Starting phenix.real_space_refine
on Wed Mar 12 18:53:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wz4_32904/03_2025/7wz4_32904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wz4_32904/03_2025/7wz4_32904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2025/7wz4_32904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2025/7wz4_32904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2025/7wz4_32904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wz4_32904/03_2025/7wz4_32904.cif"
  }
  resolution = 3.0
  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=   0.036
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      57      5.16       5
     C    5185      2.51       5
     N    1419      2.21       5
     O    1526      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8187
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1692
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 60
    Chain: "A"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1715
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2577
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 431
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 5.66, per 1000 atoms: 0.69
  Number of scatterers: 8187
  At special positions: 0
  Unit cell: (90.95, 119.85, 125.8, 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      57     16.00
     O    1526      8.00
     N    1419      7.00
     C    5185      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  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: 2.09
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1994

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 13 sheets defined
      37.2% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'R' and resid 34 through 59
      removed outlier: 3.512A  pdb=" N   TYR R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER R  39 " --> pdb=" O   SER R  35 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLY R  40 " --> pdb=" O   LEU R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 63
    Processing helix  chain 'R' and resid 64 through 88
      removed outlier: 3.819A  pdb=" N   PHE R  69 " --> pdb=" O   THR R  65 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   MET R  85 " --> pdb=" O   CYS R  81 " (cutoff:3.500A)
      Proline residue:  R  86  - end of helix
    Processing helix  chain 'R' and resid 116 through 144
      removed outlier: 3.591A  pdb=" N   CYS R 132 " --> pdb=" O   LEU R 128 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 153
    Processing helix  chain 'R' and resid 154 through 175
      removed outlier: 3.743A  pdb=" N   TRP R 166 " --> pdb=" O   LEU R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 227
      removed outlier: 4.173A  pdb=" N   LEU R 195 " --> pdb=" O   HIS R 191 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU R 196 " --> pdb=" O   TYR R 192 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA R 197 " --> pdb=" O   PRO R 193 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA R 198 " --> pdb=" O   ALA R 194 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL R 216 " --> pdb=" O   TYR R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 283 through 308
      removed outlier: 3.652A  pdb=" N   LEU R 287 " --> pdb=" O   GLY R 283 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 317 through 337
      Proline residue:  R 333  - end of helix
    Processing helix  chain 'R' and resid 340 through 351
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.647A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.374A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.831A  pdb=" N   SER A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.013A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.520A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.583A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.558A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.532A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.135A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.719A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.737A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.664A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.746A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.712A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.081A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.984A  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: 6.609A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.650A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.531A  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: 6.649A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.945A  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: 3.653A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.975A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.380A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.823A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1152 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: 2.25

  Time building geometry restraints manager: 2.46 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: 2671
        1.34 -     1.46: 1981
        1.46 -     1.58: 3611
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 8343
  Sorted by residual:
  bond pdb=" N   TRP R 179 "
       pdb=" CA  TRP R 179 "
    ideal  model  delta    sigma   weight residual
    1.455  1.481 -0.026 1.25e-02 6.40e+03 4.31e+00
  bond pdb=" CA  THR B 181 "
       pdb=" CB  THR B 181 "
    ideal  model  delta    sigma   weight residual
    1.527  1.562 -0.034 2.48e-02 1.63e+03 1.93e+00
  bond pdb=" C   TRP R 179 "
       pdb=" O   TRP R 179 "
    ideal  model  delta    sigma   weight residual
    1.234  1.244 -0.010 1.22e-02 6.72e+03 7.18e-01
  bond pdb=" CA  GLY B  41 "
       pdb=" C   GLY B  41 "
    ideal  model  delta    sigma   weight residual
    1.523  1.513  0.010 1.19e-02 7.06e+03 6.94e-01
  bond pdb=" CB  ASP G  26 "
       pdb=" CG  ASP G  26 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.61e-01
  ... (remaining 8338 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11125
        1.88 -     3.75: 166
        3.75 -     5.63: 16
        5.63 -     7.50: 2
        7.50 -     9.38: 1
  Bond angle restraints: 11310
  Sorted by residual:
  angle pdb=" N   THR R 337 "
        pdb=" CA  THR R 337 "
        pdb=" C   THR R 337 "
      ideal   model   delta    sigma   weight residual
     110.44  114.15   -3.71 1.20e+00 6.94e-01 9.57e+00
  angle pdb=" CA  TRP R 179 "
        pdb=" C   TRP R 179 "
        pdb=" O   TRP R 179 "
      ideal   model   delta    sigma   weight residual
     120.99  117.82    3.17 1.12e+00 7.97e-01 8.01e+00
  angle pdb=" CA  LEU R 152 "
        pdb=" CB  LEU R 152 "
        pdb=" CG  LEU R 152 "
      ideal   model   delta    sigma   weight residual
     116.30  125.68   -9.38 3.50e+00 8.16e-02 7.18e+00
  angle pdb=" N   ALA S  92 "
        pdb=" CA  ALA S  92 "
        pdb=" C   ALA S  92 "
      ideal   model   delta    sigma   weight residual
     107.88  111.57   -3.69 1.41e+00 5.03e-01 6.85e+00
  angle pdb=" C   GLY S 197 "
        pdb=" N   THR S 198 "
        pdb=" CA  THR S 198 "
      ideal   model   delta    sigma   weight residual
     123.05  126.89   -3.84 1.57e+00 4.06e-01 5.99e+00
  ... (remaining 11305 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 4544
       17.44 -    34.88: 331
       34.88 -    52.32: 62
       52.32 -    69.76: 8
       69.76 -    87.20: 6
  Dihedral angle restraints: 4951
    sinusoidal: 1858
      harmonic: 3093
  Sorted by residual:
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.53   21.47     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  ARG S 179 "
           pdb=" C   ARG S 179 "
           pdb=" N   MET S 180 "
           pdb=" CA  MET S 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.59   17.41     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  LEU R  83 "
           pdb=" C   LEU R  83 "
           pdb=" N   TRP R  84 "
           pdb=" CA  TRP R  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.36  -16.64     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 4948 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 822
       0.032 -    0.065: 323
       0.065 -    0.097: 98
       0.097 -    0.129: 57
       0.129 -    0.161: 5
  Chirality restraints: 1305
  Sorted by residual:
  chirality pdb=" CB  THR B 181 "
            pdb=" CA  THR B 181 "
            pdb=" OG1 THR B 181 "
            pdb=" CG2 THR B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  MET R  85 "
            pdb=" N   MET R  85 "
            pdb=" C   MET R  85 "
            pdb=" CB  MET R  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.34e-01
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.97e-01
  ... (remaining 1302 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 338 "    0.010 2.00e-02 2.50e+03   1.01e-02 2.56e+00
        pdb=" CG  TRP R 338 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 338 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 338 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 338 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 338 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 338 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 338 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 338 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 338 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "   -0.006 2.00e-02 2.50e+03   1.24e-02 1.55e+00
        pdb=" C   THR B  87 "    0.022 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "    0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO S  41 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 78
        2.66 -     3.22: 7228
        3.22 -     3.78: 11695
        3.78 -     4.34: 16121
        4.34 -     4.90: 28264
  Nonbonded interactions: 63386
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" NH2 ARG S 190 "
            pdb=" OD2 ASP S 211 "
     model   vdw
     2.282 3.120
  ... (remaining 63381 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:             2.460
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.550
  Find NCS groups from input model:        0.100
  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:13.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8343  Z= 0.222
  Angle     :  0.590   9.377  11310  Z= 0.347
  Chirality :  0.042   0.161   1305
  Planarity :  0.003   0.031   1431
  Dihedral  : 12.942  87.201   2951
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.23 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1051
  helix:  2.46 (0.28), residues: 349
  sheet:  0.58 (0.31), residues: 283
  loop : -0.68 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP R 338 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.008   0.001   TYR B 105 
 ARG   0.006   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  155 ARG cc_start: 0.4093 (mmt180) cc_final: 0.3818 (mmt180)
REVERT: R  217 ARG cc_start: 0.6608 (ttm-80) cc_final: 0.6404 (ptm160)
REVERT: R  339 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7705 (mmt-90)
REVERT: A   26 ASP cc_start: 0.7396 (m-30) cc_final: 0.7170 (m-30)
REVERT: A  308 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7592 (mt-10)
REVERT: B   19 ARG cc_start: 0.7362 (ttm170) cc_final: 0.7070 (ttm110)
REVERT: B  127 LYS cc_start: 0.8971 (mttm) cc_final: 0.8691 (mttt)
REVERT: B  134 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7489 (mtp-110)
REVERT: G   58 GLU cc_start: 0.7835 (pm20) cc_final: 0.6927 (mm-30)
REVERT: S  211 ASP cc_start: 0.8392 (m-30) cc_final: 0.8109 (m-30)
  outliers start: 1
  outliers final: 2
  residues processed: 159
  average time/residue: 1.3091
  time to fit residues: 219.6948
Evaluate side-chains
  130 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  179 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 44 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0980
   chunk 61 optimal weight:    0.0060
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
R  67 ASN
B  16 ASN
B  32 GLN
B 340 ASN
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.163741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.107188 restraints weight = 9341.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.90
r_work: 0.3152 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8343  Z= 0.149
  Angle     :  0.502   8.563  11310  Z= 0.262
  Chirality :  0.041   0.132   1305
  Planarity :  0.003   0.029   1431
  Dihedral  :  4.546  50.579   1160
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.84 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.36 (0.27), residues: 1051
  helix:  2.84 (0.28), residues: 345
  sheet:  0.60 (0.30), residues: 290
  loop : -0.56 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 338 
 HIS   0.003   0.001   HIS R 131 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.005   0.000   ARG B 251 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R   85 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.5635 (mmm)
REVERT: R  339 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7837 (mmt-90)
REVERT: A   22 ASN cc_start: 0.7061 (m-40) cc_final: 0.6721 (m110)
REVERT: A   28 GLU cc_start: 0.5774 (mt-10) cc_final: 0.5546 (tt0)
REVERT: A   51 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7530 (ttpp)
REVERT: A  309 ASP cc_start: 0.7820 (p0) cc_final: 0.7488 (p0)
REVERT: A  313 ARG cc_start: 0.7691 (ptp90) cc_final: 0.7448 (ptp90)
REVERT: B   19 ARG cc_start: 0.6859 (ttm170) cc_final: 0.6611 (ttm110)
REVERT: B  127 LYS cc_start: 0.8750 (mttm) cc_final: 0.8311 (mttt)
REVERT: B  134 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7663 (mtp-110)
REVERT: B  175 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6927 (mp10)
REVERT: G   58 GLU cc_start: 0.7711 (pm20) cc_final: 0.6890 (mm-30)
REVERT: S    3 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7626 (pt0)
  outliers start: 16
  outliers final: 6
  residues processed: 140
  average time/residue: 1.4786
  time to fit residues: 218.0294
Evaluate side-chains
  130 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.163217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.106122 restraints weight = 9466.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.97
r_work: 0.3135 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8343  Z= 0.162
  Angle     :  0.485   8.028  11310  Z= 0.254
  Chirality :  0.040   0.134   1305
  Planarity :  0.003   0.028   1431
  Dihedral  :  4.438  55.579   1160
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.11 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.50 (0.27), residues: 1051
  helix:  3.04 (0.28), residues: 345
  sheet:  0.64 (0.30), residues: 292
  loop : -0.53 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.010   0.001   TYR S 178 
 ARG   0.006   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R   85 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.6138 (mpp)
REVERT: R  344 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5686 (mtt180)
REVERT: A   22 ASN cc_start: 0.7090 (m-40) cc_final: 0.6773 (m110)
REVERT: A   28 GLU cc_start: 0.5939 (mt-10) cc_final: 0.5721 (tt0)
REVERT: A  251 ASP cc_start: 0.7481 (t0) cc_final: 0.7091 (t0)
REVERT: A  309 ASP cc_start: 0.7516 (p0) cc_final: 0.7162 (p0)
REVERT: A  313 ARG cc_start: 0.7719 (ptp90) cc_final: 0.7384 (ptp90)
REVERT: B  127 LYS cc_start: 0.8777 (mttm) cc_final: 0.8301 (mttt)
REVERT: B  134 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7709 (mtp-110)
REVERT: B  175 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7043 (mp10)
REVERT: G   58 GLU cc_start: 0.7681 (pm20) cc_final: 0.6869 (mm-30)
REVERT: S   43 LYS cc_start: 0.8606 (mptt) cc_final: 0.8389 (mmtp)
  outliers start: 25
  outliers final: 12
  residues processed: 139
  average time/residue: 1.4759
  time to fit residues: 216.4519
Evaluate side-chains
  132 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.161627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.104893 restraints weight = 9446.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.95
r_work: 0.3122 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8343  Z= 0.192
  Angle     :  0.504   7.698  11310  Z= 0.262
  Chirality :  0.041   0.133   1305
  Planarity :  0.003   0.032   1431
  Dihedral  :  4.418  49.483   1160
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 12.69 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.53 (0.27), residues: 1051
  helix:  3.06 (0.28), residues: 346
  sheet:  0.64 (0.30), residues: 291
  loop : -0.50 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.010   0.001   TYR S 178 
 ARG   0.005   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  344 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5740 (mtt180)
REVERT: A   22 ASN cc_start: 0.7148 (m-40) cc_final: 0.6824 (m110)
REVERT: A   26 ASP cc_start: 0.7078 (m-30) cc_final: 0.6818 (m-30)
REVERT: A   28 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5789 (tt0)
REVERT: A  251 ASP cc_start: 0.7527 (t0) cc_final: 0.7195 (t0)
REVERT: A  309 ASP cc_start: 0.7506 (p0) cc_final: 0.7128 (p0)
REVERT: A  313 ARG cc_start: 0.7734 (ptp90) cc_final: 0.7318 (ptp90)
REVERT: B   46 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.6606 (mtp85)
REVERT: B  127 LYS cc_start: 0.8806 (mttm) cc_final: 0.8332 (mttt)
REVERT: B  134 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7736 (mtp-110)
REVERT: B  175 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7052 (mp10)
REVERT: B  215 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7641 (mt-10)
REVERT: B  219 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7276 (mpt90)
REVERT: G   58 GLU cc_start: 0.7715 (pm20) cc_final: 0.6904 (mm-30)
REVERT: S    3 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7596 (pt0)
  outliers start: 32
  outliers final: 19
  residues processed: 143
  average time/residue: 1.6304
  time to fit residues: 244.9229
Evaluate side-chains
  142 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 104 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
S 174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.159608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.103253 restraints weight = 9382.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.88
r_work: 0.3098 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8343  Z= 0.247
  Angle     :  0.523   7.124  11310  Z= 0.276
  Chirality :  0.042   0.204   1305
  Planarity :  0.003   0.034   1431
  Dihedral  :  4.278  46.808   1157
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.42 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.42 (0.26), residues: 1051
  helix:  3.07 (0.28), residues: 345
  sheet:  0.58 (0.31), residues: 289
  loop : -0.64 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP S  47 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.012   0.001   TYR B 105 
 ARG   0.006   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 1.058 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  344 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5633 (mtt180)
REVERT: A   22 ASN cc_start: 0.7163 (m-40) cc_final: 0.6840 (m110)
REVERT: A   26 ASP cc_start: 0.6965 (m-30) cc_final: 0.6691 (m-30)
REVERT: A  251 ASP cc_start: 0.7449 (t0) cc_final: 0.7180 (t0)
REVERT: A  309 ASP cc_start: 0.7439 (p0) cc_final: 0.7056 (p0)
REVERT: A  313 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7472 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.6613 (mtp85)
REVERT: B  127 LYS cc_start: 0.8845 (mttm) cc_final: 0.8392 (mttt)
REVERT: B  134 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7638 (mtp-110)
REVERT: B  175 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7071 (mp10)
REVERT: B  219 ARG cc_start: 0.7633 (mmt180) cc_final: 0.7376 (mtt-85)
REVERT: G   21 MET cc_start: 0.6545 (ttt) cc_final: 0.6164 (mmt)
REVERT: G   58 GLU cc_start: 0.7723 (pm20) cc_final: 0.6917 (mm-30)
REVERT: S    3 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7612 (pt0)
REVERT: S  154 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8374 (tt)
REVERT: S  211 ASP cc_start: 0.8217 (m-30) cc_final: 0.7985 (m-30)
  outliers start: 30
  outliers final: 17
  residues processed: 140
  average time/residue: 1.5531
  time to fit residues: 228.9052
Evaluate side-chains
  142 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.160939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105034 restraints weight = 9390.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.88
r_work: 0.3124 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8343  Z= 0.178
  Angle     :  0.497   8.465  11310  Z= 0.258
  Chirality :  0.041   0.156   1305
  Planarity :  0.003   0.036   1431
  Dihedral  :  4.120  45.970   1157
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.76 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.47 (0.27), residues: 1051
  helix:  3.12 (0.28), residues: 345
  sheet:  0.54 (0.30), residues: 291
  loop : -0.56 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.006   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.941 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  344 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5672 (mtt180)
REVERT: A   22 ASN cc_start: 0.7152 (m-40) cc_final: 0.6812 (m110)
REVERT: A   26 ASP cc_start: 0.7141 (m-30) cc_final: 0.6811 (m-30)
REVERT: A  251 ASP cc_start: 0.7456 (t0) cc_final: 0.7187 (t0)
REVERT: A  271 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7035 (tttt)
REVERT: A  296 TYR cc_start: 0.5520 (OUTLIER) cc_final: 0.5311 (t80)
REVERT: A  309 ASP cc_start: 0.7339 (p0) cc_final: 0.6965 (p0)
REVERT: A  313 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7451 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.6595 (mtp85)
REVERT: B  127 LYS cc_start: 0.8784 (mttm) cc_final: 0.8304 (mttt)
REVERT: B  175 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7104 (mp10)
REVERT: B  219 ARG cc_start: 0.7657 (mmt180) cc_final: 0.7370 (mpt90)
REVERT: B  234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8909 (m-80)
REVERT: G   21 MET cc_start: 0.6467 (ttt) cc_final: 0.6152 (mmt)
REVERT: G   58 GLU cc_start: 0.7695 (pm20) cc_final: 0.6900 (mm-30)
REVERT: S    3 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7567 (pt0)
REVERT: S  211 ASP cc_start: 0.8206 (m-30) cc_final: 0.7994 (m-30)
  outliers start: 30
  outliers final: 19
  residues processed: 140
  average time/residue: 1.4141
  time to fit residues: 208.4526
Evaluate side-chains
  144 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 37 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.157366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.106029 restraints weight = 9526.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.54
r_work: 0.3048 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8343  Z= 0.236
  Angle     :  0.521   7.026  11310  Z= 0.273
  Chirality :  0.042   0.143   1305
  Planarity :  0.003   0.036   1431
  Dihedral  :  4.241  45.888   1157
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 15.80 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.38 (0.26), residues: 1051
  helix:  3.10 (0.28), residues: 345
  sheet:  0.44 (0.30), residues: 292
  loop : -0.63 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.010   0.001   TYR S 178 
 ARG   0.007   0.000   ARG B 134 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.941 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  344 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5896 (mtt180)
REVERT: A   22 ASN cc_start: 0.7543 (m-40) cc_final: 0.7226 (m110)
REVERT: A   26 ASP cc_start: 0.7399 (m-30) cc_final: 0.7107 (m-30)
REVERT: A   51 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7554 (ttpp)
REVERT: A  251 ASP cc_start: 0.7716 (t0) cc_final: 0.7431 (t0)
REVERT: A  309 ASP cc_start: 0.7436 (p0) cc_final: 0.7052 (p0)
REVERT: A  313 ARG cc_start: 0.7821 (ptp90) cc_final: 0.7529 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7065 (mtp85)
REVERT: B  127 LYS cc_start: 0.8955 (mttm) cc_final: 0.8500 (mttt)
REVERT: B  134 ARG cc_start: 0.8193 (mtp-110) cc_final: 0.7919 (mtm110)
REVERT: B  175 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7378 (mp10)
REVERT: B  219 ARG cc_start: 0.7822 (mmt180) cc_final: 0.7575 (mtt-85)
REVERT: B  234 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.9035 (m-80)
REVERT: G   21 MET cc_start: 0.6739 (ttt) cc_final: 0.6312 (mmt)
REVERT: G   58 GLU cc_start: 0.7804 (pm20) cc_final: 0.6950 (mm-30)
REVERT: S    3 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7777 (pt0)
REVERT: S  154 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8554 (tt)
REVERT: S  211 ASP cc_start: 0.8281 (m-30) cc_final: 0.8068 (m-30)
  outliers start: 35
  outliers final: 19
  residues processed: 144
  average time/residue: 1.4459
  time to fit residues: 219.2202
Evaluate side-chains
  147 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  221 VAL
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 76 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 65 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0980
   chunk 59 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.161302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.110330 restraints weight = 9569.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.54
r_work: 0.3083 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8343  Z= 0.133
  Angle     :  0.469   8.664  11310  Z= 0.243
  Chirality :  0.040   0.136   1305
  Planarity :  0.003   0.034   1431
  Dihedral  :  3.724  31.350   1155
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.11 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.58 (0.27), residues: 1051
  helix:  3.19 (0.28), residues: 345
  sheet:  0.54 (0.30), residues: 295
  loop : -0.44 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.010   0.001   TYR S 178 
 ARG   0.007   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.911 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  344 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5865 (mtm180)
REVERT: A   22 ASN cc_start: 0.7529 (m-40) cc_final: 0.7287 (m110)
REVERT: A   26 ASP cc_start: 0.7377 (m-30) cc_final: 0.7072 (m-30)
REVERT: A   51 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7548 (ttpp)
REVERT: A  271 LYS cc_start: 0.7541 (ttmt) cc_final: 0.7175 (tttt)
REVERT: A  309 ASP cc_start: 0.7297 (p0) cc_final: 0.6925 (p0)
REVERT: A  313 ARG cc_start: 0.7827 (ptp90) cc_final: 0.7518 (ptp-170)
REVERT: B  127 LYS cc_start: 0.8860 (mttm) cc_final: 0.8374 (mttt)
REVERT: B  134 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.8018 (mtm110)
REVERT: B  219 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7580 (mpt90)
REVERT: B  234 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8982 (m-80)
REVERT: G   21 MET cc_start: 0.6667 (ttt) cc_final: 0.6310 (mmt)
REVERT: G   58 GLU cc_start: 0.7858 (pm20) cc_final: 0.6996 (mm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 139
  average time/residue: 1.3802
  time to fit residues: 202.1454
Evaluate side-chains
  136 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0270
   chunk 23 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.3842

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
S 174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.156863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.105082 restraints weight = 9713.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.57
r_work: 0.3028 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8343  Z= 0.271
  Angle     :  0.537   7.552  11310  Z= 0.282
  Chirality :  0.042   0.139   1305
  Planarity :  0.003   0.037   1431
  Dihedral  :  4.047  27.606   1155
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.22 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.39 (0.27), residues: 1051
  helix:  3.10 (0.28), residues: 344
  sheet:  0.36 (0.30), residues: 297
  loop : -0.54 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.011   0.001   TYR B 105 
 ARG   0.007   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 1.113 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  344 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5917 (mtt180)
REVERT: A   22 ASN cc_start: 0.7558 (m-40) cc_final: 0.7246 (m110)
REVERT: A   26 ASP cc_start: 0.7405 (m-30) cc_final: 0.7068 (m-30)
REVERT: A   33 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8018 (mt-10)
REVERT: A   51 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7522 (ttpt)
REVERT: A  186 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: A  271 LYS cc_start: 0.7546 (ttmt) cc_final: 0.7224 (tttt)
REVERT: A  309 ASP cc_start: 0.7348 (p0) cc_final: 0.6966 (p0)
REVERT: A  313 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7480 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7083 (mtp85)
REVERT: B  127 LYS cc_start: 0.8989 (mttm) cc_final: 0.8546 (mttt)
REVERT: B  234 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9024 (m-80)
REVERT: G   21 MET cc_start: 0.6780 (ttt) cc_final: 0.6369 (mmt)
REVERT: G   58 GLU cc_start: 0.7802 (pm20) cc_final: 0.6971 (mm-30)
REVERT: S    3 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7722 (pt0)
REVERT: S  154 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8565 (tt)
  outliers start: 25
  outliers final: 15
  residues processed: 141
  average time/residue: 1.6620
  time to fit residues: 246.6027
Evaluate side-chains
  142 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 103 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.159346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.108417 restraints weight = 9495.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.53
r_work: 0.3069 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8343  Z= 0.171
  Angle     :  0.496   9.116  11310  Z= 0.258
  Chirality :  0.040   0.138   1305
  Planarity :  0.003   0.036   1431
  Dihedral  :  3.893  32.985   1155
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.80 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.46 (0.27), residues: 1051
  helix:  3.14 (0.28), residues: 345
  sheet:  0.44 (0.30), residues: 292
  loop : -0.52 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.010   0.001   TYR S 178 
 ARG   0.007   0.000   ARG B 197 

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

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

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2102 Ramachandran restraints generated.
    1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.859 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  344 ARG cc_start: 0.6190 (OUTLIER) cc_final: 0.5882 (mtm180)
REVERT: A   22 ASN cc_start: 0.7527 (m-40) cc_final: 0.7183 (m110)
REVERT: A   26 ASP cc_start: 0.7289 (m-30) cc_final: 0.6890 (m-30)
REVERT: A   51 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7537 (ttpt)
REVERT: A  309 ASP cc_start: 0.7292 (p0) cc_final: 0.6916 (p0)
REVERT: A  313 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7500 (ptp-170)
REVERT: B   27 ASP cc_start: 0.7745 (t0) cc_final: 0.7304 (p0)
REVERT: B   46 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7018 (mtp85)
REVERT: B  127 LYS cc_start: 0.8911 (mttm) cc_final: 0.8439 (mttt)
REVERT: B  134 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.8004 (mtm110)
REVERT: B  219 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7494 (mmt180)
REVERT: B  234 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8983 (m-80)
REVERT: G   21 MET cc_start: 0.6723 (ttt) cc_final: 0.6345 (mmt)
REVERT: G   58 GLU cc_start: 0.7820 (pm20) cc_final: 0.6990 (mm-30)
REVERT: S    3 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7661 (pt0)
  outliers start: 22
  outliers final: 14
  residues processed: 139
  average time/residue: 1.4379
  time to fit residues: 210.2521
Evaluate side-chains
  139 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  301 VAL
Chi-restraints excluded: chain R residue  337 THR
Chi-restraints excluded: chain R residue  344 ARG
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0870
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  32 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.159203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.107461 restraints weight = 9689.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.59
r_work: 0.3071 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8343  Z= 0.168
  Angle     :  0.489   7.219  11310  Z= 0.257
  Chirality :  0.040   0.137   1305
  Planarity :  0.003   0.036   1431
  Dihedral  :  3.846  32.986   1155
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.38 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.52 (0.27), residues: 1051
  helix:  3.17 (0.28), residues: 345
  sheet:  0.52 (0.30), residues: 291
  loop : -0.50 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.007   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7104.62 seconds
wall clock time: 124 minutes 46.67 seconds (7486.67 seconds total)