Starting phenix.real_space_refine
on Thu Feb 13 01:34:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvm_14180/02_2025/7qvm_14180.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvm_14180/02_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_14180/02_2025/7qvm_14180.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvm_14180/02_2025/7qvm_14180.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvm_14180/02_2025/7qvm_14180.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvm_14180/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.92, per 1000 atoms: 0.69
  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: 2.17
  Conformation dependent library (CDL) restraints added in 1.0 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: 1.13
  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: 2.51

  Time building geometry restraints manager: 2.54 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:             6.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.150
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.120
-------------------------------------------------------------------------------
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   0.066   8708  Z= 0.208
  Angle     :  0.640   6.556  11809  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 

*********************** 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  : 0.944 
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: 0.2468
  time to fit residues: 65.7679
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  : 1.015 
-------------------------------------------------------------------------------
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 = 51)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.088530 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: 0.7771
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   8708  Z= 0.184
  Angle     :  0.589   6.503  11809  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 

*********************** 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  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.8958 (ptp-110) cc_final: 0.8562 (ptp-110)
REVERT: A  246 GLU cc_start: 0.9228 (pt0) cc_final: 0.9005 (pt0)
REVERT: A  277 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8809 (mm-30)
REVERT: B   23 LYS cc_start: 0.9169 (tppt) cc_final: 0.8820 (mtpt)
REVERT: B  197 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8208 (mmm160)
REVERT: G   18 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8419 (tp-100)
REVERT: G   20 LYS cc_start: 0.9055 (ptpp) cc_final: 0.8488 (pttm)
REVERT: G   21 MET cc_start: 0.9363 (tpp) cc_final: 0.9062 (ttp)
REVERT: G   47 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8084 (tm-30)
REVERT: L    5 ASN cc_start: 0.9044 (p0) cc_final: 0.8197 (m110)
REVERT: R   40 ARG cc_start: 0.8523 (ptt90) cc_final: 0.8196 (ptm-80)
REVERT: R   42 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8636 (mt-10)
REVERT: R   79 LYS cc_start: 0.8077 (tttt) cc_final: 0.7579 (mmmt)
REVERT: R   92 GLN cc_start: 0.8381 (tp40) cc_final: 0.7796 (tp40)
REVERT: R  226 LYS cc_start: 0.6432 (tppt) cc_final: 0.6056 (mmtm)
REVERT: R  275 LYS cc_start: 0.7356 (tttt) cc_final: 0.7108 (tttt)
REVERT: R  332 PHE cc_start: 0.5286 (t80) cc_final: 0.4986 (t80)
REVERT: S   76 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8679 (mtmm)
REVERT: S   83 MET cc_start: 0.7866 (tpt) cc_final: 0.7587 (tpt)
  outliers start: 6
  outliers final: 4
  residues processed: 194
  average time/residue: 0.2577
  time to fit residues: 64.8262
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  : 1.001 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 75 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.123145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.087579 restraints weight = 17275.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 3.18
r_work: 0.3307 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8708  Z= 0.195
  Angle     :  0.575  13.284  11809  Z= 0.293
  Chirality :  0.042   0.277   1351
  Planarity :  0.004   0.044   1486
  Dihedral  :  4.169  20.852   1169
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.94 %
    Favored  : 85.01 %
  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:  0.58 (0.26), residues: 1068
  helix:  2.38 (0.28), residues: 353
  sheet: -0.29 (0.32), residues: 242
  loop : -0.79 (0.29), residues: 473

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   0.003   0.000   ARG A 209 

*********************** 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
  197 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 178
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9000 (ptp-110) cc_final: 0.8642 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9187 (tppt) cc_final: 0.8821 (mtpt)
REVERT: G   13 ARG cc_start: 0.9002 (mpp-170) cc_final: 0.8775 (mtt90)
REVERT: G   20 LYS cc_start: 0.8985 (ptpp) cc_final: 0.8515 (pttm)
REVERT: G   41 CYS cc_start: 0.7288 (t) cc_final: 0.7027 (t)
REVERT: G   47 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: L    5 ASN cc_start: 0.8973 (p0) cc_final: 0.8149 (m110)
REVERT: R   40 ARG cc_start: 0.8553 (ptt90) cc_final: 0.8098 (ptm-80)
REVERT: R   78 MET cc_start: 0.7615 (mtp) cc_final: 0.7377 (ttt)
REVERT: R   79 LYS cc_start: 0.8121 (tttt) cc_final: 0.7578 (mmmt)
REVERT: R   92 GLN cc_start: 0.8385 (tp40) cc_final: 0.7507 (tp-100)
REVERT: R  119 GLN cc_start: 0.5283 (OUTLIER) cc_final: 0.4827 (mt0)
REVERT: R  226 LYS cc_start: 0.6463 (tppt) cc_final: 0.6153 (mmtm)
REVERT: R  275 LYS cc_start: 0.7453 (tttt) cc_final: 0.7250 (tttt)
REVERT: R  332 PHE cc_start: 0.5220 (t80) cc_final: 0.4982 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 191
  average time/residue: 0.2579
  time to fit residues: 64.0067
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  : 1.042 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
B 340 ASN
S 219 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.118505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.082382 restraints weight = 17303.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.17
r_work: 0.3203 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   8708  Z= 0.396
  Angle     :  0.646   9.729  11809  Z= 0.335
  Chirality :  0.045   0.205   1351
  Planarity :  0.004   0.045   1486
  Dihedral  :  4.563  23.580   1169
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.50 %
    Favored  : 81.23 %
  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:  0.33 (0.27), residues: 1068
  helix:  2.20 (0.28), residues: 360
  sheet: -0.70 (0.31), residues: 268
  loop : -0.82 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.014   0.002   PHE S  68 
 TYR   0.025   0.002   TYR S  50 
 ARG   0.004   0.001   ARG B 197 

*********************** 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
  182 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9066 (ptp-110) cc_final: 0.8680 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9248 (tppt) cc_final: 0.9029 (tppt)
REVERT: B  118 ASP cc_start: 0.8364 (t0) cc_final: 0.8127 (m-30)
REVERT: G   13 ARG cc_start: 0.9143 (mpp-170) cc_final: 0.8779 (mtt90)
REVERT: G   21 MET cc_start: 0.9384 (tpp) cc_final: 0.9034 (ttp)
REVERT: G   41 CYS cc_start: 0.7493 (t) cc_final: 0.7159 (t)
REVERT: G   47 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: R   40 ARG cc_start: 0.8575 (ptt90) cc_final: 0.8175 (ptm-80)
REVERT: R   78 MET cc_start: 0.7617 (mtp) cc_final: 0.7332 (ttt)
REVERT: R   79 LYS cc_start: 0.8171 (tttt) cc_final: 0.7629 (mmmt)
REVERT: R  226 LYS cc_start: 0.6436 (tppt) cc_final: 0.6177 (mmtm)
REVERT: R  275 LYS cc_start: 0.7470 (tttt) cc_final: 0.7233 (tttt)
REVERT: S  219 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8570 (pp30)
  outliers start: 21
  outliers final: 17
  residues processed: 174
  average time/residue: 0.2689
  time to fit residues: 60.4487
Evaluate side-chains
  170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
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 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   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
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain S residue  222 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 69 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 5 optimal weight:    0.2980
   chunk 96 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 321 ASN
S 219 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.121340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.085617 restraints weight = 16919.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 3.08
r_work: 0.3270 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8708  Z= 0.203
  Angle     :  0.584   8.961  11809  Z= 0.301
  Chirality :  0.042   0.187   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.323  21.973   1169
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.15 %
    Favored  : 80.15 %
  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:  2.27 (0.28), residues: 359
  sheet: -0.62 (0.31), residues: 266
  loop : -0.74 (0.31), residues: 443

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   0.012   0.001   PHE R 292 
 TYR   0.027   0.001   TYR A 303 
 ARG   0.004   0.000   ARG S 148 

*********************** 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
  195 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9031 (ptp-110) cc_final: 0.8660 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9215 (tppt) cc_final: 0.8991 (tppt)
REVERT: B   63 TRP cc_start: 0.8036 (m100) cc_final: 0.7741 (m100)
REVERT: G   13 ARG cc_start: 0.9171 (mpp-170) cc_final: 0.8886 (mtt90)
REVERT: G   18 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8305 (tp-100)
REVERT: G   20 LYS cc_start: 0.9111 (ptmt) cc_final: 0.8868 (ptpt)
REVERT: G   21 MET cc_start: 0.9350 (tpp) cc_final: 0.9020 (tmm)
REVERT: G   41 CYS cc_start: 0.7344 (t) cc_final: 0.7038 (t)
REVERT: G   47 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8164 (tm-30)
REVERT: R   40 ARG cc_start: 0.8560 (ptt90) cc_final: 0.8101 (ptm-80)
REVERT: R   78 MET cc_start: 0.7609 (mtp) cc_final: 0.7352 (ttt)
REVERT: R   79 LYS cc_start: 0.8161 (tttt) cc_final: 0.7617 (mmmt)
REVERT: R  226 LYS cc_start: 0.6450 (tppt) cc_final: 0.6159 (mmtm)
REVERT: R  275 LYS cc_start: 0.7452 (tttt) cc_final: 0.7223 (tttt)
  outliers start: 25
  outliers final: 16
  residues processed: 185
  average time/residue: 0.2518
  time to fit residues: 60.7985
Evaluate side-chains
  177 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 103 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.121606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.086076 restraints weight = 17003.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 3.10
r_work: 0.3277 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8708  Z= 0.207
  Angle     :  0.583   8.452  11809  Z= 0.301
  Chirality :  0.042   0.181   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.239  21.631   1169
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.34 %
    Favored  : 79.18 %
  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   0.024   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.001   PHE B 292 
 TYR   0.019   0.001   TYR A 303 
 ARG   0.008   0.001   ARG B 197 

*********************** 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
  187 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9023 (ptp-110) cc_final: 0.8640 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9219 (tppt) cc_final: 0.8982 (tppt)
REVERT: B   63 TRP cc_start: 0.8047 (m100) cc_final: 0.7741 (m100)
REVERT: B   89 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8090 (ptpp)
REVERT: B  118 ASP cc_start: 0.8356 (m-30) cc_final: 0.8112 (m-30)
REVERT: G   20 LYS cc_start: 0.9072 (ptmt) cc_final: 0.8850 (ptpp)
REVERT: G   41 CYS cc_start: 0.7341 (t) cc_final: 0.7044 (t)
REVERT: G   47 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: R   40 ARG cc_start: 0.8553 (ptt90) cc_final: 0.8075 (ptm-80)
REVERT: R   78 MET cc_start: 0.7611 (mtp) cc_final: 0.7400 (ttt)
REVERT: R   79 LYS cc_start: 0.8172 (tttt) cc_final: 0.7626 (mmmt)
REVERT: R  226 LYS cc_start: 0.6442 (tppt) cc_final: 0.6144 (mmtm)
REVERT: R  275 LYS cc_start: 0.7543 (tttt) cc_final: 0.7311 (tttt)
  outliers start: 23
  outliers final: 15
  residues processed: 178
  average time/residue: 0.2615
  time to fit residues: 60.4997
Evaluate side-chains
  174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 MET
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  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 S residue  157 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
G  18 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 = 0.4001 r_free = 0.4001 target = 0.121722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.086223 restraints weight = 17005.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 3.09
r_work: 0.3281 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8708  Z= 0.208
  Angle     :  0.600   8.730  11809  Z= 0.309
  Chirality :  0.042   0.183   1351
  Planarity :  0.004   0.047   1486
  Dihedral  :  4.222  21.579   1169
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.09 %
    Favored  : 78.43 %
  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:  0.51 (0.27), residues: 1068
  helix:  2.33 (0.28), residues: 359
  sheet: -0.55 (0.31), residues: 266
  loop : -0.73 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.015   0.001   TYR A 303 
 ARG   0.008   0.001   ARG B 197 

*********************** 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
  188 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9014 (ptp-110) cc_final: 0.8610 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9222 (tppt) cc_final: 0.8979 (tppt)
REVERT: B   63 TRP cc_start: 0.8090 (m100) cc_final: 0.7726 (m100)
REVERT: B   89 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8107 (ptpp)
REVERT: B  118 ASP cc_start: 0.8369 (m-30) cc_final: 0.8110 (m-30)
REVERT: B  214 ARG cc_start: 0.7954 (mpp80) cc_final: 0.7706 (mpp80)
REVERT: G   18 GLN cc_start: 0.8555 (tp40) cc_final: 0.8262 (tp-100)
REVERT: G   21 MET cc_start: 0.9396 (tpp) cc_final: 0.8992 (tmm)
REVERT: G   41 CYS cc_start: 0.7362 (t) cc_final: 0.7021 (t)
REVERT: G   47 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: R   78 MET cc_start: 0.7592 (mtp) cc_final: 0.7387 (ttt)
REVERT: R   79 LYS cc_start: 0.8163 (tttt) cc_final: 0.7625 (mmmt)
REVERT: R   92 GLN cc_start: 0.8164 (tp40) cc_final: 0.7391 (tp-100)
REVERT: R  226 LYS cc_start: 0.6420 (tppt) cc_final: 0.6134 (mmtm)
REVERT: R  275 LYS cc_start: 0.7536 (tttt) cc_final: 0.7287 (tttt)
REVERT: S   47 TRP cc_start: 0.8113 (t60) cc_final: 0.7904 (t60)
REVERT: S  219 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8478 (pp30)
  outliers start: 23
  outliers final: 17
  residues processed: 180
  average time/residue: 0.2561
  time to fit residues: 60.4766
Evaluate side-chains
  180 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  255 CYS
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  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    9 ILE
Chi-restraints excluded: chain G residue   28 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 S residue  157 ASN
Chi-restraints excluded: chain S residue  219 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 40 optimal weight:    0.0970
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 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 = 0.4022 r_free = 0.4022 target = 0.122970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.087192 restraints weight = 17178.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 3.17
r_work: 0.3295 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8708  Z= 0.189
  Angle     :  0.611   8.405  11809  Z= 0.310
  Chirality :  0.042   0.205   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.208  25.501   1169
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.85 %
    Favored  : 78.21 %
  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:  0.52 (0.27), residues: 1068
  helix:  2.26 (0.27), residues: 360
  sheet: -0.50 (0.32), residues: 259
  loop : -0.68 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.005   0.001   HIS S 220 
 PHE   0.021   0.001   PHE B 292 
 TYR   0.023   0.001   TYR A 303 
 ARG   0.009   0.000   ARG B 197 

*********************** 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
  183 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9043 (ptp-110) cc_final: 0.8674 (ptp-110)
REVERT: A  323 MET cc_start: 0.8693 (tpp) cc_final: 0.8444 (tpp)
REVERT: B   23 LYS cc_start: 0.9206 (tppt) cc_final: 0.8959 (tppt)
REVERT: B   63 TRP cc_start: 0.8078 (m100) cc_final: 0.7690 (m100)
REVERT: B   89 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8110 (ptpp)
REVERT: B  118 ASP cc_start: 0.8336 (m-30) cc_final: 0.8059 (m-30)
REVERT: B  214 ARG cc_start: 0.7975 (mpp80) cc_final: 0.7740 (mpp80)
REVERT: G   20 LYS cc_start: 0.9020 (ptpt) cc_final: 0.8701 (pttm)
REVERT: G   41 CYS cc_start: 0.7250 (t) cc_final: 0.6946 (t)
REVERT: G   47 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: R   78 MET cc_start: 0.7534 (mtp) cc_final: 0.7332 (ttt)
REVERT: R   79 LYS cc_start: 0.8146 (tttt) cc_final: 0.7607 (mmmt)
REVERT: R   92 GLN cc_start: 0.8156 (tp40) cc_final: 0.7430 (tp-100)
REVERT: R  226 LYS cc_start: 0.6338 (tppt) cc_final: 0.6064 (mmtm)
REVERT: R  275 LYS cc_start: 0.7446 (tttt) cc_final: 0.7154 (tttt)
REVERT: R  332 PHE cc_start: 0.4617 (t80) cc_final: 0.4415 (t80)
  outliers start: 18
  outliers final: 16
  residues processed: 176
  average time/residue: 0.2572
  time to fit residues: 59.0794
Evaluate side-chains
  180 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 163
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  324 THR
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  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   80 HIS
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.2388

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.121132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.085423 restraints weight = 17227.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 3.16
r_work: 0.3262 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8708  Z= 0.257
  Angle     :  0.650   9.126  11809  Z= 0.330
  Chirality :  0.043   0.266   1351
  Planarity :  0.004   0.050   1486
  Dihedral  :  4.374  26.290   1169
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.71 %
    Favored  : 77.02 %
  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:  0.42 (0.27), residues: 1068
  helix:  2.27 (0.27), residues: 359
  sheet: -0.63 (0.30), residues: 287
  loop : -0.76 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP S  47 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.018   0.001   PHE S  68 
 TYR   0.018   0.001   TYR A 303 
 ARG   0.010   0.001   ARG B 197 

*********************** 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
  180 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.986 
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: 0.8735 (ptp-110)
REVERT: A  323 MET cc_start: 0.8734 (tpp) cc_final: 0.8465 (tpp)
REVERT: B   23 LYS cc_start: 0.9219 (tppt) cc_final: 0.8972 (tppt)
REVERT: B   63 TRP cc_start: 0.8087 (m100) cc_final: 0.7727 (m100)
REVERT: B   89 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8114 (ptpp)
REVERT: B  118 ASP cc_start: 0.8387 (m-30) cc_final: 0.8107 (m-30)
REVERT: B  214 ARG cc_start: 0.7989 (mpp80) cc_final: 0.7746 (mpp80)
REVERT: G   20 LYS cc_start: 0.9036 (ptpt) cc_final: 0.8692 (pttm)
REVERT: G   41 CYS cc_start: 0.7347 (t) cc_final: 0.7000 (t)
REVERT: G   47 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: R   78 MET cc_start: 0.7543 (mtp) cc_final: 0.7316 (ttt)
REVERT: R   79 LYS cc_start: 0.8167 (tttt) cc_final: 0.7629 (mmmt)
REVERT: R  226 LYS cc_start: 0.6343 (tppt) cc_final: 0.6071 (mmtm)
REVERT: R  275 LYS cc_start: 0.7460 (tttt) cc_final: 0.7168 (tttt)
REVERT: S  219 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8517 (pp30)
  outliers start: 21
  outliers final: 16
  residues processed: 170
  average time/residue: 0.2644
  time to fit residues: 58.1617
Evaluate side-chains
  176 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  324 THR
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  213 VAL
Chi-restraints excluded: chain G residue   28 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
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 4 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 66 optimal weight:    8.9990
   chunk 83 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   chunk 103 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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**
G  18 GLN
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.120811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.085219 restraints weight = 17233.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 3.15
r_work: 0.3258 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8708  Z= 0.274
  Angle     :  0.676  13.277  11809  Z= 0.340
  Chirality :  0.044   0.247   1351
  Planarity :  0.004   0.055   1486
  Dihedral  :  4.439  27.076   1169
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.25 %
    Favored  : 76.59 %
  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:  0.35 (0.27), residues: 1068
  helix:  2.22 (0.27), residues: 359
  sheet: -0.67 (0.30), residues: 287
  loop : -0.80 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.029   0.002   PHE S  68 
 TYR   0.017   0.001   TYR A 303 
 ARG   0.011   0.001   ARG B 197 

********************** 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
  179 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9099 (ptp-110) cc_final: 0.8706 (ptp-110)
REVERT: A  323 MET cc_start: 0.8747 (tpp) cc_final: 0.8476 (tpp)
REVERT: B   23 LYS cc_start: 0.9224 (tppt) cc_final: 0.8977 (tppt)
REVERT: B   63 TRP cc_start: 0.8100 (m100) cc_final: 0.7746 (m100)
REVERT: B   89 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8135 (ptpp)
REVERT: B  118 ASP cc_start: 0.8366 (m-30) cc_final: 0.8079 (m-30)
REVERT: B  214 ARG cc_start: 0.7974 (mpp80) cc_final: 0.7746 (mpp80)
REVERT: G   20 LYS cc_start: 0.9046 (ptpt) cc_final: 0.8700 (pttm)
REVERT: G   41 CYS cc_start: 0.7343 (t) cc_final: 0.7019 (t)
REVERT: G   47 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8219 (tm-30)
REVERT: R   78 MET cc_start: 0.7571 (mtp) cc_final: 0.7338 (ttt)
REVERT: R   79 LYS cc_start: 0.8176 (tttt) cc_final: 0.7637 (mmmt)
REVERT: R  226 LYS cc_start: 0.6439 (tppt) cc_final: 0.6160 (mmtm)
REVERT: R  275 LYS cc_start: 0.7503 (tttt) cc_final: 0.7196 (tttt)
REVERT: S  219 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8445 (pp30)
  outliers start: 20
  outliers final: 17
  residues processed: 170
  average time/residue: 0.2754
  time to fit residues: 60.1121
Evaluate side-chains
  176 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  249 MET
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   28 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   68 PHE
Chi-restraints excluded: chain S residue   76 LYS
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:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 17 optimal weight:    0.0980
   chunk 104 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** R 119 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 = 0.3997 r_free = 0.3997 target = 0.121188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.085483 restraints weight = 17287.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.17
r_work: 0.3263 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8708  Z= 0.253
  Angle     :  0.671   9.339  11809  Z= 0.340
  Chirality :  0.043   0.266   1351
  Planarity :  0.004   0.054   1486
  Dihedral  :  4.433  26.607   1169
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.04 %
    Favored  : 76.70 %
  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:  0.37 (0.27), residues: 1068
  helix:  2.22 (0.27), residues: 359
  sheet: -0.65 (0.30), residues: 287
  loop : -0.80 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP S  47 
 HIS   0.004   0.001   HIS S 220 
 PHE   0.027   0.001   PHE S  68 
 TYR   0.017   0.001   TYR A 303 
 ARG   0.011   0.001   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5786.06 seconds
wall clock time: 103 minutes 9.97 seconds (6189.97 seconds total)