Starting phenix.real_space_refine
on Sat Jul 26 15:20:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rql_19445/07_2025/8rql_19445.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rql_19445/07_2025/8rql_19445.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rql_19445/07_2025/8rql_19445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rql_19445/07_2025/8rql_19445.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rql_19445/07_2025/8rql_19445.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rql_19445/07_2025/8rql_19445.cif"
  }
  resolution = 3.03
  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=  -0.001 sd=   0.033
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: 5
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5537      2.51       5
     N    1460      2.21       5
     O    1588      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8646
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2142
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 3, 'TRANS': 274}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 121
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 65
    Chain: "A"
      Number of atoms: 1683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1683
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2572
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "G"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 55}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1755
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 40
          Unusual residues: {'FLF': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.73, per 1000 atoms: 0.66
  Number of scatterers: 8646
  At special positions: 0
  Unit cell: (87.556, 119.77, 123.074, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      55     16.00
     F       6      9.00
     O    1588      8.00
     N    1460      7.00
     C    5537      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: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      40.1% alpha, 22.1% 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 3 through 38
      removed outlier: 4.341A  pdb=" N   THR R  10 " --> pdb=" O   LYS R   6 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE R  11 " --> pdb=" O   SER R   7 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASP R  34 " --> pdb=" O   VAL R  30 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   TRP R  35 " --> pdb=" O   ASN R  31 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL R  36 " --> pdb=" O   CYS R  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 69
      removed outlier: 3.628A  pdb=" N   SER R  57 " --> pdb=" O   ILE R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 77
      removed outlier: 3.805A  pdb=" N   PHE R  76 " --> pdb=" O   PHE R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 112
      removed outlier: 3.971A  pdb=" N   PHE R  95 " --> pdb=" O   VAL R  91 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA R 100 " --> pdb=" O   SER R  96 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 116 through 125
    Processing helix  chain 'R' and resid 125 through 158
      removed outlier: 3.921A  pdb=" N   VAL R 130 " --> pdb=" O   VAL R 126 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   LEU R 131 " --> pdb=" O   LYS R 127 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LEU R 134 " --> pdb=" O   VAL R 130 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE R 152 " --> pdb=" O   ILE R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 176 through 183
    Processing helix  chain 'R' and resid 187 through 212
      removed outlier: 3.524A  pdb=" N   LEU R 200 " --> pdb=" O   ALA R 196 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU R 201 " --> pdb=" O   MET R 197 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   PHE R 203 " --> pdb=" O   LEU R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 224 through 253
    Processing helix  chain 'R' and resid 260 through 282
      removed outlier: 3.547A  pdb=" N   LEU R 264 " --> pdb=" O   ASN R 260 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   TYR R 272 " --> pdb=" O   MET R 268 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
      removed outlier: 3.836A  pdb=" N   SER R 277 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   CYS R 278 " --> pdb=" O   SER R 274 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL R 279 " --> pdb=" O   CYS R 275 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 303
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 96 through 102
      removed outlier: 3.594A  pdb=" N   GLU A 101 " --> pdb=" O   HIS A  98 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASP A 102 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 4.242A  pdb=" N   HIS A 119 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   GLU A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 136
      removed outlier: 3.872A  pdb=" N   SER A 135 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   THR A 136 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 132 through 136'
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.655A  pdb=" N   GLU A 151 " --> pdb=" O   ASP A 147 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   THR A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
    Processing helix  chain 'A' and resid 170 through 185
      removed outlier: 4.105A  pdb=" N   LEU A 185 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 227
    Processing helix  chain 'B' and resid 21 through 42
      removed outlier: 3.757A  pdb=" N   ARG B  25 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLU B  27 " --> pdb=" O   GLN B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 51
    Processing helix  chain 'B' and resid 52 through 54
      No H-bonds generated for 'chain 'B' and resid 52 through 54'
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.523A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.867A  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
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55
      removed outlier: 3.538A  pdb=" N   LYS A  54 " --> pdb=" O   GLN A  73 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN A  73 " --> pdb=" O   LYS A  54 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   CYS A 105 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 111
    Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 68
    Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 80
      removed outlier: 6.767A  pdb=" N   ALA B  90 " --> pdb=" O   TYR B  76 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   MET B  78 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL B  88 " --> pdb=" O   MET B  78 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   TRP B  80 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   LEU B  86 " --> pdb=" O   TRP B  80 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS B  95 " --> pdb=" O   SER B  91 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ASP B 100 " --> pdb=" O   LYS B 106 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   LYS B 106 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 122
      removed outlier: 4.507A  pdb=" N   GLY B 133 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   ILE B 137 " --> pdb=" O   GLY B 133 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASN B 142 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL B 152 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 168
      removed outlier: 4.406A  pdb=" N   THR B 182 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ASP B 187 " --> pdb=" O   GLN B 193 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   GLN B 193 " --> pdb=" O   ASP B 187 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 204 through 209
      removed outlier: 3.851A  pdb=" N   GLN B 237 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASP B 229 " --> pdb=" O   CYS B 235 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   CYS B 235 " --> pdb=" O   ASP B 229 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 251
      removed outlier: 6.898A  pdb=" N   ASP B 271 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLU B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 295
      removed outlier: 6.526A  pdb=" N   GLY B 305 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL B 293 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   LEU B 303 " --> pdb=" O   VAL B 293 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   PHE B 295 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   LEU B 301 " --> pdb=" O   PHE B 295 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   CYS B 311 " --> pdb=" O   VAL B 324 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   VAL B 324 " --> pdb=" O   CYS B 311 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   VAL B 313 " --> pdb=" O   ALA B 322 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.835A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (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: 4.065A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.555A  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: 4.065A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1320 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: 2.63

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1384
        1.32 -     1.44: 2482
        1.44 -     1.56: 4878
        1.56 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 8824
  Sorted by residual:
  bond pdb=" N   FLF R 401 "
       pdb=" C1' FLF R 401 "
    ideal  model  delta    sigma   weight residual
    1.377  1.451 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" N   FLF R 401 "
       pdb=" C6  FLF R 401 "
    ideal  model  delta    sigma   weight residual
    1.378  1.450 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" N   ILE R 179 "
       pdb=" CA  ILE R 179 "
    ideal  model  delta    sigma   weight residual
    1.460  1.502 -0.043 1.21e-02 6.83e+03 1.24e+01
  bond pdb=" N   ILE R 148 "
       pdb=" CA  ILE R 148 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.06e-02 8.90e+03 8.95e+00
  bond pdb=" C   ASN R 149 "
       pdb=" O   ASN R 149 "
    ideal  model  delta    sigma   weight residual
    1.234  1.195  0.039 1.35e-02 5.49e+03 8.39e+00
  ... (remaining 8819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 11904
        2.66 -     5.32: 58
        5.32 -     7.98: 3
        7.98 -    10.64: 2
       10.64 -    13.30: 2
  Bond angle restraints: 11969
  Sorted by residual:
  angle pdb=" N   ILE R 145 "
        pdb=" CA  ILE R 145 "
        pdb=" C   ILE R 145 "
      ideal   model   delta    sigma   weight residual
     110.62  102.10    8.52 1.14e+00 7.69e-01 5.58e+01
  angle pdb=" N   ILE R 148 "
        pdb=" CA  ILE R 148 "
        pdb=" C   ILE R 148 "
      ideal   model   delta    sigma   weight residual
     112.98  107.36    5.62 1.25e+00 6.40e-01 2.02e+01
  angle pdb=" C2  FLF R 401 "
        pdb=" C1  FLF R 401 "
        pdb=" C7  FLF R 401 "
      ideal   model   delta    sigma   weight residual
     118.34  105.04   13.30 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" N   ILE R 179 "
        pdb=" CA  ILE R 179 "
        pdb=" CB  ILE R 179 "
      ideal   model   delta    sigma   weight residual
     110.58  117.02   -6.44 1.50e+00 4.44e-01 1.84e+01
  angle pdb=" CA  ALA R 146 "
        pdb=" C   ALA R 146 "
        pdb=" O   ALA R 146 "
      ideal   model   delta    sigma   weight residual
     121.07  116.50    4.57 1.10e+00 8.26e-01 1.73e+01
  ... (remaining 11964 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 4756
       17.54 -    35.09: 354
       35.09 -    52.63: 48
       52.63 -    70.17: 4
       70.17 -    87.72: 4
  Dihedral angle restraints: 5166
    sinusoidal: 1907
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CB  CYS S  22 "
           pdb=" SG  CYS S  22 "
           pdb=" SG  CYS S  96 "
           pdb=" CB  CYS S  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.33   30.67     1      1.00e+01 1.00e-02 1.34e+01
  dihedral pdb=" CA  PHE A  76 "
           pdb=" C   PHE A  76 "
           pdb=" N   LYS A  77 "
           pdb=" CA  LYS A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.44   16.56     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  ARG R  83 "
           pdb=" CB  ARG R  83 "
           pdb=" CG  ARG R  83 "
           pdb=" CD  ARG R  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.78   59.22     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5163 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 974
       0.033 -    0.065: 281
       0.065 -    0.098: 78
       0.098 -    0.131: 48
       0.131 -    0.164: 3
  Chirality restraints: 1384
  Sorted by residual:
  chirality pdb=" CB  ILE R 148 "
            pdb=" CA  ILE R 148 "
            pdb=" CG1 ILE R 148 "
            pdb=" CG2 ILE R 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.69e-01
  chirality pdb=" CA  ILE R 145 "
            pdb=" N   ILE R 145 "
            pdb=" C   ILE R 145 "
            pdb=" CB  ILE R 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CB  ILE R 179 "
            pdb=" CA  ILE R 179 "
            pdb=" CG1 ILE R 179 "
            pdb=" CG2 ILE R 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 1381 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R 144 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.76e+00
        pdb=" C   ASN R 144 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASN R 144 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE R 145 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 145 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   ILE R 145 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ILE R 145 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA R 146 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R  81 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   MET R  81 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   MET R  81 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE R  82 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 127
        2.66 -     3.22: 8395
        3.22 -     3.78: 13445
        3.78 -     4.34: 18910
        4.34 -     4.90: 31516
  Nonbonded interactions: 72393
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 180 "
            pdb=" OG1 THR B 181 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" OG1 THR B 291 "
            pdb=" O   VAL B 332 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" O   ASP B 350 "
            pdb=" OG  SER B 351 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OE2 GLU A  71 "
            pdb=" NH1 ARG A  82 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" O   THR B 103 "
            pdb=" OG1 THR B 104 "
     model   vdw
     2.198 3.040
  ... (remaining 72388 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.320
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8826  Z= 0.172
  Angle     :  0.527  13.297  11973  Z= 0.310
  Chirality :  0.039   0.164   1384
  Planarity :  0.002   0.026   1500
  Dihedral  : 12.193  87.715   3048
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.44 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.26), residues: 1106
  helix:  1.86 (0.28), residues: 384
  sheet: -0.92 (0.28), residues: 291
  loop : -0.33 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.002   0.001   HIS R  94 
 PHE   0.011   0.001   PHE B 216 
 TYR   0.008   0.001   TYR B  76 
 ARG   0.006   0.000   ARG R 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14998 (  466)
  hydrogen bonds       : angle       6.52461 ( 1320)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       0.26171 (    4)
  covalent geometry    : bond        0.00293 ( 8824)
  covalent geometry    : angle       0.52695 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 223
  time to evaluate  : 0.898 
Fit side-chains
REVERT: R   63 PHE cc_start: 0.7390 (t80) cc_final: 0.7186 (t80)
REVERT: R   78 THR cc_start: 0.5616 (m) cc_final: 0.5307 (p)
REVERT: R   83 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6913 (ttm170)
REVERT: R   87 ASN cc_start: 0.8717 (m110) cc_final: 0.8192 (m-40)
REVERT: R  284 ASN cc_start: 0.7823 (t0) cc_final: 0.7503 (t0)
REVERT: A   73 GLN cc_start: 0.8547 (mt0) cc_final: 0.8281 (mt0)
REVERT: A  120 GLU cc_start: 0.7035 (mp0) cc_final: 0.6792 (tt0)
REVERT: A  123 HIS cc_start: 0.6358 (t-90) cc_final: 0.6084 (t-90)
REVERT: A  135 SER cc_start: 0.8278 (t) cc_final: 0.7940 (p)
REVERT: A  181 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7825 (tp40)
REVERT: A  220 LYS cc_start: 0.6409 (ttpt) cc_final: 0.5948 (mptt)
REVERT: B   53 ASN cc_start: 0.7093 (m-40) cc_final: 0.6770 (p0)
REVERT: B   59 ARG cc_start: 0.7169 (mmm160) cc_final: 0.6893 (mmp-170)
REVERT: B   63 ARG cc_start: 0.7723 (ttt180) cc_final: 0.7000 (mmm160)
REVERT: B  141 TYR cc_start: 0.8370 (m-80) cc_final: 0.7916 (m-80)
REVERT: G   47 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7624 (mp0)
REVERT: S   65 LYS cc_start: 0.7686 (tptt) cc_final: 0.7452 (tptt)
  outliers start: 2
  outliers final: 1
  residues processed: 224
  average time/residue: 0.2001
  time to fit residues: 62.0899
Evaluate side-chains
  167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue  179 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
R  31 ASN
R  87 ASN
R 284 ASN
A 130 ASN
S 171 GLN
S 182 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.163443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.127776 restraints weight = 11043.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.48
r_work: 0.3364 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8826  Z= 0.162
  Angle     :  0.542   7.323  11973  Z= 0.298
  Chirality :  0.043   0.188   1384
  Planarity :  0.004   0.049   1500
  Dihedral  :  6.080  84.280   1209
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.04 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1106
  helix:  2.12 (0.26), residues: 390
  sheet: -0.70 (0.28), residues: 271
  loop : -0.55 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 124 
 HIS   0.004   0.001   HIS A  80 
 PHE   0.022   0.002   PHE A 211 
 TYR   0.015   0.002   TYR A 195 
 ARG   0.005   0.001   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  466)
  hydrogen bonds       : angle       4.79529 ( 1320)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       1.00251 (    4)
  covalent geometry    : bond        0.00371 ( 8824)
  covalent geometry    : angle       0.54176 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: R   87 ASN cc_start: 0.8966 (m-40) cc_final: 0.8755 (m110)
REVERT: R  120 LEU cc_start: 0.8308 (mp) cc_final: 0.8056 (mm)
REVERT: R  243 PHE cc_start: 0.7249 (m-80) cc_final: 0.6961 (m-80)
REVERT: R  286 LYS cc_start: 0.8850 (tttm) cc_final: 0.8638 (tttm)
REVERT: A   35 LYS cc_start: 0.8365 (mttt) cc_final: 0.8037 (mttp)
REVERT: A   73 GLN cc_start: 0.8687 (mt0) cc_final: 0.8332 (mt0)
REVERT: A  120 GLU cc_start: 0.7601 (mp0) cc_final: 0.7242 (tt0)
REVERT: A  181 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8030 (tp40)
REVERT: B   53 ASN cc_start: 0.7378 (m-40) cc_final: 0.7160 (p0)
REVERT: B   59 ARG cc_start: 0.7392 (mmm160) cc_final: 0.7080 (mmp-170)
REVERT: B   63 ARG cc_start: 0.8400 (ttt180) cc_final: 0.7552 (mmm160)
REVERT: B  118 MET cc_start: 0.9020 (mtp) cc_final: 0.8775 (mtp)
REVERT: B  147 GLU cc_start: 0.7804 (mp0) cc_final: 0.7100 (mp0)
REVERT: B  254 ASN cc_start: 0.8016 (t0) cc_final: 0.7813 (t0)
REVERT: G   47 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7784 (mp0)
REVERT: S  128 MET cc_start: 0.8504 (mmm) cc_final: 0.7688 (mmt)
REVERT: S  146 SER cc_start: 0.9046 (m) cc_final: 0.8666 (t)
REVERT: S  174 GLN cc_start: 0.7706 (mt0) cc_final: 0.7174 (pt0)
  outliers start: 15
  outliers final: 8
  residues processed: 161
  average time/residue: 0.1839
  time to fit residues: 42.2289
Evaluate side-chains
  143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  192 GLN
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue   88 SER
Chi-restraints excluded: chain S residue  142 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0970
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R 151 HIS
A 197 HIS
S  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.160084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.126430 restraints weight = 11288.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.36
r_work: 0.3347 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8826  Z= 0.156
  Angle     :  0.513   6.141  11973  Z= 0.285
  Chirality :  0.042   0.164   1384
  Planarity :  0.004   0.037   1500
  Dihedral  :  5.858  77.366   1205
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.02 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1106
  helix:  2.06 (0.26), residues: 388
  sheet: -0.69 (0.29), residues: 271
  loop : -0.69 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 124 
 HIS   0.004   0.001   HIS A  98 
 PHE   0.021   0.002   PHE R  63 
 TYR   0.024   0.002   TYR R 240 
 ARG   0.006   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 (  466)
  hydrogen bonds       : angle       4.79688 ( 1320)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       0.69222 (    4)
  covalent geometry    : bond        0.00354 ( 8824)
  covalent geometry    : angle       0.51303 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.935 
Fit side-chains
REVERT: R   87 ASN cc_start: 0.8985 (m-40) cc_final: 0.8750 (m110)
REVERT: R  119 PHE cc_start: 0.6973 (t80) cc_final: 0.6058 (t80)
REVERT: R  120 LEU cc_start: 0.8437 (mp) cc_final: 0.8130 (mm)
REVERT: R  140 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7113 (t80)
REVERT: A   26 ASP cc_start: 0.7551 (m-30) cc_final: 0.7342 (m-30)
REVERT: A   35 LYS cc_start: 0.8459 (mttt) cc_final: 0.8123 (mttp)
REVERT: A   73 GLN cc_start: 0.8732 (mt0) cc_final: 0.8426 (mt0)
REVERT: A  120 GLU cc_start: 0.7700 (mp0) cc_final: 0.7310 (tt0)
REVERT: B   59 ARG cc_start: 0.7448 (mmm160) cc_final: 0.7187 (mmp-170)
REVERT: B   63 ARG cc_start: 0.8427 (ttt180) cc_final: 0.7582 (mtp85)
REVERT: B  147 GLU cc_start: 0.7958 (mp0) cc_final: 0.7207 (mp0)
REVERT: G   47 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7820 (mp0)
REVERT: S  146 SER cc_start: 0.9062 (m) cc_final: 0.8698 (t)
REVERT: S  174 GLN cc_start: 0.7728 (mt0) cc_final: 0.7176 (pt0)
  outliers start: 24
  outliers final: 12
  residues processed: 157
  average time/residue: 0.2086
  time to fit residues: 45.3462
Evaluate side-chains
  144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue   91 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0470
   chunk 48 optimal weight:    0.4980
   chunk 94 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
S  39 GLN
S 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.126004 restraints weight = 11204.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.36
r_work: 0.3350 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8826  Z= 0.122
  Angle     :  0.475   6.076  11973  Z= 0.264
  Chirality :  0.040   0.141   1384
  Planarity :  0.003   0.029   1500
  Dihedral  :  5.611  76.447   1205
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.56 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.25), residues: 1106
  helix:  2.28 (0.26), residues: 388
  sheet: -0.71 (0.29), residues: 271
  loop : -0.75 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 356 
 HIS   0.003   0.001   HIS A  98 
 PHE   0.011   0.001   PHE R  76 
 TYR   0.015   0.001   TYR S 103 
 ARG   0.006   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03716 (  466)
  hydrogen bonds       : angle       4.60678 ( 1320)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.59463 (    4)
  covalent geometry    : bond        0.00274 ( 8824)
  covalent geometry    : angle       0.47518 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.040 
Fit side-chains
REVERT: R  119 PHE cc_start: 0.7068 (t80) cc_final: 0.6039 (t80)
REVERT: R  140 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7096 (t80)
REVERT: R  286 LYS cc_start: 0.8934 (tttp) cc_final: 0.8672 (tttm)
REVERT: A   35 LYS cc_start: 0.8436 (mttt) cc_final: 0.8100 (mttp)
REVERT: A   73 GLN cc_start: 0.8715 (mt0) cc_final: 0.8509 (mt0)
REVERT: A  120 GLU cc_start: 0.7709 (mp0) cc_final: 0.7306 (tt0)
REVERT: B   59 ARG cc_start: 0.7386 (mmm160) cc_final: 0.7184 (mmp-170)
REVERT: B   63 ARG cc_start: 0.8425 (ttt180) cc_final: 0.7669 (mtp85)
REVERT: B  237 GLN cc_start: 0.8556 (mt0) cc_final: 0.8282 (mt0)
REVERT: G   47 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7844 (mp0)
REVERT: G   58 GLU cc_start: 0.4801 (mp0) cc_final: 0.3717 (mp0)
REVERT: S  146 SER cc_start: 0.9060 (m) cc_final: 0.8730 (t)
REVERT: S  174 GLN cc_start: 0.7722 (mt0) cc_final: 0.7209 (pt0)
  outliers start: 26
  outliers final: 15
  residues processed: 156
  average time/residue: 0.1993
  time to fit residues: 43.5647
Evaluate side-chains
  150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 97 optimal weight:    0.0970
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 80 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
R 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.160882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.127033 restraints weight = 11289.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.34
r_work: 0.3344 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8826  Z= 0.128
  Angle     :  0.488   5.805  11973  Z= 0.268
  Chirality :  0.041   0.180   1384
  Planarity :  0.003   0.031   1500
  Dihedral  :  5.549  75.820   1205
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.89 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1106
  helix:  2.28 (0.26), residues: 392
  sheet: -0.75 (0.29), residues: 271
  loop : -0.71 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A 119 
 PHE   0.010   0.001   PHE B 216 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.006   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03680 (  466)
  hydrogen bonds       : angle       4.61730 ( 1320)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.58632 (    4)
  covalent geometry    : bond        0.00290 ( 8824)
  covalent geometry    : angle       0.48791 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 1.023 
Fit side-chains
REVERT: R  119 PHE cc_start: 0.7021 (t80) cc_final: 0.5882 (t80)
REVERT: R  140 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7102 (t80)
REVERT: R  212 MET cc_start: 0.6922 (mmm) cc_final: 0.6720 (mmt)
REVERT: R  243 PHE cc_start: 0.7214 (m-80) cc_final: 0.6950 (m-80)
REVERT: R  286 LYS cc_start: 0.9047 (tttp) cc_final: 0.8838 (tttm)
REVERT: A   35 LYS cc_start: 0.8449 (mttt) cc_final: 0.8123 (mttp)
REVERT: A   73 GLN cc_start: 0.8724 (mt0) cc_final: 0.8523 (mt0)
REVERT: A  120 GLU cc_start: 0.7682 (mp0) cc_final: 0.7287 (tt0)
REVERT: B   63 ARG cc_start: 0.8410 (ttt180) cc_final: 0.7621 (mtp85)
REVERT: B  254 ASN cc_start: 0.7938 (t0) cc_final: 0.7641 (t0)
REVERT: G   17 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6949 (mm-30)
REVERT: G   22 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: G   47 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7877 (mp0)
REVERT: G   58 GLU cc_start: 0.4820 (mp0) cc_final: 0.3542 (mp0)
REVERT: S  146 SER cc_start: 0.9075 (m) cc_final: 0.8747 (t)
REVERT: S  174 GLN cc_start: 0.7755 (mt0) cc_final: 0.7266 (pt0)
  outliers start: 26
  outliers final: 18
  residues processed: 152
  average time/residue: 0.2069
  time to fit residues: 44.4090
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   88 SER
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  181 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 92 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.122782 restraints weight = 11331.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.26
r_work: 0.3304 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8826  Z= 0.192
  Angle     :  0.551   7.767  11973  Z= 0.298
  Chirality :  0.042   0.217   1384
  Planarity :  0.004   0.046   1500
  Dihedral  :  5.733  73.993   1205
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.56 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.25), residues: 1106
  helix:  1.99 (0.25), residues: 392
  sheet: -0.82 (0.29), residues: 273
  loop : -0.80 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP S  47 
 HIS   0.005   0.001   HIS A 119 
 PHE   0.015   0.002   PHE A 211 
 TYR   0.015   0.002   TYR B  76 
 ARG   0.006   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04113 (  466)
  hydrogen bonds       : angle       4.85963 ( 1320)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.70186 (    4)
  covalent geometry    : bond        0.00447 ( 8824)
  covalent geometry    : angle       0.55079 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 1.069 
Fit side-chains
REVERT: R   10 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7926 (t)
REVERT: R   87 ASN cc_start: 0.9088 (m-40) cc_final: 0.8813 (m110)
REVERT: R  140 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7287 (t80)
REVERT: R  243 PHE cc_start: 0.7331 (m-80) cc_final: 0.7107 (m-80)
REVERT: A    5 VAL cc_start: 0.8429 (t) cc_final: 0.8049 (p)
REVERT: A   35 LYS cc_start: 0.8594 (mttt) cc_final: 0.8335 (mttp)
REVERT: A  102 ASP cc_start: 0.7889 (m-30) cc_final: 0.7627 (p0)
REVERT: A  120 GLU cc_start: 0.7717 (mp0) cc_final: 0.7355 (tt0)
REVERT: A  135 SER cc_start: 0.8239 (t) cc_final: 0.8001 (p)
REVERT: B  254 ASN cc_start: 0.8165 (t0) cc_final: 0.7934 (t0)
REVERT: G   17 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6952 (mm-30)
REVERT: G   22 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7209 (tm-30)
REVERT: G   42 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8097 (tm-30)
REVERT: G   47 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8041 (mp0)
REVERT: G   58 GLU cc_start: 0.5351 (mp0) cc_final: 0.4993 (mt-10)
REVERT: S  146 SER cc_start: 0.9071 (m) cc_final: 0.8753 (t)
REVERT: S  174 GLN cc_start: 0.7832 (mt0) cc_final: 0.7414 (pt0)
  outliers start: 29
  outliers final: 21
  residues processed: 171
  average time/residue: 0.2056
  time to fit residues: 49.6998
Evaluate side-chains
  167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   10 THR
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  208 HIS
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   88 SER
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  181 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0000
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
R 151 HIS
S 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.158855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.125004 restraints weight = 11341.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.29
r_work: 0.3334 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8826  Z= 0.130
  Angle     :  0.523  10.871  11973  Z= 0.283
  Chirality :  0.041   0.233   1384
  Planarity :  0.003   0.046   1500
  Dihedral  :  5.564  74.574   1205
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.21 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1106
  helix:  2.16 (0.25), residues: 393
  sheet: -0.76 (0.29), residues: 277
  loop : -0.72 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A  98 
 PHE   0.010   0.001   PHE B 216 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.012   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03680 (  466)
  hydrogen bonds       : angle       4.66182 ( 1320)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       0.81397 (    4)
  covalent geometry    : bond        0.00298 ( 8824)
  covalent geometry    : angle       0.52288 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 1.011 
Fit side-chains
REVERT: R   78 THR cc_start: 0.6195 (m) cc_final: 0.5944 (p)
REVERT: R   87 ASN cc_start: 0.9046 (m-40) cc_final: 0.8837 (m110)
REVERT: R  140 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7231 (t80)
REVERT: A   35 LYS cc_start: 0.8594 (mttt) cc_final: 0.8344 (mttp)
REVERT: A  102 ASP cc_start: 0.7844 (m-30) cc_final: 0.7598 (p0)
REVERT: A  120 GLU cc_start: 0.7756 (mp0) cc_final: 0.7379 (tt0)
REVERT: B  254 ASN cc_start: 0.8097 (t0) cc_final: 0.7828 (t0)
REVERT: G   17 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6922 (mm-30)
REVERT: G   22 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7215 (tm-30)
REVERT: G   47 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8021 (mp0)
REVERT: S  146 SER cc_start: 0.9008 (m) cc_final: 0.8707 (t)
REVERT: S  174 GLN cc_start: 0.7852 (mt0) cc_final: 0.7437 (pt0)
  outliers start: 23
  outliers final: 18
  residues processed: 157
  average time/residue: 0.1980
  time to fit residues: 43.5236
Evaluate side-chains
  160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  251 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  181 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 81 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0010
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.6986

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

Flipped N/Q/H residues before XYZ refinement:
R  31 ASN
R 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.159981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.126076 restraints weight = 11420.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.29
r_work: 0.3327 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8826  Z= 0.137
  Angle     :  0.522  11.039  11973  Z= 0.282
  Chirality :  0.041   0.246   1384
  Planarity :  0.003   0.043   1500
  Dihedral  :  5.518  75.453   1205
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.32 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.25), residues: 1106
  helix:  2.20 (0.25), residues: 394
  sheet: -0.77 (0.29), residues: 273
  loop : -0.71 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 119 
 PHE   0.012   0.001   PHE R  63 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.008   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03651 (  466)
  hydrogen bonds       : angle       4.64092 ( 1320)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.62128 (    4)
  covalent geometry    : bond        0.00315 ( 8824)
  covalent geometry    : angle       0.52174 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.900 
Fit side-chains
REVERT: R  140 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7292 (t80)
REVERT: R  243 PHE cc_start: 0.7417 (m-80) cc_final: 0.7111 (m-80)
REVERT: A   29 ARG cc_start: 0.6926 (mtm110) cc_final: 0.6706 (mtm110)
REVERT: A   35 LYS cc_start: 0.8606 (mttt) cc_final: 0.8357 (mttp)
REVERT: A  102 ASP cc_start: 0.7877 (m-30) cc_final: 0.7642 (p0)
REVERT: A  120 GLU cc_start: 0.7723 (mp0) cc_final: 0.7405 (tt0)
REVERT: B  254 ASN cc_start: 0.8149 (t0) cc_final: 0.7870 (t0)
REVERT: G   17 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7013 (mm-30)
REVERT: G   47 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8027 (mp0)
REVERT: S  146 SER cc_start: 0.9013 (m) cc_final: 0.8707 (t)
REVERT: S  174 GLN cc_start: 0.7859 (mt0) cc_final: 0.7448 (pt0)
  outliers start: 24
  outliers final: 20
  residues processed: 154
  average time/residue: 0.1959
  time to fit residues: 42.0890
Evaluate side-chains
  154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  113 ASN
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  251 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  181 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 82 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
R  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.158978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125189 restraints weight = 11392.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.28
r_work: 0.3320 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8826  Z= 0.154
  Angle     :  0.543  10.998  11973  Z= 0.292
  Chirality :  0.042   0.257   1384
  Planarity :  0.003   0.042   1500
  Dihedral  :  5.510  75.465   1205
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.99 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1106
  helix:  2.18 (0.25), residues: 393
  sheet: -0.84 (0.29), residues: 275
  loop : -0.75 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 119 
 PHE   0.014   0.001   PHE B 251 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.007   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  466)
  hydrogen bonds       : angle       4.69567 ( 1320)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       0.75021 (    4)
  covalent geometry    : bond        0.00360 ( 8824)
  covalent geometry    : angle       0.54261 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.906 
Fit side-chains
REVERT: R  140 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7302 (t80)
REVERT: R  243 PHE cc_start: 0.7333 (m-80) cc_final: 0.7064 (m-80)
REVERT: A   35 LYS cc_start: 0.8607 (mttt) cc_final: 0.8361 (mttp)
REVERT: A  120 GLU cc_start: 0.7729 (mp0) cc_final: 0.7405 (tt0)
REVERT: B  254 ASN cc_start: 0.8155 (t0) cc_final: 0.7901 (t0)
REVERT: B  278 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8455 (mp)
REVERT: G   17 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7006 (mm-30)
REVERT: G   47 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8029 (mp0)
REVERT: S  146 SER cc_start: 0.9026 (m) cc_final: 0.8708 (t)
REVERT: S  174 GLN cc_start: 0.7856 (mt0) cc_final: 0.7439 (pt0)
  outliers start: 25
  outliers final: 22
  residues processed: 153
  average time/residue: 0.1996
  time to fit residues: 42.7369
Evaluate side-chains
  157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  251 PHE
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  181 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0570
   chunk 29 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
R  87 ASN
R 208 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.126665 restraints weight = 11256.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.27
r_work: 0.3317 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8826  Z= 0.129
  Angle     :  0.531  10.944  11973  Z= 0.284
  Chirality :  0.041   0.262   1384
  Planarity :  0.003   0.047   1500
  Dihedral  :  5.408  76.329   1205
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.87 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1106
  helix:  2.33 (0.25), residues: 393
  sheet: -0.82 (0.29), residues: 275
  loop : -0.73 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A  98 
 PHE   0.015   0.001   PHE R 119 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.014   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  466)
  hydrogen bonds       : angle       4.57185 ( 1320)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.76322 (    4)
  covalent geometry    : bond        0.00296 ( 8824)
  covalent geometry    : angle       0.53045 (11969)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.911 
Fit side-chains
REVERT: R  140 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7047 (t80)
REVERT: R  243 PHE cc_start: 0.7326 (m-80) cc_final: 0.7065 (m-80)
REVERT: A   35 LYS cc_start: 0.8598 (mttt) cc_final: 0.8331 (mttp)
REVERT: A  120 GLU cc_start: 0.7707 (mp0) cc_final: 0.7381 (tt0)
REVERT: B  254 ASN cc_start: 0.8078 (t0) cc_final: 0.7799 (t0)
REVERT: B  278 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8443 (mp)
REVERT: G   17 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6980 (mm-30)
REVERT: G   47 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7975 (mp0)
REVERT: S  146 SER cc_start: 0.9030 (m) cc_final: 0.8706 (t)
  outliers start: 23
  outliers final: 19
  residues processed: 150
  average time/residue: 0.1928
  time to fit residues: 40.5265
Evaluate side-chains
  153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   19 ILE
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  251 PHE
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue  132 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  181 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 6 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.159621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125924 restraints weight = 11374.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.28
r_work: 0.3301 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8826  Z= 0.141
  Angle     :  0.534  11.079  11973  Z= 0.288
  Chirality :  0.042   0.257   1384
  Planarity :  0.004   0.059   1500
  Dihedral  :  5.431  76.677   1205
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.65 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1106
  helix:  2.30 (0.25), residues: 393
  sheet: -0.84 (0.29), residues: 277
  loop : -0.71 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.009   0.001   HIS R 208 
 PHE   0.032   0.001   PHE R  26 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.013   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  466)
  hydrogen bonds       : angle       4.60757 ( 1320)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       0.71944 (    4)
  covalent geometry    : bond        0.00328 ( 8824)
  covalent geometry    : angle       0.53421 (11969)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5596.60 seconds
wall clock time: 96 minutes 23.70 seconds (5783.70 seconds total)