: 0.7034 (mp-120)
  outliers start: 16
  outliers final: 5
  residues processed: 102
  average time/residue: 1.4030
  time to fit residues: 150.5213
Evaluate side-chains
  87 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  155 GLN
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue  241 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0270
   chunk 85 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.6640

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  56 GLN
B  86 GLN
B 249 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.086629 restraints weight = 8967.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.04
r_work: 0.2832 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7668  Z= 0.169
  Angle     :  0.513   8.302  10488  Z= 0.261
  Chirality :  0.041   0.135   1258
  Planarity :  0.004   0.041   1251
  Dihedral  :  6.941  58.466   1387
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.22 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.28), residues: 925
  helix:  1.96 (0.25), residues: 421
  sheet:  0.67 (0.36), residues: 222
  loop : -0.91 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 220 
 HIS   0.001   0.000   HIS A 202 
 PHE   0.018   0.001   PHE D 209 
 TYR   0.008   0.001   TYR D  91 
 ARG   0.005   0.000   ARG D  93 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.805 
Fit side-chains
REVERT: C   43 GLN cc_start: 0.8745 (mm110) cc_final: 0.8438 (mm110)
REVERT: C   46 GLU cc_start: 0.8840 (tt0) cc_final: 0.8481 (tt0)
REVERT: C   57 ASP cc_start: 0.8149 (t70) cc_final: 0.7853 (t0)
REVERT: C   67 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.5536 (ptt90)
REVERT: D    3 GLN cc_start: 0.8435 (mm110) cc_final: 0.8180 (mp-120)
REVERT: D   45 LYS cc_start: 0.8585 (mttt) cc_final: 0.8320 (mtpm)
REVERT: D  126 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7090 (pttp)
REVERT: D  179 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7056 (tp)
REVERT: B  154 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.6581 (mpp-170)
REVERT: B  157 MET cc_start: 0.7030 (mtm) cc_final: 0.6690 (mtt)
REVERT: B  198 ASN cc_start: 0.8307 (t0) cc_final: 0.7988 (p0)
REVERT: B  232 GLN cc_start: 0.7570 (mt0) cc_final: 0.7028 (mp-120)
REVERT: B  263 CYS cc_start: 0.8603 (m) cc_final: 0.8312 (m)
  outliers start: 17
  outliers final: 6
  residues processed: 96
  average time/residue: 1.3274
  time to fit residues: 134.1679
Evaluate side-chains
  88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain D residue  109 THR
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
C  35 ASN
D 155 GLN
B  56 GLN
B  86 GLN
B 249 ASN
A 249 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.081950 restraints weight = 8916.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.96
r_work: 0.2780 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7668  Z= 0.307
  Angle     :  0.591   7.942  10488  Z= 0.298
  Chirality :  0.044   0.148   1258
  Planarity :  0.005   0.046   1251
  Dihedral  :  7.432  59.497   1387
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.32 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.22 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.28), residues: 925
  helix:  1.70 (0.25), residues: 423
  sheet:  0.66 (0.36), residues: 222
  loop : -1.03 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 220 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.021   0.002   PHE D 209 
 TYR   0.010   0.002   TYR C  95 
 ARG   0.005   0.000   ARG D  93 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLN cc_start: 0.8747 (mm110) cc_final: 0.8448 (mm110)
REVERT: C   46 GLU cc_start: 0.8876 (tt0) cc_final: 0.8491 (tt0)
REVERT: C   57 ASP cc_start: 0.8110 (t70) cc_final: 0.7774 (t0)
REVERT: C   67 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.5665 (ptt90)
REVERT: D    3 GLN cc_start: 0.8460 (mm110) cc_final: 0.8217 (mp10)
REVERT: D   45 LYS cc_start: 0.8587 (mttt) cc_final: 0.8290 (mtpm)
REVERT: D  155 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7310 (mp10)
REVERT: D  179 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6936 (tp)
REVERT: B  157 MET cc_start: 0.7197 (mtm) cc_final: 0.6790 (mtt)
REVERT: B  232 GLN cc_start: 0.7616 (mt0) cc_final: 0.7082 (mp-120)
  outliers start: 19
  outliers final: 9
  residues processed: 100
  average time/residue: 1.3126
  time to fit residues: 138.6554
Evaluate side-chains
  91 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain D residue  109 THR
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  155 GLN
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue   86 GLN
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  241 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 81 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
D 155 GLN
B  56 GLN
B  86 GLN
B 249 ASN
A 249 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.083372 restraints weight = 8934.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 1.98
r_work: 0.2800 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2681 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7668  Z= 0.212
  Angle     :  0.539   8.026  10488  Z= 0.274
  Chirality :  0.042   0.139   1258
  Planarity :  0.004   0.040   1251
  Dihedral  :  7.219  59.851   1387
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.32 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.31 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.28), residues: 925
  helix:  1.87 (0.25), residues: 423
  sheet:  0.67 (0.36), residues: 222
  loop : -0.99 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 220 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.024   0.001   PHE D 209 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.006   0.000   ARG D  93 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 GLN cc_start: 0.8740 (mm110) cc_final: 0.8436 (mm110)
REVERT: C   46 GLU cc_start: 0.8861 (tt0) cc_final: 0.8474 (tt0)
REVERT: C   57 ASP cc_start: 0.8157 (t70) cc_final: 0.7826 (t0)
REVERT: C   67 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.5516 (ptt90)
REVERT: D   45 LYS cc_start: 0.8573 (mttt) cc_final: 0.8289 (mtpm)
REVERT: D  155 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7371 (mp10)
REVERT: D  179 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7040 (tp)
REVERT: B  157 MET cc_start: 0.7126 (mtm) cc_final: 0.6740 (mtt)
REVERT: B  232 GLN cc_start: 0.7607 (mt0) cc_final: 0.7077 (mp-120)
  outliers start: 19
  outliers final: 7
  residues processed: 98
  average time/residue: 1.2881
  time to fit residues: 133.0234
Evaluate side-chains
  90 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain D residue  109 THR
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  155 GLN
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  208 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  241 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
D 155 GLN
B  56 GLN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
A 249 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.082801 restraints weight = 8937.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 1.97
r_work: 0.2797 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7668  Z= 0.255
  Angle     :  0.552   7.855  10488  Z= 0.281
  Chirality :  0.042   0.140   1258
  Planarity :  0.004   0.041   1251
  Dihedral  :  7.258  59.954   1387
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.32 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.44 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.28), residues: 925
  helix:  1.87 (0.25), residues: 423
  sheet:  0.68 (0.36), residues: 222
  loop : -1.02 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 220 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.026   0.002   PHE D 209 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.007   0.000   ARG D  93 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 GLN cc_start: 0.8758 (mm110) cc_final: 0.8500 (mm110)
REVERT: C   46 GLU cc_start: 0.8871 (tt0) cc_final: 0.8493 (tt0)
REVERT: C   57 ASP cc_start: 0.8155 (t70) cc_final: 0.7830 (t0)
REVERT: C   67 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.5649 (ptt90)
REVERT: D   45 LYS cc_start: 0.8597 (mttt) cc_final: 0.8322 (mtpm)
REVERT: D  179 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7111 (tp)
REVERT: B  157 MET cc_start: 0.7230 (mtm) cc_final: 0.6853 (mtt)
  outliers start: 17
  outliers final: 13
  residues processed: 98
  average time/residue: 1.3192
  time to fit residues: 136.4005
Evaluate side-chains
  92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue  109 THR
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  155 GLN
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  208 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  156 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
B  56 GLN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
A 249 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.119837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.082250 restraints weight = 9056.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.00
r_work: 0.2785 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7668  Z= 0.290
  Angle     :  0.569   7.833  10488  Z= 0.290
  Chirality :  0.043   0.143   1258
  Planarity :  0.004   0.041   1251
  Dihedral  :  7.320  59.518   1387
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.43 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.07 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.28), residues: 925
  helix:  1.82 (0.25), residues: 423
  sheet:  0.70 (0.36), residues: 222
  loop : -1.07 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 220 
 HIS   0.002   0.001   HIS D 189 
 PHE   0.022   0.002   PHE D 209 
 TYR   0.010   0.002   TYR D  91 
 ARG   0.006   0.000   ARG D  93 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 GLN cc_start: 0.8767 (mm110) cc_final: 0.8478 (mm110)
REVERT: C   46 GLU cc_start: 0.8864 (tt0) cc_final: 0.8512 (tt0)
REVERT: C   57 ASP cc_start: 0.8161 (t70) cc_final: 0.7828 (t0)
REVERT: C   67 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.5615 (ptt90)
REVERT: D   45 LYS cc_start: 0.8598 (mttt) cc_final: 0.8318 (mtpm)
REVERT: D  179 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7046 (tp)
REVERT: B  157 MET cc_start: 0.7227 (mtm) cc_final: 0.6851 (mtt)
  outliers start: 21
  outliers final: 11
  residues processed: 97
  average time/residue: 1.3159
  time to fit residues: 134.9102
Evaluate side-chains
  91 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain D residue  109 THR
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  208 SER
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  156 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 70 optimal weight:    0.2980
   chunk 19 optimal weight:    8.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
A 249 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.122215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.084778 restraints weight = 9066.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.99
r_work: 0.2831 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7668  Z= 0.168
  Angle     :  0.513   7.981  10488  Z= 0.262
  Chirality :  0.040   0.136   1258
  Planarity :  0.004   0.040   1251
  Dihedral  :  7.012  59.951   1387
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.43 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.92 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.28), residues: 925
  helix:  2.05 (0.25), residues: 423
  sheet:  0.71 (0.35), residues: 224
  loop : -0.95 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 220 
 HIS   0.001   0.000   HIS D 189 
 PHE   0.027   0.001   PHE D 209 
 TYR   0.008   0.001   TYR D  91 
 ARG   0.008   0.000   ARG D  93 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 GLN cc_start: 0.8756 (mm110) cc_final: 0.8471 (mm110)
REVERT: C   46 GLU cc_start: 0.8811 (tt0) cc_final: 0.8439 (tt0)
REVERT: C   57 ASP cc_start: 0.8162 (t70) cc_final: 0.7839 (t0)
REVERT: C   67 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.5484 (ptt90)
REVERT: D   45 LYS cc_start: 0.8580 (mttt) cc_final: 0.8312 (mtpm)
REVERT: D  179 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7045 (tp)
REVERT: B  157 MET cc_start: 0.7114 (mtm) cc_final: 0.6737 (mtt)
  outliers start: 15
  outliers final: 9
  residues processed: 89
  average time/residue: 1.2861
  time to fit residues: 120.8271
Evaluate side-chains
  85 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain D residue  109 THR
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain A residue   59 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
D 147 GLN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
A 249 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.119574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.082091 restraints weight = 9072.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.98
r_work: 0.2787 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7668  Z= 0.299
  Angle     :  0.578   7.927  10488  Z= 0.293
  Chirality :  0.043   0.143   1258
  Planarity :  0.004   0.043   1251
  Dihedral  :  7.316  58.643   1387
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.32 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.04 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.28), residues: 925
  helix:  1.85 (0.25), residues: 423
  sheet:  0.67 (0.36), residues: 222
  loop : -1.06 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.027   0.002   PHE D 209 
 TYR   0.011   0.002   TYR D  91 
 ARG   0.008   0.000   ARG D  93 

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 GLN cc_start: 0.8750 (mm110) cc_final: 0.8461 (mm110)
REVERT: C   46 GLU cc_start: 0.8861 (tt0) cc_final: 0.8504 (tt0)
REVERT: C   57 ASP cc_start: 0.8129 (t70) cc_final: 0.7789 (t0)
REVERT: C   67 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.5683 (ptt90)
REVERT: D   45 LYS cc_start: 0.8609 (mttt) cc_final: 0.8328 (mtpm)
REVERT: D  179 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7031 (tp)
REVERT: B  157 MET cc_start: 0.7187 (mtm) cc_final: 0.6783 (mtt)
  outliers start: 13
  outliers final: 9
  residues processed: 91
  average time/residue: 1.3066
  time to fit residues: 125.5739
Evaluate side-chains
  89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain D residue  109 THR
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain A residue   59 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9944

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

Flipped N/Q/H residues before XYZ refinement:
D 147 GLN
** B  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
A 249 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.120747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.083911 restraints weight = 8955.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.03
r_work: 0.2793 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7668  Z= 0.219
  Angle     :  0.535   7.850  10488  Z= 0.273
  Chirality :  0.041   0.138   1258
  Planarity :  0.004   0.040   1251
  Dihedral  :  7.159  59.512   1387
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.43 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.65 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.28), residues: 925
  helix:  1.94 (0.25), residues: 423
  sheet:  0.61 (0.35), residues: 224
  loop : -1.03 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 220 
 HIS   0.001   0.000   HIS A 202 
 PHE   0.028   0.001   PHE D 209 
 TYR   0.009   0.001   TYR C  95 
 ARG   0.008   0.000   ARG D  93 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5939.47 seconds
wall clock time: 102 minutes 4.39 seconds (6124.39 seconds total)