Starting phenix.real_space_refine
on Wed Feb 12 02:12:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvv_32859/02_2025/7wvv_32859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvv_32859/02_2025/7wvv_32859.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvv_32859/02_2025/7wvv_32859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvv_32859/02_2025/7wvv_32859.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvv_32859/02_2025/7wvv_32859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvv_32859/02_2025/7wvv_32859.cif"
  }
  resolution = 2.9
  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=   0.005
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      53      5.16       5
     C    4528      2.51       5
     N    1184      2.21       5
     O    1255      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 7020
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 46
          Classifications: {'peptide': 5}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2319
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 1778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1778
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2510
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 367
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 4.73, per 1000 atoms: 0.67
  Number of scatterers: 7020
  At special positions: 0
  Unit cell: (112.86, 119.13, 85.69, 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      53     16.00
     O    1255      8.00
     N    1184      7.00
     C    4528      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 912.2 milliseconds
  

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      47.7% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 55
      Proline residue:  R  29  - end of helix
      removed outlier: 3.954A  pdb=" N   PHE R  53 " --> pdb=" O   TRP R  49 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   MET R  55 " --> pdb=" O   ALA R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 77
      removed outlier: 3.769A  pdb=" N   THR R  77 " --> pdb=" O   SER R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 86
      removed outlier: 3.699A  pdb=" N   LEU R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
      removed outlier: 3.649A  pdb=" N   ARG R 137 " --> pdb=" O   ALA R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 163
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 180 through 185
    Processing helix  chain 'R' and resid 186 through 210
    Processing helix  chain 'R' and resid 210 through 231
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 274
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 3.741A  pdb=" N   ILE R 282 " --> pdb=" O   LYS R 278 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 316
    Processing helix  chain 'A' and resid 7 through 32
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.710A  pdb=" N   LYS A  51 " --> pdb=" O   ASN A  47 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 217
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 4.048A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.981A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   HIS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
      removed outlier: 3.609A  pdb=" N   LEU A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.629A  pdb=" N   VAL A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 3.570A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 13 through 24
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.575A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192
      removed outlier: 8.887A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.522A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.805A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.420A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.474A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.505A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.996A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.165A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1119 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2230
        1.34 -     1.46: 1716
        1.46 -     1.58: 3146
        1.58 -     1.70: 0
        1.70 -     1.82: 77
  Bond restraints: 7169
  Sorted by residual:
  bond pdb=" SD  FME L   1 "
       pdb=" CE  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.752  0.053 2.00e-02 2.50e+03 7.03e+00
  bond pdb=" CG  FME L   1 "
       pdb=" SD  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.771  0.046 2.00e-02 2.50e+03 5.40e+00
  bond pdb=" N   FME L   1 "
       pdb=" CN  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.376 -0.041 2.00e-02 2.50e+03 4.27e+00
  bond pdb=" N   FME L   1 "
       pdb=" CA  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.436  0.022 1.90e-02 2.77e+03 1.36e+00
  bond pdb=" CN  FME L   1 "
       pdb=" O1  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.221  1.241 -0.020 2.00e-02 2.50e+03 9.64e-01
  ... (remaining 7164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 9436
        1.07 -     2.14: 223
        2.14 -     3.22: 47
        3.22 -     4.29: 11
        4.29 -     5.36: 9
  Bond angle restraints: 9726
  Sorted by residual:
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     113.72  110.98    2.74 1.30e+00 5.92e-01 4.44e+00
  angle pdb=" CB  MET R 197 "
        pdb=" CG  MET R 197 "
        pdb=" SD  MET R 197 "
      ideal   model   delta    sigma   weight residual
     112.70  118.06   -5.36 3.00e+00 1.11e-01 3.19e+00
  angle pdb=" NE  ARG B  49 "
        pdb=" CZ  ARG B  49 "
        pdb=" NH1 ARG B  49 "
      ideal   model   delta    sigma   weight residual
     121.50  119.72    1.78 1.00e+00 1.00e+00 3.18e+00
  angle pdb=" C   ASP A 329 "
        pdb=" N   THR A 330 "
        pdb=" CA  THR A 330 "
      ideal   model   delta    sigma   weight residual
     121.54  124.88   -3.34 1.91e+00 2.74e-01 3.05e+00
  angle pdb=" N   GLY R 232 "
        pdb=" CA  GLY R 232 "
        pdb=" C   GLY R 232 "
      ideal   model   delta    sigma   weight residual
     113.18  117.16   -3.98 2.37e+00 1.78e-01 2.81e+00
  ... (remaining 9721 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 3867
       17.35 -    34.71: 300
       34.71 -    52.06: 44
       52.06 -    69.42: 5
       69.42 -    86.77: 3
  Dihedral angle restraints: 4219
    sinusoidal: 1585
      harmonic: 2634
  Sorted by residual:
  dihedral pdb=" CA  ASP B 254 "
           pdb=" CB  ASP B 254 "
           pdb=" CG  ASP B 254 "
           pdb=" OD1 ASP B 254 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.95   59.95     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CB  GLU B 138 "
           pdb=" CG  GLU B 138 "
           pdb=" CD  GLU B 138 "
           pdb=" OE1 GLU B 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.77  -86.77     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CG  ARG B  48 "
           pdb=" CD  ARG B  48 "
           pdb=" NE  ARG B  48 "
           pdb=" CZ  ARG B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.11  -42.89     2      1.50e+01 4.44e-03 9.88e+00
  ... (remaining 4216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 711
       0.028 -    0.055: 261
       0.055 -    0.083: 94
       0.083 -    0.110: 59
       0.110 -    0.138: 15
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 1137 not shown)

  Planarity restraints: 1212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 148 "    0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO R 149 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO R 149 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 149 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.025 5.00e-02 4.00e+02   3.71e-02 2.21e+00
        pdb=" N   PRO B 236 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 164 "   -0.007 2.00e-02 2.50e+03   1.40e-02 1.97e+00
        pdb=" C   THR B 164 "    0.024 2.00e-02 2.50e+03
        pdb=" O   THR B 164 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   THR B 165 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1209 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1840
        2.81 -     3.33: 6808
        3.33 -     3.85: 11965
        3.85 -     4.38: 13859
        4.38 -     4.90: 24483
  Nonbonded interactions: 58955
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   PRO R 286 "
            pdb=" OG  SER R 289 "
     model   vdw
     2.328 3.040
  ... (remaining 58950 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:             1.040
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.710
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
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      :  0.002   0.053   7169  Z= 0.125
  Angle     :  0.446   5.362   9726  Z= 0.246
  Chirality :  0.039   0.138   1140
  Planarity :  0.003   0.038   1212
  Dihedral  : 12.210  86.772   2508
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.28), residues: 898
  helix:  1.85 (0.26), residues: 394
  sheet:  0.37 (0.40), residues: 183
  loop : -1.18 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 169 
 HIS   0.003   0.000   HIS B  91 
 PHE   0.019   0.001   PHE R 257 
 TYR   0.007   0.001   TYR A 231 
 ARG   0.006   0.000   ARG B  49 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.785 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.9911
  time to fit residues: 133.3728
Evaluate side-chains
  100 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0970
   chunk 52 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 295 ASN
A 347 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.175493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.138639 restraints weight = 7038.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.78
r_work: 0.3495 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7169  Z= 0.177
  Angle     :  0.508   7.154   9726  Z= 0.271
  Chirality :  0.041   0.131   1140
  Planarity :  0.004   0.041   1212
  Dihedral  :  3.707  22.177    967
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.99 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.28), residues: 898
  helix:  1.65 (0.25), residues: 405
  sheet:  0.23 (0.38), residues: 183
  loop : -1.30 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE R 163 
 TYR   0.007   0.001   TYR B 289 
 ARG   0.006   0.000   ARG R  26 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.773 
Fit side-chains
REVERT: R  214 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7797 (tpt)
  outliers start: 12
  outliers final: 4
  residues processed: 121
  average time/residue: 0.9966
  time to fit residues: 128.6998
Evaluate side-chains
  111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 230 ASN
C  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.161091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.121330 restraints weight = 7113.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.83
r_work: 0.3277 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7169  Z= 0.321
  Angle     :  0.585   7.146   9726  Z= 0.313
  Chirality :  0.043   0.145   1140
  Planarity :  0.004   0.040   1212
  Dihedral  :  4.268  22.916    967
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.02 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.28), residues: 898
  helix:  1.40 (0.25), residues: 407
  sheet: -0.17 (0.37), residues: 190
  loop : -1.27 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.016   0.002   PHE A 197 
 TYR   0.015   0.002   TYR B  59 
 ARG   0.007   0.001   ARG R  26 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.737 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7424 (m)
REVERT: R  214 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7933 (tpt)
  outliers start: 27
  outliers final: 13
  residues processed: 124
  average time/residue: 1.0463
  time to fit residues: 138.4328
Evaluate side-chains
  115 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   35 VAL
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   93 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0000
   chunk 48 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 84 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.164829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.124322 restraints weight = 7068.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.93
r_work: 0.3414 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7169  Z= 0.183
  Angle     :  0.507   8.265   9726  Z= 0.269
  Chirality :  0.041   0.143   1140
  Planarity :  0.004   0.039   1212
  Dihedral  :  4.071  26.604    967
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.52 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.28), residues: 898
  helix:  1.48 (0.25), residues: 410
  sheet: -0.16 (0.37), residues: 190
  loop : -1.34 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.002   0.000   HIS B  54 
 PHE   0.011   0.001   PHE A 197 
 TYR   0.008   0.001   TYR B 264 
 ARG   0.005   0.000   ARG B 219 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.742 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7314 (m)
REVERT: R  214 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7878 (tpt)
  outliers start: 22
  outliers final: 9
  residues processed: 119
  average time/residue: 1.0251
  time to fit residues: 129.8949
Evaluate side-chains
  109 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain C residue   38 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.163190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.122619 restraints weight = 7010.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.91
r_work: 0.3292 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7169  Z= 0.218
  Angle     :  0.518   8.784   9726  Z= 0.273
  Chirality :  0.041   0.138   1140
  Planarity :  0.004   0.041   1212
  Dihedral  :  4.092  26.489    967
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.33 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.28), residues: 898
  helix:  1.55 (0.25), residues: 409
  sheet: -0.29 (0.36), residues: 194
  loop : -1.31 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.002   0.001   HIS C  44 
 PHE   0.011   0.001   PHE A 197 
 TYR   0.008   0.001   TYR R 221 
 ARG   0.006   0.000   ARG B 219 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.780 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.7320 (m)
REVERT: R  214 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7838 (tpt)
  outliers start: 25
  outliers final: 13
  residues processed: 117
  average time/residue: 0.9826
  time to fit residues: 122.8007
Evaluate side-chains
  111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   38 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 45 optimal weight:    0.1980
   chunk 1 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
R 294 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.165208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.124730 restraints weight = 7073.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.93
r_work: 0.3323 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7169  Z= 0.170
  Angle     :  0.494   9.346   9726  Z= 0.261
  Chirality :  0.040   0.139   1140
  Planarity :  0.004   0.041   1212
  Dihedral  :  4.012  27.176    967
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.00 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.28), residues: 898
  helix:  1.66 (0.26), residues: 410
  sheet: -0.22 (0.36), residues: 192
  loop : -1.33 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.000   HIS B  54 
 PHE   0.010   0.001   PHE A 197 
 TYR   0.006   0.001   TYR R 221 
 ARG   0.007   0.000   ARG B 219 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.762 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7254 (m)
REVERT: R  214 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7690 (tpt)
REVERT: A   17 LYS cc_start: 0.7147 (tppt) cc_final: 0.6896 (mptp)
REVERT: A  290 GLU cc_start: 0.7971 (pm20) cc_final: 0.7488 (pm20)
  outliers start: 24
  outliers final: 12
  residues processed: 122
  average time/residue: 1.0584
  time to fit residues: 137.2981
Evaluate side-chains
  108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   38 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 78 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.163799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.125009 restraints weight = 7072.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 1.81
r_work: 0.3324 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7169  Z= 0.205
  Angle     :  0.514   9.979   9726  Z= 0.271
  Chirality :  0.040   0.140   1140
  Planarity :  0.004   0.042   1212
  Dihedral  :  4.060  26.946    967
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.22 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.28), residues: 898
  helix:  1.67 (0.25), residues: 409
  sheet: -0.32 (0.36), residues: 194
  loop : -1.35 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  91 
 HIS   0.002   0.001   HIS A 189 
 PHE   0.011   0.001   PHE A 197 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.007   0.000   ARG B 219 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.819 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7315 (m)
REVERT: R  214 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7778 (tpt)
REVERT: A   17 LYS cc_start: 0.7181 (tppt) cc_final: 0.6948 (mptp)
REVERT: A   21 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7358 (tmmm)
REVERT: A  241 MET cc_start: 0.7414 (tpt) cc_final: 0.6783 (tpt)
REVERT: B  219 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7479 (tpp-160)
  outliers start: 22
  outliers final: 12
  residues processed: 115
  average time/residue: 1.0482
  time to fit residues: 128.3040
Evaluate side-chains
  109 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain C residue   38 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0170
   chunk 0 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
R 294 ASN
A 257 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.162378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.123463 restraints weight = 7066.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.81
r_work: 0.3308 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7169  Z= 0.219
  Angle     :  0.521  10.339   9726  Z= 0.276
  Chirality :  0.041   0.138   1140
  Planarity :  0.004   0.043   1212
  Dihedral  :  4.107  27.393    967
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.35 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.28), residues: 898
  helix:  1.66 (0.25), residues: 409
  sheet: -0.32 (0.36), residues: 189
  loop : -1.40 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A 189 
 PHE   0.013   0.001   PHE A 197 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.007   0.000   ARG B 219 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.739 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7336 (m)
REVERT: R  214 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7763 (tpt)
REVERT: A   17 LYS cc_start: 0.7187 (tppt) cc_final: 0.6951 (mptp)
REVERT: A   21 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7393 (tmmm)
REVERT: A  290 GLU cc_start: 0.7947 (pm20) cc_final: 0.7486 (pm20)
REVERT: B   78 LYS cc_start: 0.8562 (mptm) cc_final: 0.8352 (mptt)
REVERT: B  219 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7509 (tpp-160)
  outliers start: 26
  outliers final: 13
  residues processed: 121
  average time/residue: 1.0780
  time to fit residues: 138.7528
Evaluate side-chains
  112 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  315 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0470
   chunk 61 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.162325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.123476 restraints weight = 7178.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.82
r_work: 0.3302 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7169  Z= 0.218
  Angle     :  0.534  11.138   9726  Z= 0.282
  Chirality :  0.041   0.143   1140
  Planarity :  0.004   0.043   1212
  Dihedral  :  4.129  28.058    967
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.02 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.28), residues: 898
  helix:  1.63 (0.25), residues: 410
  sheet: -0.30 (0.37), residues: 189
  loop : -1.41 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  91 
 HIS   0.002   0.001   HIS C  44 
 PHE   0.012   0.001   PHE A 197 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 219 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.781 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7368 (m)
REVERT: R  214 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7867 (tpt)
REVERT: A   17 LYS cc_start: 0.7208 (tppt) cc_final: 0.6975 (mptp)
REVERT: A   21 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7402 (tmmm)
REVERT: B  219 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7511 (tpp-160)
REVERT: B  234 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7848 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 115
  average time/residue: 1.0691
  time to fit residues: 130.8687
Evaluate side-chains
  113 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 42 optimal weight:    0.3980
   chunk 88 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.162842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.123802 restraints weight = 7185.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.84
r_work: 0.3315 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7169  Z= 0.206
  Angle     :  0.532  10.856   9726  Z= 0.282
  Chirality :  0.041   0.144   1140
  Planarity :  0.004   0.043   1212
  Dihedral  :  4.144  27.987    967
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 21.43 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.28), residues: 898
  helix:  1.66 (0.25), residues: 410
  sheet: -0.29 (0.36), residues: 194
  loop : -1.42 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  91 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.012   0.001   PHE A 197 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 219 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.843 
Fit side-chains
REVERT: R  147 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7316 (m)
REVERT: R  214 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (tpt)
REVERT: A   17 LYS cc_start: 0.7210 (tppt) cc_final: 0.6985 (mptp)
REVERT: A   21 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7400 (tmmm)
REVERT: B   96 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7560 (ptp-170)
REVERT: B  219 ARG cc_start: 0.7906 (tpp80) cc_final: 0.7539 (tpp-160)
REVERT: B  234 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.7830 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 111
  average time/residue: 1.0642
  time to fit residues: 125.7909
Evaluate side-chains
  118 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  138 THR
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 87 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0370
   overall best weight:    0.7838

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.161710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.122684 restraints weight = 7117.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.82
r_work: 0.3299 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7169  Z= 0.226
  Angle     :  0.544  10.794   9726  Z= 0.288
  Chirality :  0.041   0.140   1140
  Planarity :  0.004   0.043   1212
  Dihedral  :  4.191  27.610    967
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.16 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.28), residues: 898
  helix:  1.62 (0.25), residues: 411
  sheet: -0.28 (0.36), residues: 194
  loop : -1.45 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  91 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.012   0.001   PHE A 197 
 TYR   0.022   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5618.20 seconds
wall clock time: 99 minutes 53.06 seconds (5993.06 seconds total)