Starting phenix.real_space_refine
on Fri Nov 15 01:43:54 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gyo_51700/11_2024/9gyo_51700.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gyo_51700/11_2024/9gyo_51700.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gyo_51700/11_2024/9gyo_51700.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gyo_51700/11_2024/9gyo_51700.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gyo_51700/11_2024/9gyo_51700.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gyo_51700/11_2024/9gyo_51700.cif"
  }
  resolution = 2.5
  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=   0.002
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      47      5.16       5
     C    5146      2.51       5
     N    1414      2.21       5
     O    1480      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8087
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1899
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2057
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 251}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "R"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Unusual residues: {'CLR': 3, 'FWX': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.52, per 1000 atoms: 0.68
  Number of scatterers: 8087
  At special positions: 0
  Unit cell: (73.831, 97.223, 130.849, 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      47     16.00
     O    1480      8.00
     N    1414      7.00
     C    5146      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.43
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.15
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 155 " 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: 2.10
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      42.7% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.788A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.585A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 218
      removed outlier: 3.674A  pdb=" N   ASN A 218 " --> pdb=" O   GLN A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 258
    Processing helix  chain 'A' and resid 272 through 283
      removed outlier: 3.536A  pdb=" N   LEU A 276 " --> pdb=" O   LYS A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 297
      removed outlier: 3.632A  pdb=" N   ALA A 295 " --> pdb=" O   PRO A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 331
      removed outlier: 3.623A  pdb=" N   PHE A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE A 327 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   SER A 331 " --> pdb=" O   ILE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 370
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.759A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.598A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.868A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 21 through 42
      removed outlier: 3.532A  pdb=" N   LEU R  27 " --> pdb=" O   ALA R  23 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ASP R  42 " --> pdb=" O   GLY R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 68
    Processing helix  chain 'R' and resid 70 through 75
      removed outlier: 3.921A  pdb=" N   TRP R  75 " --> pdb=" O   LEU R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 116
      Proline residue:  R  92  - end of helix
      removed outlier: 3.543A  pdb=" N   ARG R 116 " --> pdb=" O   MET R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 140
      Proline residue:  R 135  - end of helix
    Processing helix  chain 'R' and resid 141 through 144
    Processing helix  chain 'R' and resid 156 through 161
      removed outlier: 3.533A  pdb=" N   ILE R 160 " --> pdb=" O   SER R 156 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 162 through 173
    Processing helix  chain 'R' and resid 173 through 207
      removed outlier: 4.132A  pdb=" N   VAL R 206 " --> pdb=" O   LEU R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 235
    Processing helix  chain 'R' and resid 236 through 252
      removed outlier: 3.522A  pdb=" N   TYR R 240 " --> pdb=" O   CYS R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 275
    Processing helix  chain 'R' and resid 275 through 284
    Processing helix  chain 'R' and resid 284 through 289
    Processing helix  chain 'R' and resid 290 through 292
      No H-bonds generated for 'chain 'R' and resid 290 through 292'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192
      removed outlier: 3.538A  pdb=" N   PHE A 191 " --> pdb=" O   PHE A 198 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ILE A 224 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   VAL A 226 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   ALA A 228 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ILE A 223 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   PHE A 269 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE A 225 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ASN A 271 " --> pdb=" O   PHE A 225 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   VAL A 227 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 3.689A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.544A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.834A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.178A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.026A  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: 6.892A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.596A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.131A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.754A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    421 hydrogen bonds defined for protein.
    1194 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: 2.52

  Time building geometry restraints manager: 2.37 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: 2035
        1.34 -     1.46: 2473
        1.46 -     1.58: 3692
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 8265
  Sorted by residual:
  bond pdb=" C   SER R  47 "
       pdb=" N   PRO R  48 "
    ideal  model  delta    sigma   weight residual
    1.331  1.360 -0.028 8.70e-03 1.32e+04 1.06e+01
  bond pdb=" CE1 HIS B  62 "
       pdb=" NE2 HIS B  62 "
    ideal  model  delta    sigma   weight residual
    1.321  1.295  0.026 1.00e-02 1.00e+04 6.58e+00
  bond pdb=" CA  PRO R  48 "
       pdb=" C   PRO R  48 "
    ideal  model  delta    sigma   weight residual
    1.514  1.528 -0.014 5.50e-03 3.31e+04 6.19e+00
  bond pdb=" C   ARG R 254 "
       pdb=" N   PRO R 255 "
    ideal  model  delta    sigma   weight residual
    1.329  1.356 -0.027 1.18e-02 7.18e+03 5.25e+00
  bond pdb=" CA  SER B 161 "
       pdb=" CB  SER B 161 "
    ideal  model  delta    sigma   weight residual
    1.534  1.495  0.039 1.77e-02 3.19e+03 4.95e+00
  ... (remaining 8260 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 9738
        1.75 -     3.49: 1370
        3.49 -     5.24: 119
        5.24 -     6.98: 8
        6.98 -     8.73: 3
  Bond angle restraints: 11238
  Sorted by residual:
  angle pdb=" NE  ARG A 326 "
        pdb=" CZ  ARG A 326 "
        pdb=" NH2 ARG A 326 "
      ideal   model   delta    sigma   weight residual
     119.20  114.90    4.30 9.00e-01 1.23e+00 2.29e+01
  angle pdb=" CA  ASP B 323 "
        pdb=" CB  ASP B 323 "
        pdb=" CG  ASP B 323 "
      ideal   model   delta    sigma   weight residual
     112.60  116.96   -4.36 1.00e+00 1.00e+00 1.90e+01
  angle pdb=" CA  ASP G  48 "
        pdb=" CB  ASP G  48 "
        pdb=" CG  ASP G  48 "
      ideal   model   delta    sigma   weight residual
     112.60  116.90   -4.30 1.00e+00 1.00e+00 1.85e+01
  angle pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
        pdb=" CB  THR B 196 "
      ideal   model   delta    sigma   weight residual
     114.17  109.48    4.69 1.14e+00 7.69e-01 1.69e+01
  angle pdb=" CA  THR N 111 "
        pdb=" CB  THR N 111 "
        pdb=" OG1 THR N 111 "
      ideal   model   delta    sigma   weight residual
     109.60  103.51    6.09 1.50e+00 4.44e-01 1.65e+01
  ... (remaining 11233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.99: 4459
       14.99 -    29.97: 432
       29.97 -    44.96: 117
       44.96 -    59.95: 27
       59.95 -    74.94: 34
  Dihedral angle restraints: 5069
    sinusoidal: 2101
      harmonic: 2968
  Sorted by residual:
  dihedral pdb=" CD  ARG A 326 "
           pdb=" NE  ARG A 326 "
           pdb=" CZ  ARG A 326 "
           pdb=" NH1 ARG A 326 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   72.49  -72.49     1      1.00e+01 1.00e-02 6.71e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.28   23.72     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  THR B 249 "
           pdb=" C   THR B 249 "
           pdb=" N   CYS B 250 "
           pdb=" CA  CYS B 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.88   19.12     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5066 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 729
       0.043 -    0.086: 339
       0.086 -    0.129: 166
       0.129 -    0.173: 31
       0.173 -    0.216: 4
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  PRO R 142 "
            pdb=" N   PRO R 142 "
            pdb=" C   PRO R 142 "
            pdb=" CB  PRO R 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CA  PRO N  88 "
            pdb=" N   PRO N  88 "
            pdb=" C   PRO N  88 "
            pdb=" CB  PRO N  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.19 2.00e-01 2.50e+01 9.40e-01
  ... (remaining 1266 not shown)

  Planarity restraints: 1425
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 326 "   -0.972 9.50e-02 1.11e+02   4.36e-01 1.24e+02
        pdb=" NE  ARG A 326 "    0.077 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 326 "   -0.040 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 326 "    0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 326 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 FWX R 401 "    0.056 2.00e-02 2.50e+03   5.02e-02 3.78e+01
        pdb=" C10 FWX R 401 "   -0.064 2.00e-02 2.50e+03
        pdb=" C12 FWX R 401 "    0.013 2.00e-02 2.50e+03
        pdb=" C14 FWX R 401 "   -0.064 2.00e-02 2.50e+03
        pdb=" N09 FWX R 401 "   -0.002 2.00e-02 2.50e+03
        pdb=" O13 FWX R 401 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  99 "   -0.024 2.00e-02 2.50e+03   1.33e-02 4.42e+00
        pdb=" CG  TRP B  99 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  99 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  99 "    0.010 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  99 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  99 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  99 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  99 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1422 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 212
        2.69 -     3.24: 7301
        3.24 -     3.80: 12706
        3.80 -     4.35: 18006
        4.35 -     4.90: 29267
  Nonbonded interactions: 67492
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" O   ASP B 323 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" NH1 ARG A 207 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   LEU R  74 "
            pdb=" OH  TYR R  89 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   THR N 113 "
            pdb=" NH2 ARG N 118 "
     model   vdw
     2.416 3.120
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.435 3.040
  ... (remaining 67487 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:             1.430
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.530
  Find NCS groups from input model:        0.070
  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:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
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      :  0.007   0.039   8265  Z= 0.491
  Angle     :  1.196   8.728  11238  Z= 0.812
  Chirality :  0.059   0.216   1269
  Planarity :  0.013   0.436   1425
  Dihedral  : 14.414  74.935   3146
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.74 %
    Favored  : 92.55 %
  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: -1.22 (0.23), residues: 1014
  helix: -0.23 (0.22), residues: 395
  sheet: -0.29 (0.29), residues: 228
  loop : -1.63 (0.27), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP B  99 
 HIS   0.012   0.003   HIS B  62 
 PHE   0.014   0.003   PHE N  68 
 TYR   0.012   0.003   TYR B  85 
 ARG   0.051   0.002   ARG A 326 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 138
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8150 (mttp) cc_final: 0.7467 (tmmt)
REVERT: A  244 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7891 (tpt-90)
REVERT: A  290 TYR cc_start: 0.7444 (m-80) cc_final: 0.7228 (m-10)
REVERT: A  296 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7769 (mtm110)
REVERT: A  365 MET cc_start: 0.8343 (ttm) cc_final: 0.8136 (ttp)
REVERT: B    9 GLN cc_start: 0.7232 (mt0) cc_final: 0.6783 (tp40)
REVERT: B   23 LYS cc_start: 0.8171 (tttp) cc_final: 0.7944 (tttp)
REVERT: B   42 ARG cc_start: 0.7384 (tpt170) cc_final: 0.7052 (mmm160)
REVERT: B   96 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7840 (mtm-85)
REVERT: B  132 ASN cc_start: 0.5488 (OUTLIER) cc_final: 0.4659 (p0)
REVERT: B  135 VAL cc_start: 0.8526 (t) cc_final: 0.8177 (p)
REVERT: N    3 GLN cc_start: 0.8119 (mt0) cc_final: 0.7886 (mt0)
REVERT: R  263 LEU cc_start: 0.6526 (mm) cc_final: 0.6072 (tp)
  outliers start: 6
  outliers final: 1
  residues processed: 143
  average time/residue: 1.6761
  time to fit residues: 250.8464
Evaluate side-chains
  119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  132 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    0.4980
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 199 HIS
A 257 ASN
A 350 ASN
B  17 GLN
B 176 GLN
B 268 ASN
B 293 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8265  Z= 0.166
  Angle     :  0.558   7.493  11238  Z= 0.293
  Chirality :  0.041   0.178   1269
  Planarity :  0.004   0.032   1425
  Dihedral  :  6.069  49.001   1334
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.99 %
    Favored  : 87.47 %
  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:  0.53 (0.25), residues: 1014
  helix:  1.88 (0.25), residues: 405
  sheet:  0.04 (0.33), residues: 210
  loop : -1.07 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 213 
 HIS   0.007   0.001   HIS A 336 
 PHE   0.013   0.001   PHE N  29 
 TYR   0.014   0.001   TYR A 318 
 ARG   0.006   0.001   ARG B  19 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8068 (mttp) cc_final: 0.7395 (tmmt)
REVERT: A  244 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7511 (ttt-90)
REVERT: A  247 GLU cc_start: 0.8064 (tt0) cc_final: 0.7826 (mm-30)
REVERT: A  290 TYR cc_start: 0.7566 (m-80) cc_final: 0.7252 (m-80)
REVERT: A  296 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7802 (mtm110)
REVERT: B    9 GLN cc_start: 0.7037 (mt0) cc_final: 0.6622 (tp40)
REVERT: B   42 ARG cc_start: 0.7294 (tpt170) cc_final: 0.7019 (mmm160)
REVERT: B   59 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.7826 (t80)
REVERT: B  135 VAL cc_start: 0.8572 (t) cc_final: 0.8266 (p)
REVERT: B  215 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7660 (mt-10)
REVERT: G   47 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: N    3 GLN cc_start: 0.8092 (mt0) cc_final: 0.7794 (mt0)
REVERT: N  111 THR cc_start: 0.8588 (m) cc_final: 0.8277 (p)
REVERT: N  120 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7645 (mp10)
REVERT: R  198 ASP cc_start: 0.8164 (m-30) cc_final: 0.7868 (m-30)
REVERT: R  249 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7689 (tp)
  outliers start: 13
  outliers final: 1
  residues processed: 136
  average time/residue: 1.5738
  time to fit residues: 224.6681
Evaluate side-chains
  119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN
B  17 GLN
B 268 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 119 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8265  Z= 0.146
  Angle     :  0.510   7.412  11238  Z= 0.266
  Chirality :  0.040   0.181   1269
  Planarity :  0.004   0.039   1425
  Dihedral  :  5.930  50.728   1331
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.12 %
    Favored  : 84.99 %
  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:  1.10 (0.26), residues: 1014
  helix:  2.49 (0.25), residues: 405
  sheet:  0.18 (0.33), residues: 210
  loop : -0.82 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 213 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.012   0.001   PHE N  29 
 TYR   0.012   0.001   TYR A 318 
 ARG   0.010   0.000   ARG B  19 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8073 (mttp) cc_final: 0.7422 (tmmt)
REVERT: A  244 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7485 (ttt-90)
REVERT: A  247 GLU cc_start: 0.8111 (tt0) cc_final: 0.7874 (mm-30)
REVERT: A  290 TYR cc_start: 0.7547 (m-80) cc_final: 0.7177 (m-80)
REVERT: A  296 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7818 (mtm110)
REVERT: B    9 GLN cc_start: 0.6906 (mt0) cc_final: 0.6467 (tp40)
REVERT: B   42 ARG cc_start: 0.7286 (tpt170) cc_final: 0.7016 (mmm160)
REVERT: B   59 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8014 (t80)
REVERT: B  132 ASN cc_start: 0.5558 (OUTLIER) cc_final: 0.4794 (p0)
REVERT: B  135 VAL cc_start: 0.8574 (t) cc_final: 0.8292 (p)
REVERT: B  215 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7655 (mt-10)
REVERT: G   17 GLU cc_start: 0.7608 (tp30) cc_final: 0.7172 (mp0)
REVERT: G   47 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7362 (mt-10)
REVERT: N    3 GLN cc_start: 0.8158 (mt0) cc_final: 0.7822 (mt0)
REVERT: N  105 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7471 (ptt90)
REVERT: N  111 THR cc_start: 0.8486 (m) cc_final: 0.8169 (p)
REVERT: R  198 ASP cc_start: 0.8163 (m-30) cc_final: 0.7891 (m-30)
REVERT: R  249 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7670 (tp)
  outliers start: 16
  outliers final: 2
  residues processed: 137
  average time/residue: 1.3795
  time to fit residues: 199.0349
Evaluate side-chains
  126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0870
   chunk 86 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.0162

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 268 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 119 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8265  Z= 0.159
  Angle     :  0.519   7.506  11238  Z= 0.269
  Chirality :  0.040   0.181   1269
  Planarity :  0.004   0.042   1425
  Dihedral  :  6.048  50.891   1331
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.42 %
    Favored  : 83.22 %
  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:  1.45 (0.26), residues: 1014
  helix:  2.77 (0.25), residues: 400
  sheet:  0.36 (0.34), residues: 205
  loop : -0.55 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 213 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.013   0.001   PHE N  29 
 TYR   0.012   0.001   TYR A 318 
 ARG   0.004   0.000   ARG N 105 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8057 (mttp) cc_final: 0.7417 (tmmt)
REVERT: A  244 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7388 (ttt-90)
REVERT: A  247 GLU cc_start: 0.8096 (tt0) cc_final: 0.7881 (mm-30)
REVERT: A  296 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7760 (mtm110)
REVERT: B    9 GLN cc_start: 0.7091 (mt0) cc_final: 0.6643 (tp40)
REVERT: B   42 ARG cc_start: 0.7285 (tpt170) cc_final: 0.6603 (ttt90)
REVERT: B   59 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8037 (t80)
REVERT: B  132 ASN cc_start: 0.5549 (OUTLIER) cc_final: 0.4782 (p0)
REVERT: B  135 VAL cc_start: 0.8565 (t) cc_final: 0.8310 (p)
REVERT: G   17 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7234 (mp0)
REVERT: G   22 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8024 (mt-10)
REVERT: G   47 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7359 (mt-10)
REVERT: N    3 GLN cc_start: 0.8156 (mt0) cc_final: 0.7812 (mt0)
REVERT: N  111 THR cc_start: 0.8554 (m) cc_final: 0.8235 (p)
REVERT: N  120 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7650 (mp10)
REVERT: R  198 ASP cc_start: 0.8156 (m-30) cc_final: 0.7883 (m-30)
REVERT: R  249 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7644 (tp)
  outliers start: 20
  outliers final: 6
  residues processed: 136
  average time/residue: 1.4422
  time to fit residues: 206.9968
Evaluate side-chains
  126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 71 optimal weight:    0.3980
   chunk 39 optimal weight:   10.0000
   chunk 82 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 271 ASN
B  17 GLN
B 268 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 119 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8265  Z= 0.168
  Angle     :  0.531   7.921  11238  Z= 0.274
  Chirality :  0.041   0.181   1269
  Planarity :  0.004   0.043   1425
  Dihedral  :  6.171  54.208   1331
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.42 %
    Favored  : 82.74 %
  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:  1.60 (0.26), residues: 1014
  helix:  2.84 (0.25), residues: 400
  sheet:  0.39 (0.34), residues: 210
  loop : -0.40 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 213 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.014   0.001   PHE N  29 
 TYR   0.012   0.001   TYR A 318 
 ARG   0.005   0.000   ARG N 105 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8060 (mttp) cc_final: 0.7417 (tmmt)
REVERT: A  244 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7360 (ttt-90)
REVERT: A  247 GLU cc_start: 0.8082 (tt0) cc_final: 0.7879 (mm-30)
REVERT: A  296 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7759 (mtm110)
REVERT: B    9 GLN cc_start: 0.7146 (mt0) cc_final: 0.6671 (tp40)
REVERT: B   59 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8083 (t80)
REVERT: B  132 ASN cc_start: 0.5555 (OUTLIER) cc_final: 0.4752 (p0)
REVERT: B  135 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8351 (p)
REVERT: G   17 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7215 (mp0)
REVERT: G   22 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8066 (mt-10)
REVERT: G   47 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7343 (mt-10)
REVERT: N    3 GLN cc_start: 0.8158 (mt0) cc_final: 0.7820 (mt0)
REVERT: N  111 THR cc_start: 0.8575 (m) cc_final: 0.8243 (p)
REVERT: N  120 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7641 (mp10)
REVERT: R  147 ASN cc_start: 0.8104 (p0) cc_final: 0.7839 (p0)
REVERT: R  198 ASP cc_start: 0.8172 (m-30) cc_final: 0.7897 (m-30)
REVERT: R  249 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7632 (tp)
  outliers start: 24
  outliers final: 6
  residues processed: 135
  average time/residue: 1.4763
  time to fit residues: 209.7721
Evaluate side-chains
  131 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 96 optimal weight:    0.1980
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B  17 GLN
B 268 ASN
R 119 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8265  Z= 0.139
  Angle     :  0.501   7.332  11238  Z= 0.257
  Chirality :  0.040   0.180   1269
  Planarity :  0.004   0.044   1425
  Dihedral  :  6.040  57.122   1331
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.25 %
    Favored  : 82.86 %
  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:  1.68 (0.27), residues: 1014
  helix:  2.95 (0.25), residues: 400
  sheet:  0.45 (0.35), residues: 203
  loop : -0.41 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.012   0.001   TYR A 318 
 ARG   0.004   0.000   ARG N 105 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8095 (mttp) cc_final: 0.7449 (tmmt)
REVERT: A  244 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7354 (ttt-90)
REVERT: A  247 GLU cc_start: 0.8058 (tt0) cc_final: 0.7813 (mm-30)
REVERT: A  296 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7730 (mtm110)
REVERT: B    9 GLN cc_start: 0.7175 (mt0) cc_final: 0.6699 (tp40)
REVERT: B  135 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8365 (p)
REVERT: B  234 PHE cc_start: 0.9473 (OUTLIER) cc_final: 0.9171 (m-80)
REVERT: G   17 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7174 (mp0)
REVERT: G   22 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (mt-10)
REVERT: G   47 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7314 (mt-10)
REVERT: N    3 GLN cc_start: 0.8137 (mt0) cc_final: 0.7797 (mt0)
REVERT: N  111 THR cc_start: 0.8509 (m) cc_final: 0.8191 (p)
REVERT: N  120 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7656 (mp10)
REVERT: R  147 ASN cc_start: 0.8089 (p0) cc_final: 0.7819 (p0)
REVERT: R  198 ASP cc_start: 0.8128 (m-30) cc_final: 0.7867 (m-30)
REVERT: R  249 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7610 (tp)
  outliers start: 16
  outliers final: 3
  residues processed: 131
  average time/residue: 1.3980
  time to fit residues: 193.2034
Evaluate side-chains
  126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0270
   chunk 58 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 59 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.4220

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
R 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8265  Z= 0.188
  Angle     :  0.550   8.168  11238  Z= 0.283
  Chirality :  0.041   0.182   1269
  Planarity :  0.004   0.044   1425
  Dihedral  :  6.286  54.448   1331
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.25 %
    Favored  : 82.62 %
  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:  1.66 (0.27), residues: 1014
  helix:  2.84 (0.25), residues: 406
  sheet:  0.48 (0.35), residues: 203
  loop : -0.38 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 213 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.016   0.002   PHE N  29 
 TYR   0.011   0.001   TYR A 318 
 ARG   0.011   0.000   ARG B  19 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8094 (mttp) cc_final: 0.7434 (tmmt)
REVERT: A  244 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7349 (ttt-90)
REVERT: A  247 GLU cc_start: 0.8071 (tt0) cc_final: 0.7861 (mm-30)
REVERT: A  296 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7723 (mtm110)
REVERT: B    9 GLN cc_start: 0.7181 (mt0) cc_final: 0.6304 (mm-40)
REVERT: B   59 TYR cc_start: 0.9275 (OUTLIER) cc_final: 0.8149 (t80)
REVERT: B  132 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.4776 (p0)
REVERT: B  135 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8354 (p)
REVERT: G   17 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7206 (mp0)
REVERT: N    3 GLN cc_start: 0.8151 (mt0) cc_final: 0.7797 (mt0)
REVERT: N  111 THR cc_start: 0.8584 (m) cc_final: 0.8262 (p)
REVERT: N  120 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7639 (mp10)
REVERT: R  124 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6829 (mt)
REVERT: R  147 ASN cc_start: 0.8173 (p0) cc_final: 0.7791 (p0)
REVERT: R  198 ASP cc_start: 0.8167 (m-30) cc_final: 0.7899 (m-30)
REVERT: R  249 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7596 (tp)
  outliers start: 18
  outliers final: 4
  residues processed: 126
  average time/residue: 1.5030
  time to fit residues: 199.6828
Evaluate side-chains
  124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0060
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.8004

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B 268 ASN
R 119 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8265  Z= 0.219
  Angle     :  0.580   8.596  11238  Z= 0.299
  Chirality :  0.042   0.181   1269
  Planarity :  0.004   0.045   1425
  Dihedral  :  6.528  58.354   1331
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.48 %
    Favored  : 82.39 %
  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:  1.67 (0.26), residues: 1014
  helix:  2.87 (0.25), residues: 400
  sheet:  0.51 (0.35), residues: 208
  loop : -0.38 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 213 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.015   0.002   PHE N  29 
 TYR   0.012   0.002   TYR A 318 
 ARG   0.013   0.000   ARG B  19 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8097 (mttp) cc_final: 0.7435 (tmmt)
REVERT: A  244 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7337 (ttt-90)
REVERT: A  247 GLU cc_start: 0.8098 (tt0) cc_final: 0.7843 (mm-30)
REVERT: A  296 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7724 (mtm110)
REVERT: B    9 GLN cc_start: 0.7327 (mt0) cc_final: 0.6407 (mm-40)
REVERT: B   59 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8167 (t80)
REVERT: B  132 ASN cc_start: 0.5752 (OUTLIER) cc_final: 0.4717 (p0)
REVERT: B  135 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8400 (p)
REVERT: G   17 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7204 (mp0)
REVERT: N    3 GLN cc_start: 0.8118 (mt0) cc_final: 0.7765 (mt0)
REVERT: N  111 THR cc_start: 0.8686 (m) cc_final: 0.8349 (p)
REVERT: N  120 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7634 (mp10)
REVERT: R  124 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6890 (mt)
REVERT: R  147 ASN cc_start: 0.8224 (p0) cc_final: 0.7786 (p0)
REVERT: R  198 ASP cc_start: 0.8147 (m-30) cc_final: 0.7880 (m-30)
REVERT: R  249 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7580 (tp)
  outliers start: 18
  outliers final: 5
  residues processed: 125
  average time/residue: 1.4952
  time to fit residues: 196.6680
Evaluate side-chains
  122 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   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 218 ASN
B  17 GLN
B 268 ASN
R 119 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8265  Z= 0.150
  Angle     :  0.517   7.720  11238  Z= 0.264
  Chirality :  0.040   0.179   1269
  Planarity :  0.004   0.044   1425
  Dihedral  :  6.153  56.954   1331
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.55 %
    Favored  : 82.15 %
  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:  1.71 (0.27), residues: 1014
  helix:  2.91 (0.26), residues: 406
  sheet:  0.56 (0.35), residues: 199
  loop : -0.40 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 213 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.013   0.001   TYR A 318 
 ARG   0.004   0.000   ARG N 105 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8094 (mttp) cc_final: 0.7450 (tmmt)
REVERT: A  244 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7316 (ttt-90)
REVERT: A  296 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7717 (mtm110)
REVERT: B    9 GLN cc_start: 0.7310 (mt0) cc_final: 0.6436 (mm-40)
REVERT: B   59 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8052 (t80)
REVERT: B  135 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8400 (p)
REVERT: B  234 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.9194 (m-80)
REVERT: G   17 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7191 (mp0)
REVERT: G   19 LEU cc_start: 0.8658 (mt) cc_final: 0.8416 (mp)
REVERT: N    3 GLN cc_start: 0.8103 (mt0) cc_final: 0.7757 (mt0)
REVERT: N  111 THR cc_start: 0.8539 (m) cc_final: 0.8229 (p)
REVERT: N  120 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7630 (mp10)
REVERT: R  124 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6778 (mt)
REVERT: R  147 ASN cc_start: 0.8153 (p0) cc_final: 0.7856 (p0)
REVERT: R  198 ASP cc_start: 0.8171 (m-30) cc_final: 0.7898 (m-30)
REVERT: R  249 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7609 (tp)
  outliers start: 11
  outliers final: 4
  residues processed: 125
  average time/residue: 1.5751
  time to fit residues: 206.7071
Evaluate side-chains
  124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 91 optimal weight:    0.1980
   chunk 79 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 268 ASN
R 119 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8265  Z= 0.236
  Angle     :  0.599   8.936  11238  Z= 0.308
  Chirality :  0.042   0.183   1269
  Planarity :  0.004   0.045   1425
  Dihedral  :  6.521  58.015   1331
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.08 %
    Favored  : 82.27 %
  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:  1.64 (0.26), residues: 1014
  helix:  2.86 (0.25), residues: 400
  sheet:  0.47 (0.35), residues: 208
  loop : -0.39 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 213 
 HIS   0.007   0.001   HIS B  62 
 PHE   0.018   0.002   PHE N  29 
 TYR   0.011   0.002   TYR A 318 
 ARG   0.005   0.000   ARG N 105 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8085 (mttp) cc_final: 0.7439 (tmmt)
REVERT: A  244 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7317 (ttt-90)
REVERT: A  296 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7725 (mtm110)
REVERT: B    9 GLN cc_start: 0.7372 (mt0) cc_final: 0.6420 (mm-40)
REVERT: B   59 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8132 (t80)
REVERT: B  135 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8398 (p)
REVERT: B  215 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7355 (mm-30)
REVERT: G   17 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7212 (mp0)
REVERT: N    3 GLN cc_start: 0.8110 (mt0) cc_final: 0.7752 (mt0)
REVERT: N  111 THR cc_start: 0.8676 (m) cc_final: 0.8338 (p)
REVERT: N  120 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7614 (mp10)
REVERT: R  124 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6848 (mt)
REVERT: R  147 ASN cc_start: 0.8245 (p0) cc_final: 0.7787 (p0)
REVERT: R  198 ASP cc_start: 0.8151 (m-30) cc_final: 0.7881 (m-30)
REVERT: R  249 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7566 (tp)
  outliers start: 14
  outliers final: 5
  residues processed: 121
  average time/residue: 1.5365
  time to fit residues: 195.1735
Evaluate side-chains
  121 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 268 ASN
R 119 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.143776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.104592 restraints weight = 8096.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.50
r_work: 0.2917 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8265  Z= 0.161
  Angle     :  0.535   7.954  11238  Z= 0.273
  Chirality :  0.040   0.177   1269
  Planarity :  0.004   0.044   1425
  Dihedral  :  6.222  58.362   1331
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 16.90 %
    Favored  : 81.91 %
  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:  1.68 (0.27), residues: 1014
  helix:  2.87 (0.25), residues: 406
  sheet:  0.52 (0.35), residues: 199
  loop : -0.40 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 213 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.012   0.001   TYR A 318 
 ARG   0.005   0.000   ARG N 105 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3956.56 seconds
wall clock time: 71 minutes 7.01 seconds (4267.01 seconds total)