Starting phenix.real_space_refine
on Sat Jun  7 07:11:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvm_14180/06_2025/7qvm_14180.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvm_14180/06_2025/7qvm_14180.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qvm_14180/06_2025/7qvm_14180.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvm_14180/06_2025/7qvm_14180.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvm_14180/06_2025/7qvm_14180.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvm_14180/06_2025/7qvm_14180.cif"
  }
  resolution = 3.25
  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=   0.026
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      65      5.16       5
     C    5450      2.51       5
     N    1438      2.21       5
     O    1575      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8528
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1662
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 205}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "L"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 68
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 1994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1994
          Classifications: {'peptide': 250}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 10, 'TRANS': 239}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "S"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1770
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 6.60, per 1000 atoms: 0.77
  Number of scatterers: 8528
  At special positions: 0
  Unit cell: (93.093, 122.388, 127.596, 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      65     16.00
     O    1575      8.00
     N    1438      7.00
     C    5450      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS L   1 " - pdb=" SG  CYS L   6 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 112 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.44
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2054

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      37.1% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.754A  pdb=" N   LYS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 5.098A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 256
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.024A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.863A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
      removed outlier: 3.551A  pdb=" N   ALA A 301 " --> pdb=" O   TYR A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 4.030A  pdb=" N   VAL A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.723A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 4.107A  pdb=" N   ARG G  13 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 36 through 59
    Processing helix  chain 'R' and resid 60 through 65
      removed outlier: 3.654A  pdb=" N   ARG R  65 " --> pdb=" O   LEU R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 103
      removed outlier: 3.644A  pdb=" N   VAL R  93 " --> pdb=" O   ALA R  89 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU R  94 " --> pdb=" O   VAL R  90 " (cutoff:3.500A)
      Proline residue:  R  95  - end of helix
    Processing helix  chain 'R' and resid 108 through 143
      removed outlier: 3.858A  pdb=" N   THR R 127 " --> pdb=" O   MET R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 175
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 195 through 209
    Processing helix  chain 'R' and resid 209 through 230
    Processing helix  chain 'R' and resid 271 through 301
      Proline residue:  R 290  - end of helix
    Processing helix  chain 'R' and resid 308 through 317
      removed outlier: 3.795A  pdb=" N   LEU R 316 " --> pdb=" O   ILE R 312 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU R 317 " --> pdb=" O   ILE R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 319 through 333
      Proline residue:  R 326  - end of helix
      removed outlier: 3.567A  pdb=" N   THR R 333 " --> pdb=" O   TYR R 329 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 333 through 338
      removed outlier: 3.747A  pdb=" N   PHE R 337 " --> pdb=" O   THR R 333 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.532A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.568A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.843A  pdb=" N   LEU A  38 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 72
      removed outlier: 6.469A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.797A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 6.158A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.299A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.885A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.778A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 177 through 178
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 4.107A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.885A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TYR S  50 " --> pdb=" O   TYR S  59 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.321A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.962A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1209 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: 2.82

  Time building geometry restraints manager: 2.90 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: 2615
        1.34 -     1.46: 1454
        1.46 -     1.58: 4547
        1.58 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 8708
  Sorted by residual:
  bond pdb=" C   THR S  84 "
       pdb=" N   SER S  85 "
    ideal  model  delta    sigma   weight residual
    1.333  1.266  0.066 1.29e-02 6.01e+03 2.65e+01
  bond pdb=" N   ILE L   3 "
       pdb=" CA  ILE L   3 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.50e+00
  bond pdb=" N   GLN R  92 "
       pdb=" CA  GLN R  92 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.24e-02 6.50e+03 7.27e+00
  bond pdb=" N   LEU R 316 "
       pdb=" CA  LEU R 316 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.33e-02 5.65e+03 6.57e+00
  bond pdb=" N   GLN R 171 "
       pdb=" CA  GLN R 171 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.17e-02 7.31e+03 5.45e+00
  ... (remaining 8703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 11260
        1.31 -     2.62: 412
        2.62 -     3.93: 100
        3.93 -     5.24: 29
        5.24 -     6.56: 8
  Bond angle restraints: 11809
  Sorted by residual:
  angle pdb=" N   TYR L   2 "
        pdb=" CA  TYR L   2 "
        pdb=" C   TYR L   2 "
      ideal   model   delta    sigma   weight residual
     113.12  109.08    4.04 1.25e+00 6.40e-01 1.04e+01
  angle pdb=" N   ASP A   9 "
        pdb=" CA  ASP A   9 "
        pdb=" C   ASP A   9 "
      ideal   model   delta    sigma   weight residual
     111.07  107.76    3.31 1.07e+00 8.73e-01 9.59e+00
  angle pdb=" C   THR S  84 "
        pdb=" N   SER S  85 "
        pdb=" CA  SER S  85 "
      ideal   model   delta    sigma   weight residual
     122.63  127.03   -4.40 1.44e+00 4.82e-01 9.32e+00
  angle pdb=" N   MET A 249 "
        pdb=" CA  MET A 249 "
        pdb=" C   MET A 249 "
      ideal   model   delta    sigma   weight residual
     110.97  107.66    3.31 1.09e+00 8.42e-01 9.24e+00
  angle pdb=" CA  LEU L   8 "
        pdb=" C   LEU L   8 "
        pdb=" O   LEU L   8 "
      ideal   model   delta    sigma   weight residual
     121.20  118.17    3.03 1.04e+00 9.25e-01 8.50e+00
  ... (remaining 11804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4698
       17.96 -    35.92: 387
       35.92 -    53.88: 55
       53.88 -    71.84: 6
       71.84 -    89.80: 6
  Dihedral angle restraints: 5152
    sinusoidal: 1980
      harmonic: 3172
  Sorted by residual:
  dihedral pdb=" CB  CYS R 112 "
           pdb=" SG  CYS R 112 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.69   85.69     1      1.00e+01 1.00e-02 8.88e+01
  dihedral pdb=" CB  CYS L   1 "
           pdb=" SG  CYS L   1 "
           pdb=" SG  CYS L   6 "
           pdb=" CB  CYS L   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.07  -60.07     1      1.00e+01 1.00e-02 4.81e+01
  dihedral pdb=" CA  GLN S  82 "
           pdb=" C   GLN S  82 "
           pdb=" N   MET S  83 "
           pdb=" CA  MET S  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.76  -22.24     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 5149 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 895
       0.035 -    0.070: 312
       0.070 -    0.105: 94
       0.105 -    0.140: 41
       0.140 -    0.175: 9
  Chirality restraints: 1351
  Sorted by residual:
  chirality pdb=" CA  GLU G  17 "
            pdb=" N   GLU G  17 "
            pdb=" C   GLU G  17 "
            pdb=" CB  GLU G  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  MET A 249 "
            pdb=" N   MET A 249 "
            pdb=" C   MET A 249 "
            pdb=" CB  MET A 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CA  LEU A 250 "
            pdb=" N   LEU A 250 "
            pdb=" C   LEU A 250 "
            pdb=" CB  LEU A 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.29e-01
  ... (remaining 1348 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 341 "    0.013 2.00e-02 2.50e+03   2.53e-02 6.40e+00
        pdb=" C   ASP A 341 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASP A 341 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE A 342 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "    0.005 2.00e-02 2.50e+03   1.30e-02 4.24e+00
        pdb=" CG  TRP B  82 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  63 "    0.016 2.00e-02 2.50e+03   1.08e-02 2.92e+00
        pdb=" CG  TRP B  63 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  63 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  63 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  63 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  63 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  63 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  63 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 262
        2.70 -     3.25: 8817
        3.25 -     3.80: 13858
        3.80 -     4.35: 17167
        4.35 -     4.90: 29414
  Nonbonded interactions: 69518
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   ALA B 231 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" O   HIS G  44 "
     model   vdw
     2.248 3.040
  ... (remaining 69513 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             5.900
  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:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.380
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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   0.093   8713  Z= 0.208
  Angle     :  0.640   6.556  11817  Z= 0.359
  Chirality :  0.044   0.175   1351
  Planarity :  0.004   0.043   1486
  Dihedral  : 12.937  89.801   3086
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.22 (0.27), residues: 1068
  helix:  1.70 (0.29), residues: 353
  sheet: -0.52 (0.32), residues: 241
  loop : -0.63 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  63 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.017   0.001   PHE S  68 
 TYR   0.010   0.001   TYR S 178 
 ARG   0.008   0.001   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13286 (  430)
  hydrogen bonds       : angle       5.82794 ( 1209)
  SS BOND              : bond        0.00211 (    4)
  SS BOND              : angle       0.77098 (    8)
  covalent geometry    : bond        0.00323 ( 8708)
  covalent geometry    : angle       0.64002 (11809)
  Misc. bond           : bond        0.09320 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 HIS cc_start: 0.7167 (p90) cc_final: 0.6950 (p90)
REVERT: A  243 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.8291 (ptp-110)
REVERT: A  249 MET cc_start: 0.8227 (tpt) cc_final: 0.7991 (tpp)
REVERT: B   23 LYS cc_start: 0.9109 (tppt) cc_final: 0.8810 (mtmm)
REVERT: B   63 TRP cc_start: 0.7775 (m100) cc_final: 0.7539 (m100)
REVERT: B  274 THR cc_start: 0.8341 (m) cc_final: 0.7836 (p)
REVERT: G   20 LYS cc_start: 0.8863 (ptpp) cc_final: 0.8490 (pttm)
REVERT: G   41 CYS cc_start: 0.7026 (t) cc_final: 0.6759 (t)
REVERT: R   42 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8642 (mt-10)
REVERT: R   79 LYS cc_start: 0.8214 (tttt) cc_final: 0.7646 (mmmt)
REVERT: R   92 GLN cc_start: 0.7935 (tp40) cc_final: 0.7238 (tp-100)
REVERT: R  119 GLN cc_start: 0.5790 (mt0) cc_final: 0.5418 (mt0)
REVERT: R  275 LYS cc_start: 0.7453 (tttt) cc_final: 0.7212 (tttt)
REVERT: S   83 MET cc_start: 0.8025 (tpt) cc_final: 0.7554 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2333
  time to fit residues: 62.4994
Evaluate side-chains
  172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 83 optimal weight:    0.4980
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0270
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
** R 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.124039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.088528 restraints weight = 16960.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 3.12
r_work: 0.3329 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8713  Z= 0.127
  Angle     :  0.589   6.503  11817  Z= 0.305
  Chirality :  0.042   0.157   1351
  Planarity :  0.004   0.045   1486
  Dihedral  :  4.183  20.641   1169
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 10.25 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1068
  helix:  2.18 (0.28), residues: 354
  sheet: -0.43 (0.32), residues: 244
  loop : -0.71 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.019   0.001   PHE S 200 
 TYR   0.013   0.001   TYR S 102 
 ARG   0.009   0.001   ARG R  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  430)
  hydrogen bonds       : angle       4.80396 ( 1209)
  SS BOND              : bond        0.00106 (    4)
  SS BOND              : angle       0.58994 (    8)
  covalent geometry    : bond        0.00284 ( 8708)
  covalent geometry    : angle       0.58893 (11809)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 190
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.8953 (ptp-110) cc_final: 0.8563 (ptp-110)
REVERT: A  246 GLU cc_start: 0.9226 (pt0) cc_final: 0.9003 (pt0)
REVERT: A  277 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8803 (mm-30)
REVERT: B   23 LYS cc_start: 0.9168 (tppt) cc_final: 0.8819 (mtpt)
REVERT: B  197 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8210 (mmm160)
REVERT: G   18 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8420 (tp-100)
REVERT: G   20 LYS cc_start: 0.9052 (ptpp) cc_final: 0.8484 (pttm)
REVERT: G   21 MET cc_start: 0.9363 (tpp) cc_final: 0.9063 (ttp)
REVERT: G   47 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: L    5 ASN cc_start: 0.9040 (p0) cc_final: 0.8200 (m110)
REVERT: R   40 ARG cc_start: 0.8522 (ptt90) cc_final: 0.8190 (ptm-80)
REVERT: R   42 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8625 (mt-10)
REVERT: R   79 LYS cc_start: 0.8086 (tttt) cc_final: 0.7589 (mmmt)
REVERT: R   92 GLN cc_start: 0.8370 (tp40) cc_final: 0.7796 (tp40)
REVERT: R  226 LYS cc_start: 0.6428 (tppt) cc_final: 0.6052 (mmtm)
REVERT: R  275 LYS cc_start: 0.7370 (tttt) cc_final: 0.7121 (tttt)
REVERT: R  332 PHE cc_start: 0.5287 (t80) cc_final: 0.4987 (t80)
REVERT: S   83 MET cc_start: 0.7869 (tpt) cc_final: 0.7590 (tpt)
  outliers start: 6
  outliers final: 4
  residues processed: 194
  average time/residue: 0.2498
  time to fit residues: 62.9423
Evaluate side-chains
  167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 163
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
R 230 ASN
S 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.122940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.087356 restraints weight = 17283.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 3.18
r_work: 0.3303 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8713  Z= 0.135
  Angle     :  0.577  12.763  11817  Z= 0.295
  Chirality :  0.042   0.289   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.194  20.926   1169
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.05 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.27), residues: 1068
  helix:  2.38 (0.28), residues: 353
  sheet: -0.46 (0.32), residues: 253
  loop : -0.71 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.001   PHE S 200 
 TYR   0.012   0.001   TYR S 102 
 ARG   0.004   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  430)
  hydrogen bonds       : angle       4.55759 ( 1209)
  SS BOND              : bond        0.00147 (    4)
  SS BOND              : angle       0.58209 (    8)
  covalent geometry    : bond        0.00307 ( 8708)
  covalent geometry    : angle       0.57697 (11809)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 176
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9002 (ptp-110) cc_final: 0.8641 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9188 (tppt) cc_final: 0.8829 (mtpt)
REVERT: G   13 ARG cc_start: 0.8999 (mpp-170) cc_final: 0.8769 (mtt90)
REVERT: G   20 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8517 (pttm)
REVERT: G   41 CYS cc_start: 0.7271 (t) cc_final: 0.7017 (t)
REVERT: G   47 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: L    5 ASN cc_start: 0.8973 (p0) cc_final: 0.8159 (m110)
REVERT: R   40 ARG cc_start: 0.8541 (ptt90) cc_final: 0.8094 (ptm-80)
REVERT: R   78 MET cc_start: 0.7628 (mtp) cc_final: 0.7389 (ttt)
REVERT: R   79 LYS cc_start: 0.8121 (tttt) cc_final: 0.7586 (mmmt)
REVERT: R   92 GLN cc_start: 0.8382 (tp40) cc_final: 0.7519 (tp-100)
REVERT: R  119 GLN cc_start: 0.5341 (OUTLIER) cc_final: 0.4878 (mt0)
REVERT: R  226 LYS cc_start: 0.6496 (tppt) cc_final: 0.6180 (mmtm)
REVERT: R  275 LYS cc_start: 0.7472 (tttt) cc_final: 0.7269 (tttt)
REVERT: R  332 PHE cc_start: 0.5206 (t80) cc_final: 0.4991 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 188
  average time/residue: 0.2570
  time to fit residues: 62.7231
Evaluate side-chains
  171 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  119 GLN
Chi-restraints excluded: chain R residue  300 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  171 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0030
   chunk 7 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   chunk 85 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    1.5998

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

Flipped N/Q/H residues before XYZ refinement:
S 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.120383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.084664 restraints weight = 17143.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 3.10
r_work: 0.3248 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8713  Z= 0.192
  Angle     :  0.600   9.950  11817  Z= 0.310
  Chirality :  0.043   0.201   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.350  22.381   1169
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.64 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.44 (0.27), residues: 1068
  helix:  2.26 (0.28), residues: 360
  sheet: -0.58 (0.31), residues: 266
  loop : -0.77 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.012   0.002   PHE S  68 
 TYR   0.017   0.002   TYR S  50 
 ARG   0.004   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03476 (  430)
  hydrogen bonds       : angle       4.56099 ( 1209)
  SS BOND              : bond        0.00134 (    4)
  SS BOND              : angle       0.52824 (    8)
  covalent geometry    : bond        0.00442 ( 8708)
  covalent geometry    : angle       0.60040 (11809)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9034 (ptp-110) cc_final: 0.8672 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9225 (tppt) cc_final: 0.9017 (tppt)
REVERT: B  118 ASP cc_start: 0.8248 (t0) cc_final: 0.8044 (m-30)
REVERT: G   18 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8538 (tp-100)
REVERT: G   21 MET cc_start: 0.9362 (tpp) cc_final: 0.9039 (tmm)
REVERT: G   41 CYS cc_start: 0.7351 (t) cc_final: 0.7052 (t)
REVERT: G   47 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8148 (tm-30)
REVERT: R   40 ARG cc_start: 0.8582 (ptt90) cc_final: 0.8079 (ptm-80)
REVERT: R   78 MET cc_start: 0.7645 (mtp) cc_final: 0.7363 (ttt)
REVERT: R   79 LYS cc_start: 0.8162 (tttt) cc_final: 0.7626 (mmmt)
REVERT: R  226 LYS cc_start: 0.6433 (tppt) cc_final: 0.6149 (mmtm)
REVERT: R  275 LYS cc_start: 0.7480 (tttt) cc_final: 0.7246 (tttt)
  outliers start: 20
  outliers final: 15
  residues processed: 175
  average time/residue: 0.2782
  time to fit residues: 62.8178
Evaluate side-chains
  169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  300 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 69 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
S 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.122018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.086467 restraints weight = 16890.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 3.08
r_work: 0.3287 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8713  Z= 0.129
  Angle     :  0.576   9.006  11817  Z= 0.297
  Chirality :  0.042   0.183   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.202  21.263   1169
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.72 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.50 (0.26), residues: 1068
  helix:  2.29 (0.28), residues: 359
  sheet: -0.42 (0.31), residues: 255
  loop : -0.80 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.026   0.001   TYR A 303 
 ARG   0.009   0.001   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03236 (  430)
  hydrogen bonds       : angle       4.45045 ( 1209)
  SS BOND              : bond        0.00174 (    4)
  SS BOND              : angle       0.41756 (    8)
  covalent geometry    : bond        0.00295 ( 8708)
  covalent geometry    : angle       0.57599 (11809)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9017 (ptp-110) cc_final: 0.8635 (ptp-110)
REVERT: A  323 MET cc_start: 0.8691 (tpp) cc_final: 0.8449 (tpp)
REVERT: B   23 LYS cc_start: 0.9212 (tppt) cc_final: 0.8979 (tppt)
REVERT: B   63 TRP cc_start: 0.8021 (m100) cc_final: 0.7708 (m100)
REVERT: G   18 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8343 (tp-100)
REVERT: G   20 LYS cc_start: 0.9083 (ptmt) cc_final: 0.8812 (ptpp)
REVERT: G   21 MET cc_start: 0.9336 (tpp) cc_final: 0.9036 (tmm)
REVERT: G   41 CYS cc_start: 0.7241 (t) cc_final: 0.6942 (t)
REVERT: G   47 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: R   40 ARG cc_start: 0.8564 (ptt90) cc_final: 0.8091 (ptm-80)
REVERT: R   78 MET cc_start: 0.7641 (mtp) cc_final: 0.7426 (ttt)
REVERT: R   79 LYS cc_start: 0.8163 (tttt) cc_final: 0.7666 (mmmt)
REVERT: R  119 GLN cc_start: 0.5421 (OUTLIER) cc_final: 0.5093 (mt0)
REVERT: R  123 MET cc_start: 0.5866 (mmp) cc_final: 0.5631 (mmp)
REVERT: R  226 LYS cc_start: 0.6435 (tppt) cc_final: 0.6118 (mmtm)
REVERT: R  275 LYS cc_start: 0.7498 (tttt) cc_final: 0.7280 (tttt)
REVERT: S  219 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8519 (pp30)
  outliers start: 24
  outliers final: 15
  residues processed: 186
  average time/residue: 0.2587
  time to fit residues: 62.9532
Evaluate side-chains
  177 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue  119 GLN
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  300 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  219 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 103 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0870
   chunk 2 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
S 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.122147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.086579 restraints weight = 16982.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.09
r_work: 0.3293 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8713  Z= 0.126
  Angle     :  0.575   8.563  11817  Z= 0.298
  Chirality :  0.041   0.181   1351
  Planarity :  0.004   0.048   1486
  Dihedral  :  4.121  21.079   1169
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.02 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.55 (0.27), residues: 1068
  helix:  2.30 (0.28), residues: 359
  sheet: -0.36 (0.31), residues: 255
  loop : -0.76 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP S  47 
 HIS   0.005   0.001   HIS S 220 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.019   0.001   TYR A 303 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  430)
  hydrogen bonds       : angle       4.38756 ( 1209)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       0.37515 (    8)
  covalent geometry    : bond        0.00287 ( 8708)
  covalent geometry    : angle       0.57498 (11809)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9046 (ptp-110) cc_final: 0.8661 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9214 (tppt) cc_final: 0.8970 (tppt)
REVERT: B   63 TRP cc_start: 0.8063 (m100) cc_final: 0.7719 (m100)
REVERT: B  118 ASP cc_start: 0.8170 (t0) cc_final: 0.7961 (m-30)
REVERT: G   18 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8352 (tp-100)
REVERT: G   41 CYS cc_start: 0.7330 (t) cc_final: 0.7011 (t)
REVERT: G   47 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: R   40 ARG cc_start: 0.8547 (ptt90) cc_final: 0.8072 (ptm-80)
REVERT: R   78 MET cc_start: 0.7567 (mtp) cc_final: 0.7358 (ttt)
REVERT: R   79 LYS cc_start: 0.8142 (tttt) cc_final: 0.7642 (mmmt)
REVERT: R  226 LYS cc_start: 0.6305 (tppt) cc_final: 0.6037 (mmtm)
REVERT: R  275 LYS cc_start: 0.7517 (tttt) cc_final: 0.7298 (tttt)
REVERT: R  332 PHE cc_start: 0.4829 (t80) cc_final: 0.4613 (t80)
REVERT: S   83 MET cc_start: 0.8403 (mmt) cc_final: 0.8191 (mmt)
REVERT: S  219 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8486 (pp30)
  outliers start: 22
  outliers final: 16
  residues processed: 181
  average time/residue: 0.2738
  time to fit residues: 64.0845
Evaluate side-chains
  176 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  300 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain S residue  219 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    0.0470
   chunk 75 optimal weight:    0.4980
   chunk 69 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0170
   chunk 61 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.122561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.087031 restraints weight = 17004.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 3.11
r_work: 0.3298 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8713  Z= 0.123
  Angle     :  0.597  10.646  11817  Z= 0.306
  Chirality :  0.041   0.183   1351
  Planarity :  0.004   0.047   1486
  Dihedral  :  4.068  20.720   1169
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.45 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.57 (0.27), residues: 1068
  helix:  2.32 (0.28), residues: 359
  sheet: -0.36 (0.31), residues: 255
  loop : -0.75 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.016   0.001   TYR A 303 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03177 (  430)
  hydrogen bonds       : angle       4.36711 ( 1209)
  SS BOND              : bond        0.00182 (    4)
  SS BOND              : angle       0.37070 (    8)
  covalent geometry    : bond        0.00280 ( 8708)
  covalent geometry    : angle       0.59665 (11809)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9004 (ptp-110) cc_final: 0.8643 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9208 (tppt) cc_final: 0.8965 (tppt)
REVERT: B   63 TRP cc_start: 0.8031 (m100) cc_final: 0.7663 (m100)
REVERT: B   89 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8132 (ptpp)
REVERT: B  118 ASP cc_start: 0.8149 (t0) cc_final: 0.7947 (m-30)
REVERT: G   18 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8320 (tp-100)
REVERT: G   21 MET cc_start: 0.9353 (tpp) cc_final: 0.9010 (ttp)
REVERT: G   41 CYS cc_start: 0.7332 (t) cc_final: 0.6979 (t)
REVERT: G   47 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8170 (tm-30)
REVERT: R   78 MET cc_start: 0.7619 (mtp) cc_final: 0.7411 (ttt)
REVERT: R   79 LYS cc_start: 0.8169 (tttt) cc_final: 0.7670 (mmmt)
REVERT: R   92 GLN cc_start: 0.8138 (tp40) cc_final: 0.7421 (tp-100)
REVERT: R  226 LYS cc_start: 0.6439 (tppt) cc_final: 0.6142 (mmtm)
REVERT: R  275 LYS cc_start: 0.7579 (tttt) cc_final: 0.7338 (tttt)
  outliers start: 19
  outliers final: 17
  residues processed: 175
  average time/residue: 0.2582
  time to fit residues: 58.7105
Evaluate side-chains
  178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  217 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 40 optimal weight:    0.0770
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.3742

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

Flipped N/Q/H residues before XYZ refinement:
S 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.120281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.084595 restraints weight = 17380.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 3.17
r_work: 0.3249 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8713  Z= 0.175
  Angle     :  0.628   8.673  11817  Z= 0.324
  Chirality :  0.042   0.183   1351
  Planarity :  0.004   0.047   1486
  Dihedral  :  4.287  22.019   1169
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.99 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.50 (0.27), residues: 1068
  helix:  2.32 (0.28), residues: 359
  sheet: -0.56 (0.31), residues: 266
  loop : -0.73 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.021   0.002   PHE B 292 
 TYR   0.023   0.001   TYR A 303 
 ARG   0.009   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  430)
  hydrogen bonds       : angle       4.41183 ( 1209)
  SS BOND              : bond        0.00173 (    4)
  SS BOND              : angle       0.50687 (    8)
  covalent geometry    : bond        0.00405 ( 8708)
  covalent geometry    : angle       0.62801 (11809)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9057 (ptp-110) cc_final: 0.8693 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9251 (tppt) cc_final: 0.9016 (tppt)
REVERT: B   63 TRP cc_start: 0.8082 (m100) cc_final: 0.7743 (m100)
REVERT: B   89 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8126 (ptpp)
REVERT: G   18 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8453 (tp-100)
REVERT: G   20 LYS cc_start: 0.8994 (ptpt) cc_final: 0.8686 (pttm)
REVERT: G   21 MET cc_start: 0.9352 (tpp) cc_final: 0.9010 (tmm)
REVERT: G   47 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: R   78 MET cc_start: 0.7571 (mtp) cc_final: 0.7341 (ttt)
REVERT: R   79 LYS cc_start: 0.8162 (tttt) cc_final: 0.7666 (mmmt)
REVERT: R   92 GLN cc_start: 0.8254 (tp40) cc_final: 0.7517 (tp-100)
REVERT: R  226 LYS cc_start: 0.6345 (tppt) cc_final: 0.6086 (mmtm)
REVERT: R  275 LYS cc_start: 0.7512 (tttt) cc_final: 0.7268 (tttt)
REVERT: S  219 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8488 (pp30)
  outliers start: 21
  outliers final: 14
  residues processed: 173
  average time/residue: 0.2681
  time to fit residues: 60.9548
Evaluate side-chains
  173 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   80 HIS
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  219 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
S 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.118313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.082495 restraints weight = 17417.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 3.17
r_work: 0.3202 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   8713  Z= 0.249
  Angle     :  0.696   8.460  11817  Z= 0.359
  Chirality :  0.045   0.198   1351
  Planarity :  0.005   0.048   1486
  Dihedral  :  4.622  23.355   1169
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.20 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.28 (0.27), residues: 1068
  helix:  2.18 (0.28), residues: 360
  sheet: -0.77 (0.29), residues: 285
  loop : -0.82 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP S  47 
 HIS   0.010   0.001   HIS S 220 
 PHE   0.013   0.002   PHE B 199 
 TYR   0.028   0.002   TYR S  50 
 ARG   0.010   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03642 (  430)
  hydrogen bonds       : angle       4.61630 ( 1209)
  SS BOND              : bond        0.00178 (    4)
  SS BOND              : angle       2.42742 (    8)
  covalent geometry    : bond        0.00574 ( 8708)
  covalent geometry    : angle       0.69370 (11809)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9096 (ptp-110) cc_final: 0.8690 (ptp-110)
REVERT: B   63 TRP cc_start: 0.8154 (m100) cc_final: 0.7842 (m100)
REVERT: B   89 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8161 (ptpp)
REVERT: B  118 ASP cc_start: 0.8311 (t0) cc_final: 0.8069 (m-30)
REVERT: G   18 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8480 (tp-100)
REVERT: G   20 LYS cc_start: 0.9022 (ptpt) cc_final: 0.8678 (pttm)
REVERT: G   21 MET cc_start: 0.9384 (tpp) cc_final: 0.8993 (ttp)
REVERT: G   47 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: R   78 MET cc_start: 0.7556 (mtp) cc_final: 0.7322 (ttt)
REVERT: R   79 LYS cc_start: 0.8186 (tttt) cc_final: 0.7651 (mmmt)
REVERT: R  226 LYS cc_start: 0.6427 (tppt) cc_final: 0.6164 (mmtm)
REVERT: R  275 LYS cc_start: 0.7503 (tttt) cc_final: 0.7234 (tttt)
  outliers start: 26
  outliers final: 18
  residues processed: 174
  average time/residue: 0.2556
  time to fit residues: 57.9770
Evaluate side-chains
  175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   80 HIS
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue   76 LYS
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.120488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.084714 restraints weight = 17280.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.18
r_work: 0.3250 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8713  Z= 0.162
  Angle     :  0.679   9.315  11817  Z= 0.346
  Chirality :  0.043   0.243   1351
  Planarity :  0.004   0.052   1486
  Dihedral  :  4.477  22.147   1169
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 20.50 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.34 (0.27), residues: 1068
  helix:  2.13 (0.28), residues: 360
  sheet: -0.64 (0.30), residues: 269
  loop : -0.77 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP S  47 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.045   0.002   PHE B 292 
 TYR   0.016   0.001   TYR A 303 
 ARG   0.011   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  430)
  hydrogen bonds       : angle       4.54386 ( 1209)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       1.93376 (    8)
  covalent geometry    : bond        0.00375 ( 8708)
  covalent geometry    : angle       0.67772 (11809)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9089 (ptp-110) cc_final: 0.8669 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9246 (tppp) cc_final: 0.8896 (tppt)
REVERT: B   63 TRP cc_start: 0.8122 (m100) cc_final: 0.7795 (m100)
REVERT: B   89 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8115 (ptpp)
REVERT: B  118 ASP cc_start: 0.8227 (t0) cc_final: 0.8003 (m-30)
REVERT: G   13 ARG cc_start: 0.9315 (mtt90) cc_final: 0.9060 (ptp90)
REVERT: G   18 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8441 (tp-100)
REVERT: G   20 LYS cc_start: 0.9011 (ptpt) cc_final: 0.8668 (pttm)
REVERT: G   21 MET cc_start: 0.9361 (tpp) cc_final: 0.8994 (tmm)
REVERT: G   47 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: R   78 MET cc_start: 0.7518 (mtp) cc_final: 0.7288 (ttt)
REVERT: R   79 LYS cc_start: 0.8163 (tttt) cc_final: 0.7631 (mmmt)
REVERT: R  226 LYS cc_start: 0.6380 (tppt) cc_final: 0.6129 (mmtm)
REVERT: R  275 LYS cc_start: 0.7436 (tttt) cc_final: 0.7181 (tttt)
REVERT: S  219 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8461 (pp30)
  outliers start: 16
  outliers final: 13
  residues processed: 170
  average time/residue: 0.2678
  time to fit residues: 58.7948
Evaluate side-chains
  170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   80 HIS
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  219 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0870
   chunk 2 optimal weight:    8.9990
   chunk 17 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0770
   chunk 97 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 42 optimal weight:    0.2980
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.120639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.084999 restraints weight = 17382.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.18
r_work: 0.3250 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.116   8713  Z= 0.196
  Angle     :  1.006  59.198  11817  Z= 0.564
  Chirality :  0.046   0.577   1351
  Planarity :  0.004   0.052   1486
  Dihedral  :  4.500  22.064   1169
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.04 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.35 (0.27), residues: 1068
  helix:  2.14 (0.28), residues: 360
  sheet: -0.64 (0.30), residues: 269
  loop : -0.77 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.030   0.002   PHE B 292 
 TYR   0.016   0.001   TYR L   2 
 ARG   0.009   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03384 (  430)
  hydrogen bonds       : angle       4.54603 ( 1209)
  SS BOND              : bond        0.00287 (    4)
  SS BOND              : angle       1.72225 (    8)
  covalent geometry    : bond        0.00436 ( 8708)
  covalent geometry    : angle       1.00571 (11809)
  Misc. bond           : bond        0.00004 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6340.76 seconds
wall clock time: 109 minutes 16.29 seconds (6556.29 seconds total)