Starting phenix.real_space_refine
on Sat Jul 26 09:02:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ejx_31164/07_2025/7ejx_31164_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ejx_31164/07_2025/7ejx_31164.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ejx_31164/07_2025/7ejx_31164.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ejx_31164/07_2025/7ejx_31164.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ejx_31164/07_2025/7ejx_31164_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ejx_31164/07_2025/7ejx_31164_neut.cif"
  }
  resolution = 2.4
  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=   0.020
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    5321      2.51       5
     N    1429      2.21       5
     O    1527      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8334
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 1728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1728
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 218}
          Unresolved chain links: 1
          Chain breaks: 2
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 1710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1710
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 4
          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: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1768
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "R"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 120
          Unusual residues: {'CLR': 3, 'J5F': 1}
          Classifications: {'undetermined': 4, 'water': 2}
          Link IDs: {None: 5}
  Time building chain proxies: 5.74, per 1000 atoms: 0.69
  Number of scatterers: 8334
  At special positions: 0
  Unit cell: (89.64, 118.69, 125.33, 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    1527      8.00
     N    1429      7.00
     C    5321      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=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 987.4 milliseconds
  

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1982

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.5% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'R' and resid 37 through 59
      removed outlier: 4.017A  pdb=" N   LEU R  41 " --> pdb=" O   LEU R  37 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA R  42 " --> pdb=" O   TYR R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 64
      removed outlier: 5.690A  pdb=" N   THR R  64 " --> pdb=" O   LYS R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 85
      removed outlier: 3.930A  pdb=" N   PHE R  69 " --> pdb=" O   THR R  65 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE R  70 " --> pdb=" O   SER R  66 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 114 through 144
    Processing helix  chain 'R' and resid 145 through 153
    Processing helix  chain 'R' and resid 154 through 175
    Processing helix  chain 'R' and resid 192 through 228
      removed outlier: 3.802A  pdb=" N   VAL R 223 " --> pdb=" O   VAL R 219 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL R 228 " --> pdb=" O   LYS R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 283 through 309
      removed outlier: 3.650A  pdb=" N   CYS R 290 " --> pdb=" O   VAL R 286 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 314 through 338
      removed outlier: 3.838A  pdb=" N   SER R 329 " --> pdb=" O   CYS R 325 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA R 330 " --> pdb=" O   CYS R 326 " (cutoff:3.500A)
      Proline residue:  R 333  - end of helix
    Processing helix  chain 'R' and resid 340 through 351
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.609A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.545A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.160A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.922A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 329 through 352
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.841A  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 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.528A  pdb=" N   GLU G  58 " --> pdb=" O   PRO G  55 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.086A  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: 3.587A  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: 6.397A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.696A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.641A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.875A  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: 6.983A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.359A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.791A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.401A  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: 6.180A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.001A  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: 3.759A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (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: 6.728A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.464A  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: 4.179A  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: 4.056A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 4.056A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1263 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: 2.53

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1323
        1.31 -     1.43: 2309
        1.43 -     1.56: 4792
        1.56 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 8504
  Sorted by residual:
  bond pdb=" C2  J5F R 401 "
       pdb=" N12 J5F R 401 "
    ideal  model  delta    sigma   weight residual
    1.362  1.483 -0.121 2.00e-02 2.50e+03 3.65e+01
  bond pdb=" N   LEU R 176 "
       pdb=" CA  LEU R 176 "
    ideal  model  delta    sigma   weight residual
    1.455  1.499 -0.044 9.60e-03 1.09e+04 2.10e+01
  bond pdb=" N   PRO B 236 "
       pdb=" CD  PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.473  1.533 -0.060 1.40e-02 5.10e+03 1.83e+01
  bond pdb=" C   PHE B 235 "
       pdb=" N   PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.334  1.390 -0.056 1.51e-02 4.39e+03 1.36e+01
  bond pdb=" C   SER R 304 "
       pdb=" O   SER R 304 "
    ideal  model  delta    sigma   weight residual
    1.237  1.195  0.041 1.17e-02 7.31e+03 1.25e+01
  ... (remaining 8499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 11381
        2.63 -     5.25: 138
        5.25 -     7.88: 18
        7.88 -    10.50: 4
       10.50 -    13.13: 2
  Bond angle restraints: 11543
  Sorted by residual:
  angle pdb=" N   SER R 307 "
        pdb=" CA  SER R 307 "
        pdb=" C   SER R 307 "
      ideal   model   delta    sigma   weight residual
     112.54  103.34    9.20 1.22e+00 6.72e-01 5.68e+01
  angle pdb=" N   THR A 324 "
        pdb=" CA  THR A 324 "
        pdb=" C   THR A 324 "
      ideal   model   delta    sigma   weight residual
     108.56  121.45  -12.89 1.74e+00 3.30e-01 5.49e+01
  angle pdb=" CA  LEU R 176 "
        pdb=" C   LEU R 176 "
        pdb=" N   PRO R 177 "
      ideal   model   delta    sigma   weight residual
     117.95  122.35   -4.40 7.70e-01 1.69e+00 3.26e+01
  angle pdb=" N   ARG A 205 "
        pdb=" CA  ARG A 205 "
        pdb=" C   ARG A 205 "
      ideal   model   delta    sigma   weight residual
     108.63  117.24   -8.61 1.60e+00 3.91e-01 2.89e+01
  angle pdb=" N   PRO R 178 "
        pdb=" CA  PRO R 178 "
        pdb=" C   PRO R 178 "
      ideal   model   delta    sigma   weight residual
     113.40  120.37   -6.97 1.34e+00 5.57e-01 2.71e+01
  ... (remaining 11538 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 4598
       17.66 -    35.31: 442
       35.31 -    52.97: 116
       52.97 -    70.62: 24
       70.62 -    88.28: 11
  Dihedral angle restraints: 5191
    sinusoidal: 2113
      harmonic: 3078
  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  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C   LEU B 198 "
           pdb=" N   LEU B 198 "
           pdb=" CA  LEU B 198 "
           pdb=" CB  LEU B 198 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.91   -8.69     0      2.50e+00 1.60e-01 1.21e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.81   17.19     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 5188 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1204
       0.071 -    0.142: 105
       0.142 -    0.213: 16
       0.213 -    0.285: 5
       0.285 -    0.356: 2
  Chirality restraints: 1332
  Sorted by residual:
  chirality pdb=" CA  THR A 324 "
            pdb=" N   THR A 324 "
            pdb=" C   THR A 324 "
            pdb=" CB  THR A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.36 2.00e-01 2.50e+01 3.16e+00
  chirality pdb=" CA  LEU R 281 "
            pdb=" N   LEU R 281 "
            pdb=" C   LEU R 281 "
            pdb=" CB  LEU R 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CA  LEU B 198 "
            pdb=" N   LEU B 198 "
            pdb=" C   LEU B 198 "
            pdb=" CB  LEU B 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1329 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 281 "    0.012 2.00e-02 2.50e+03   2.41e-02 5.80e+00
        pdb=" C   LEU R 281 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   LEU R 281 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER R 282 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C13 J5F R 401 "    0.020 2.00e-02 2.50e+03   1.53e-02 3.51e+00
        pdb=" C2  J5F R 401 "   -0.007 2.00e-02 2.50e+03
        pdb=" C20 J5F R 401 "    0.002 2.00e-02 2.50e+03
        pdb=" C3  J5F R 401 "    0.015 2.00e-02 2.50e+03
        pdb=" N12 J5F R 401 "   -0.027 2.00e-02 2.50e+03
        pdb=" O1  J5F R 401 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 280 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   ARG R 280 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ARG R 280 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU R 281 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 81
        2.59 -     3.17: 7031
        3.17 -     3.75: 12803
        3.75 -     4.32: 18907
        4.32 -     4.90: 31478
  Nonbonded interactions: 70300
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.016 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.044 3.040
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.073 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OG  SER S 149 "
            pdb=" O   LYS S 151 "
     model   vdw
     2.141 3.040
  ... (remaining 70295 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:             3.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.900
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
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      :  0.004   0.121   8506  Z= 0.263
  Angle     :  0.713  13.127  11547  Z= 0.420
  Chirality :  0.047   0.356   1332
  Planarity :  0.002   0.024   1438
  Dihedral  : 15.550  88.279   3203
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.52 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.27), residues: 1045
  helix:  3.06 (0.27), residues: 354
  sheet:  0.94 (0.32), residues: 265
  loop : -0.43 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 322 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.009   0.001   PHE B 234 
 TYR   0.009   0.001   TYR S 103 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18814 (  448)
  hydrogen bonds       : angle       6.64796 ( 1263)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.74149 (    4)
  covalent geometry    : bond        0.00429 ( 8504)
  covalent geometry    : angle       0.71294 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.894 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: A    6 SER cc_start: 0.8274 (t) cc_final: 0.7999 (p)
REVERT: A   17 LYS cc_start: 0.7391 (mmtt) cc_final: 0.7011 (mtpt)
REVERT: A   24 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7538 (ttp80)
REVERT: A  208 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7333 (ttp-110)
REVERT: A  269 ASN cc_start: 0.8514 (m110) cc_final: 0.8307 (m110)
REVERT: B   44 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7951 (mt0)
REVERT: G   47 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7908 (mt-10)
REVERT: S  120 SER cc_start: 0.8590 (t) cc_final: 0.8118 (p)
REVERT: S  174 GLN cc_start: 0.8282 (tt0) cc_final: 0.8040 (tt0)
  outliers start: 11
  outliers final: 5
  residues processed: 146
  average time/residue: 1.2025
  time to fit residues: 186.6642
Evaluate side-chains
  120 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    0.4980
   chunk 81 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0170
   chunk 94 optimal weight:    6.9990
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
B 237 ASN
B 340 ASN
S 130 GLN
S 182 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.129436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.086786 restraints weight = 10316.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.19
r_work: 0.2928 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8506  Z= 0.122
  Angle     :  0.566  14.812  11547  Z= 0.287
  Chirality :  0.042   0.244   1332
  Planarity :  0.004   0.034   1438
  Dihedral  :  6.598  57.143   1390
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.34 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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:  1.74 (0.27), residues: 1045
  helix:  3.18 (0.26), residues: 363
  sheet:  0.61 (0.31), residues: 264
  loop : -0.31 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.010   0.001   PHE B 151 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.005   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  448)
  hydrogen bonds       : angle       4.64669 ( 1263)
  SS BOND              : bond        0.00320 (    2)
  SS BOND              : angle       0.88125 (    4)
  covalent geometry    : bond        0.00260 ( 8504)
  covalent geometry    : angle       0.56624 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.901 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  196 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7606 (pp)
REVERT: R  204 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7305 (tm-30)
REVERT: A    6 SER cc_start: 0.8323 (t) cc_final: 0.7964 (p)
REVERT: A   17 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7139 (mtpt)
REVERT: A   24 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.7482 (ttp80)
REVERT: A  208 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7282 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8028 (mt0)
REVERT: G   17 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7255 (mm-30)
REVERT: G   47 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8145 (mt-10)
REVERT: S   93 MET cc_start: 0.8843 (tpp) cc_final: 0.8302 (tpp)
  outliers start: 31
  outliers final: 15
  residues processed: 143
  average time/residue: 1.4110
  time to fit residues: 214.1212
Evaluate side-chains
  125 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  204 GLN
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0000
   chunk 43 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 97 optimal weight:    0.4980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
R  49 ASN
R 332 ASN
A 244 HIS
A 269 ASN
B  75 GLN
S  13 GLN
S  39 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.128862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.085388 restraints weight = 10412.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.26
r_work: 0.2873 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8506  Z= 0.127
  Angle     :  0.533  11.075  11547  Z= 0.275
  Chirality :  0.041   0.237   1332
  Planarity :  0.003   0.034   1438
  Dihedral  :  6.168  50.865   1386
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.23 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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:  1.73 (0.26), residues: 1045
  helix:  3.31 (0.26), residues: 363
  sheet:  0.31 (0.29), residues: 280
  loop : -0.26 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.012   0.001   TYR S 178 
 ARG   0.007   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03826 (  448)
  hydrogen bonds       : angle       4.40000 ( 1263)
  SS BOND              : bond        0.00488 (    2)
  SS BOND              : angle       1.06065 (    4)
  covalent geometry    : bond        0.00280 ( 8504)
  covalent geometry    : angle       0.53299 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 119
  time to evaluate  : 1.036 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  196 LEU cc_start: 0.8020 (tt) cc_final: 0.7557 (pp)
REVERT: R  342 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7385 (tm-30)
REVERT: A    6 SER cc_start: 0.8340 (t) cc_final: 0.7926 (p)
REVERT: A   17 LYS cc_start: 0.7512 (mmtt) cc_final: 0.6973 (mttp)
REVERT: A   24 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7285 (ttp80)
REVERT: A  208 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7090 (ttp-110)
REVERT: A  269 ASN cc_start: 0.8813 (m-40) cc_final: 0.8546 (m110)
REVERT: B   44 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7978 (mt0)
REVERT: B  276 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8436 (p)
REVERT: G   17 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7207 (mm-30)
REVERT: G   47 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: S   93 MET cc_start: 0.8723 (tpp) cc_final: 0.8223 (tpp)
  outliers start: 36
  outliers final: 18
  residues processed: 145
  average time/residue: 1.5012
  time to fit residues: 230.7885
Evaluate side-chains
  133 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  342 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9980
   chunk 68 optimal weight:    0.4980
   chunk 61 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0270
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
R  49 ASN
R 332 ASN
A 244 HIS
S  13 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.129911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.086777 restraints weight = 10375.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.21
r_work: 0.2927 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8506  Z= 0.110
  Angle     :  0.504   8.949  11547  Z= 0.260
  Chirality :  0.040   0.196   1332
  Planarity :  0.003   0.035   1438
  Dihedral  :  6.229  55.894   1386
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 19.00 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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:  1.78 (0.27), residues: 1045
  helix:  3.33 (0.26), residues: 365
  sheet:  0.29 (0.29), residues: 280
  loop : -0.19 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B  54 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.008   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03453 (  448)
  hydrogen bonds       : angle       4.24792 ( 1263)
  SS BOND              : bond        0.00368 (    2)
  SS BOND              : angle       0.69296 (    4)
  covalent geometry    : bond        0.00238 ( 8504)
  covalent geometry    : angle       0.50380 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 1.212 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  196 LEU cc_start: 0.8024 (tt) cc_final: 0.7549 (pp)
REVERT: R  341 GLU cc_start: 0.7901 (tp30) cc_final: 0.7429 (mm-30)
REVERT: R  342 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7483 (tm-30)
REVERT: A    6 SER cc_start: 0.8358 (t) cc_final: 0.8041 (p)
REVERT: A   17 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7221 (mttp)
REVERT: A   24 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7548 (ttp80)
REVERT: A  208 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7306 (ttp-110)
REVERT: A  324 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8455 (t)
REVERT: B   44 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8071 (mt0)
REVERT: G   17 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7257 (mm-30)
REVERT: G   42 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7936 (mt-10)
REVERT: G   47 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8082 (mt-10)
REVERT: S   93 MET cc_start: 0.8818 (tpp) cc_final: 0.8404 (tpp)
  outliers start: 41
  outliers final: 19
  residues processed: 148
  average time/residue: 1.8237
  time to fit residues: 284.5995
Evaluate side-chains
  133 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  342 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Chi-restraints excluded: chain S residue  211 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
R  49 ASN
R 191 HIS
A 204 GLN
A 244 HIS
B  75 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.081018 restraints weight = 10204.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.18
r_work: 0.2830 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   8506  Z= 0.249
  Angle     :  0.607   7.748  11547  Z= 0.317
  Chirality :  0.044   0.195   1332
  Planarity :  0.004   0.036   1438
  Dihedral  :  6.711  54.316   1386
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 19.00 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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:  1.62 (0.26), residues: 1045
  helix:  3.16 (0.26), residues: 365
  sheet:  0.22 (0.29), residues: 283
  loop : -0.26 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.013   0.002   TYR S 103 
 ARG   0.007   0.001   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04412 (  448)
  hydrogen bonds       : angle       4.60637 ( 1263)
  SS BOND              : bond        0.00535 (    2)
  SS BOND              : angle       1.14845 (    4)
  covalent geometry    : bond        0.00585 ( 8504)
  covalent geometry    : angle       0.60672 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.902 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  196 LEU cc_start: 0.8069 (tt) cc_final: 0.7574 (pp)
REVERT: A    6 SER cc_start: 0.8631 (t) cc_final: 0.8174 (p)
REVERT: A   17 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7291 (mtpt)
REVERT: A   24 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7528 (ttp80)
REVERT: A  208 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7327 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8095 (mt0)
REVERT: B  276 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8619 (p)
REVERT: G   17 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7266 (mm-30)
REVERT: G   42 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8049 (mt-10)
REVERT: G   47 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: S   19 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8234 (tttm)
  outliers start: 41
  outliers final: 20
  residues processed: 144
  average time/residue: 1.1863
  time to fit residues: 181.7474
Evaluate side-chains
  133 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
S  13 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.125719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.081898 restraints weight = 10344.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.19
r_work: 0.2844 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8506  Z= 0.191
  Angle     :  0.570   7.465  11547  Z= 0.299
  Chirality :  0.043   0.248   1332
  Planarity :  0.004   0.045   1438
  Dihedral  :  6.666  53.226   1386
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 19.23 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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 (0.26), residues: 1045
  helix:  3.11 (0.26), residues: 365
  sheet:  0.17 (0.29), residues: 281
  loop : -0.32 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.012   0.001   TYR S 103 
 ARG   0.007   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04082 (  448)
  hydrogen bonds       : angle       4.51240 ( 1263)
  SS BOND              : bond        0.00469 (    2)
  SS BOND              : angle       0.96802 (    4)
  covalent geometry    : bond        0.00444 ( 8504)
  covalent geometry    : angle       0.56994 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 111
  time to evaluate  : 0.987 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  196 LEU cc_start: 0.8068 (tt) cc_final: 0.7567 (pp)
REVERT: R  342 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7528 (tm-30)
REVERT: A    6 SER cc_start: 0.8537 (t) cc_final: 0.8098 (p)
REVERT: A   17 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7291 (mtpt)
REVERT: A   24 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7545 (ttp80)
REVERT: A  208 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7371 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8173 (mt0)
REVERT: B  276 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8595 (p)
REVERT: G   17 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7272 (mm-30)
REVERT: G   42 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8029 (mt-10)
REVERT: G   47 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8151 (mt-10)
REVERT: S   19 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8238 (tttm)
  outliers start: 37
  outliers final: 21
  residues processed: 138
  average time/residue: 1.2164
  time to fit residues: 178.6365
Evaluate side-chains
  134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  342 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   88 SER
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.127366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.083781 restraints weight = 10324.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.20
r_work: 0.2875 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8506  Z= 0.142
  Angle     :  0.534   7.653  11547  Z= 0.280
  Chirality :  0.041   0.192   1332
  Planarity :  0.004   0.041   1438
  Dihedral  :  6.461  52.551   1386
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.36 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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 (0.26), residues: 1045
  helix:  3.16 (0.26), residues: 366
  sheet:  0.18 (0.29), residues: 280
  loop : -0.30 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.009   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  448)
  hydrogen bonds       : angle       4.37314 ( 1263)
  SS BOND              : bond        0.00378 (    2)
  SS BOND              : angle       0.74895 (    4)
  covalent geometry    : bond        0.00320 ( 8504)
  covalent geometry    : angle       0.53382 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.971 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  196 LEU cc_start: 0.7998 (tt) cc_final: 0.7494 (pp)
REVERT: R  342 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7489 (tm-30)
REVERT: A    6 SER cc_start: 0.8468 (t) cc_final: 0.8066 (p)
REVERT: A   17 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7273 (mtpt)
REVERT: A   24 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7502 (ttp80)
REVERT: A  208 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7332 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8172 (mt0)
REVERT: B  219 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8222 (mtp85)
REVERT: G   17 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7254 (mm-30)
REVERT: G   42 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7974 (mt-10)
REVERT: G   47 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: S   19 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8230 (tttm)
REVERT: S  120 SER cc_start: 0.8712 (t) cc_final: 0.8080 (p)
  outliers start: 32
  outliers final: 18
  residues processed: 133
  average time/residue: 1.3842
  time to fit residues: 195.7529
Evaluate side-chains
  128 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  342 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.127421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.083917 restraints weight = 10385.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.20
r_work: 0.2878 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8506  Z= 0.141
  Angle     :  0.536   7.954  11547  Z= 0.281
  Chirality :  0.041   0.164   1332
  Planarity :  0.004   0.041   1438
  Dihedral  :  6.407  51.271   1386
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.82 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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:  1.62 (0.26), residues: 1045
  helix:  3.17 (0.26), residues: 366
  sheet:  0.26 (0.29), residues: 276
  loop : -0.30 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.008   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  448)
  hydrogen bonds       : angle       4.33946 ( 1263)
  SS BOND              : bond        0.00358 (    2)
  SS BOND              : angle       0.77819 (    4)
  covalent geometry    : bond        0.00319 ( 8504)
  covalent geometry    : angle       0.53580 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 107
  time to evaluate  : 0.934 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  196 LEU cc_start: 0.8003 (tt) cc_final: 0.7513 (pp)
REVERT: R  341 GLU cc_start: 0.7887 (tp30) cc_final: 0.7424 (mm-30)
REVERT: R  342 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7476 (tm-30)
REVERT: A    6 SER cc_start: 0.8469 (t) cc_final: 0.8084 (p)
REVERT: A   17 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7273 (mtpt)
REVERT: A   24 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7506 (ttp80)
REVERT: A  208 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7333 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8176 (mt0)
REVERT: G   17 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7248 (mm-30)
REVERT: G   42 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7970 (mt-10)
REVERT: G   47 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8120 (mt-10)
REVERT: S   19 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8230 (tttm)
  outliers start: 32
  outliers final: 21
  residues processed: 132
  average time/residue: 1.3292
  time to fit residues: 185.8617
Evaluate side-chains
  130 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  342 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.126311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.082507 restraints weight = 10421.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.20
r_work: 0.2856 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8506  Z= 0.172
  Angle     :  0.561   8.103  11547  Z= 0.293
  Chirality :  0.042   0.172   1332
  Planarity :  0.004   0.040   1438
  Dihedral  :  6.497  52.159   1386
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.50 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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:  1.56 (0.26), residues: 1045
  helix:  3.11 (0.26), residues: 366
  sheet:  0.23 (0.29), residues: 277
  loop : -0.32 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.011   0.001   TYR S 103 
 ARG   0.009   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  448)
  hydrogen bonds       : angle       4.41497 ( 1263)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       0.87932 (    4)
  covalent geometry    : bond        0.00398 ( 8504)
  covalent geometry    : angle       0.56067 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.237 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  342 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7486 (tm-30)
REVERT: A    6 SER cc_start: 0.8519 (t) cc_final: 0.8123 (p)
REVERT: A   17 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7199 (mttp)
REVERT: A   24 ARG cc_start: 0.7778 (ttp-110) cc_final: 0.7538 (ttp80)
REVERT: A  208 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7354 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8164 (mt0)
REVERT: G   17 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7246 (mm-30)
REVERT: G   42 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8039 (mt-10)
REVERT: G   47 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8145 (mt-10)
REVERT: S   19 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8217 (tttm)
  outliers start: 28
  outliers final: 20
  residues processed: 128
  average time/residue: 1.8763
  time to fit residues: 254.6393
Evaluate side-chains
  130 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  342 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   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 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.084095 restraints weight = 10310.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.20
r_work: 0.2881 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8506  Z= 0.138
  Angle     :  0.548   8.193  11547  Z= 0.284
  Chirality :  0.041   0.189   1332
  Planarity :  0.004   0.039   1438
  Dihedral  :  6.352  51.565   1386
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.96 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    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:  1.61 (0.26), residues: 1045
  helix:  3.14 (0.26), residues: 366
  sheet:  0.26 (0.29), residues: 276
  loop : -0.28 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.009   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03612 (  448)
  hydrogen bonds       : angle       4.33311 ( 1263)
  SS BOND              : bond        0.00349 (    2)
  SS BOND              : angle       0.63963 (    4)
  covalent geometry    : bond        0.00313 ( 8504)
  covalent geometry    : angle       0.54808 (11543)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 1.968 
Fit side-chains
TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it.
REVERT: R  341 GLU cc_start: 0.7896 (tp30) cc_final: 0.7434 (mm-30)
REVERT: R  342 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7480 (tm-30)
REVERT: A    6 SER cc_start: 0.8457 (t) cc_final: 0.8090 (p)
REVERT: A   17 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7185 (mttp)
REVERT: A   24 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7477 (ttp80)
REVERT: A  208 ARG cc_start: 0.8095 (ttm170) cc_final: 0.7323 (ttp-110)
REVERT: B   44 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8157 (mt0)
REVERT: G   17 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7233 (mm-30)
REVERT: G   42 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7967 (mt-10)
REVERT: G   47 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: S   19 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8187 (tttm)
  outliers start: 25
  outliers final: 20
  residues processed: 127
  average time/residue: 2.0479
  time to fit residues: 275.5195
Evaluate side-chains
  129 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  342 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0570
   chunk 1 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0870
   chunk 84 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.083473 restraints weight = 10475.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.20
r_work: 0.2884 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8506  Z= 0.147
  Angle     :  0.553   8.870  11547  Z= 0.286
  Chirality :  0.041   0.188   1332
  Planarity :  0.004   0.039   1438
  Dihedral  :  6.332  51.651   1386
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.62 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1045
  helix:  3.15 (0.26), residues: 366
  sheet:  0.25 (0.29), residues: 276
  loop : -0.29 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.011   0.001   TYR S 178 
 ARG   0.009   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  448)
  hydrogen bonds       : angle       4.35643 ( 1263)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.67718 (    4)
  covalent geometry    : bond        0.00335 ( 8504)
  covalent geometry    : angle       0.55312 (11543)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11196.25 seconds
wall clock time: 199 minutes 56.94 seconds (11996.94 seconds total)