Starting phenix.real_space_refine
on Fri Aug 22 22:21:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z3m_39747/08_2025/8z3m_39747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z3m_39747/08_2025/8z3m_39747.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z3m_39747/08_2025/8z3m_39747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z3m_39747/08_2025/8z3m_39747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z3m_39747/08_2025/8z3m_39747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z3m_39747/08_2025/8z3m_39747.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    5379      2.51       5
     N    1433      2.21       5
     O    1537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8395
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1783
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 203
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'ARG:plan': 6, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 118
    Chain: "B"
      Number of atoms: 2458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2458
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'ARG:plan': 10, 'GLN:plan1': 4}
          Unresolved non-hydrogen planarities: 96
    Chain: "G"
      Number of atoms: 334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 334
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "S"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1662
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 80
    Chain: "R"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2158
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 279}
          Unresolved non-hydrogen bonds: 207
          Unresolved non-hydrogen angles: 253
          Unresolved non-hydrogen dihedrals: 174
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 12, 'PHE:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 145
  Time building chain proxies: 2.12, per 1000 atoms: 0.25
  Number of scatterers: 8395
  At special positions: 0
  Unit cell: (94.3, 119.72, 127.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1537      8.00
     N    1433      7.00
     C    5379      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " 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: 0.71
  Conformation dependent library (CDL) restraints added in 488.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      38.3% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.586A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 57
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 3.866A  pdb=" N   ASN A 214 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 243
    Processing helix  chain 'A' and resid 259 through 268
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 3.814A  pdb=" N   ALA A 281 " --> pdb=" O   PRO A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 317
      removed outlier: 3.556A  pdb=" N   GLU A 309 " --> pdb=" O   PHE A 305 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 12 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 4.088A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.107A  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 helix  chain 'R' and resid 18 through 48
      removed outlier: 3.553A  pdb=" N   SER R  22 " --> pdb=" O   LEU R  18 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 50 through 79
      removed outlier: 4.095A  pdb=" N   VAL R  54 " --> pdb=" O   ASN R  50 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 94
    Processing helix  chain 'R' and resid 94 through 120
      removed outlier: 4.414A  pdb=" N   ILE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 129
    Processing helix  chain 'R' and resid 130 through 149
      removed outlier: 3.568A  pdb=" N   ASN R 149 " --> pdb=" O   GLU R 145 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 155
      removed outlier: 3.677A  pdb=" N   PHE R 154 " --> pdb=" O   SER R 150 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   HIS R 155 " --> pdb=" O   ALA R 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 150 through 155'
    Processing helix  chain 'R' and resid 175 through 188
    Processing helix  chain 'R' and resid 190 through 210
    Processing helix  chain 'R' and resid 215 through 254
      Proline residue:  R 239  - end of helix
    Processing helix  chain 'R' and resid 258 through 275
      removed outlier: 3.715A  pdb=" N   GLU R 262 " --> pdb=" O   CYS R 258 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   SER R 266 " --> pdb=" O   GLU R 262 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   ALA R 267 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 288
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 300
      removed outlier: 3.623A  pdb=" N   ARG R 294 " --> pdb=" O   ASN R 290 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 189
      removed outlier: 6.740A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   PHE A 197 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   VAL A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 218 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   ILE A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   ASP A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ILE A 219 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 255 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   PHE A 221 " --> pdb=" O   PHE A 255 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ASN A 257 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   VAL A 223 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.581A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.835A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.012A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.535A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.880A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.635A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.754A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.696A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
      removed outlier: 4.205A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1348
        1.29 -     1.42: 2372
        1.42 -     1.55: 4808
        1.55 -     1.69: 0
        1.69 -     1.82: 64
  Bond restraints: 8592
  Sorted by residual:
  bond pdb=" C   PHE R 159 "
       pdb=" O   PHE R 159 "
    ideal  model  delta    sigma   weight residual
    1.236  1.157  0.079 1.14e-02 7.69e+03 4.76e+01
  bond pdb=" CA  ALA R 249 "
       pdb=" C   ALA R 249 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.081 1.26e-02 6.30e+03 4.18e+01
  bond pdb=" CA  TRP R  83 "
       pdb=" C   TRP R  83 "
    ideal  model  delta    sigma   weight residual
    1.524  1.444  0.079 1.30e-02 5.92e+03 3.71e+01
  bond pdb=" N   ILE R  84 "
       pdb=" CA  ILE R  84 "
    ideal  model  delta    sigma   weight residual
    1.459  1.389  0.070 1.25e-02 6.40e+03 3.10e+01
  bond pdb=" CA  TYR R 251 "
       pdb=" C   TYR R 251 "
    ideal  model  delta    sigma   weight residual
    1.523  1.451  0.072 1.30e-02 5.92e+03 3.06e+01
  ... (remaining 8587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 11602
        2.70 -     5.40: 123
        5.40 -     8.09: 9
        8.09 -    10.79: 4
       10.79 -    13.49: 3
  Bond angle restraints: 11741
  Sorted by residual:
  angle pdb=" N   ASN R 164 "
        pdb=" CA  ASN R 164 "
        pdb=" C   ASN R 164 "
      ideal   model   delta    sigma   weight residual
     112.47  124.79  -12.32 1.24e+00 6.50e-01 9.88e+01
  angle pdb=" N   HIS R  79 "
        pdb=" CA  HIS R  79 "
        pdb=" C   HIS R  79 "
      ideal   model   delta    sigma   weight residual
     110.59   99.39   11.20 1.45e+00 4.76e-01 5.97e+01
  angle pdb=" N   TYR R 163 "
        pdb=" CA  TYR R 163 "
        pdb=" C   TYR R 163 "
      ideal   model   delta    sigma   weight residual
     110.68  120.36   -9.68 1.39e+00 5.18e-01 4.85e+01
  angle pdb=" N   ILE R  84 "
        pdb=" CA  ILE R  84 "
        pdb=" C   ILE R  84 "
      ideal   model   delta    sigma   weight residual
     109.34   95.85   13.49 2.08e+00 2.31e-01 4.20e+01
  angle pdb=" N   LYS A 270 "
        pdb=" CA  LYS A 270 "
        pdb=" C   LYS A 270 "
      ideal   model   delta    sigma   weight residual
     113.40  122.74   -9.34 1.47e+00 4.63e-01 4.04e+01
  ... (remaining 11736 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.20: 4464
       15.20 -    30.41: 403
       30.41 -    45.61: 90
       45.61 -    60.82: 12
       60.82 -    76.02: 8
  Dihedral angle restraints: 4977
    sinusoidal: 1644
      harmonic: 3333
  Sorted by residual:
  dihedral pdb=" N   LYS A 270 "
           pdb=" C   LYS A 270 "
           pdb=" CA  LYS A 270 "
           pdb=" CB  LYS A 270 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.69  -15.89     0      2.50e+00 1.60e-01 4.04e+01
  dihedral pdb=" C   LYS A 270 "
           pdb=" N   LYS A 270 "
           pdb=" CA  LYS A 270 "
           pdb=" CB  LYS A 270 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.84   15.24     0      2.50e+00 1.60e-01 3.72e+01
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.33  -38.33     1      1.00e+01 1.00e-02 2.07e+01
  ... (remaining 4974 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1351
       0.151 -    0.302: 12
       0.302 -    0.453: 1
       0.453 -    0.603: 2
       0.603 -    0.754: 1
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" CA  LYS A 270 "
            pdb=" N   LYS A 270 "
            pdb=" C   LYS A 270 "
            pdb=" CB  LYS A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CA  TYR R 163 "
            pdb=" N   TYR R 163 "
            pdb=" C   TYR R 163 "
            pdb=" CB  TYR R 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.38e+00
  chirality pdb=" CA  ASN R 164 "
            pdb=" N   ASN R 164 "
            pdb=" C   ASN R 164 "
            pdb=" CB  ASN R 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.24e+00
  ... (remaining 1364 not shown)

  Planarity restraints: 1496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  78 "    0.013 2.00e-02 2.50e+03   2.76e-02 7.62e+00
        pdb=" C   LEU R  78 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU R  78 "    0.018 2.00e-02 2.50e+03
        pdb=" N   HIS R  79 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 181 "   -0.012 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   MET R 181 "    0.044 2.00e-02 2.50e+03
        pdb=" O   MET R 181 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASN R 182 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL S  64 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.87e+00
        pdb=" C   VAL S  64 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL S  64 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LYS S  65 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1493 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 33
        2.47 -     3.08: 5810
        3.08 -     3.69: 13056
        3.69 -     4.29: 18809
        4.29 -     4.90: 31468
  Nonbonded interactions: 69176
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 263 "
            pdb=" CD1 LEU A 267 "
     model   vdw
     1.867 3.460
  nonbonded pdb=" O   ARG S  67 "
            pdb=" OG1 THR S  84 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   LEU R 272 "
            pdb=" OG1 THR R 275 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.286 3.040
  ... (remaining 69171 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.180
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
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      :  0.006   0.081   8594  Z= 0.374
  Angle     :  0.722  13.488  11745  Z= 0.443
  Chirality :  0.056   0.754   1367
  Planarity :  0.004   0.050   1496
  Dihedral  : 12.812  76.019   2823
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.12 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.26), residues: 1133
  helix:  1.67 (0.27), residues: 392
  sheet:  0.31 (0.30), residues: 269
  loop : -0.78 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  49 
 TYR   0.016   0.001   TYR R 163 
 PHE   0.032   0.002   PHE S  68 
 TRP   0.018   0.001   TRP B 332 
 HIS   0.007   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 8592)
  covalent geometry    : angle       0.72159 (11741)
  SS BOND              : bond        0.00377 (    2)
  SS BOND              : angle       1.00131 (    4)
  hydrogen bonds       : bond        0.13649 (  442)
  hydrogen bonds       : angle       5.92383 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.7706 (t0) cc_final: 0.7403 (t0)
REVERT: A  307 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7871 (tmm-80)
REVERT: B   88 ASN cc_start: 0.7549 (m110) cc_final: 0.7313 (m110)
REVERT: B  100 VAL cc_start: 0.8389 (p) cc_final: 0.8154 (m)
REVERT: B  175 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7586 (mm-40)
REVERT: B  178 THR cc_start: 0.8654 (m) cc_final: 0.8451 (t)
REVERT: B  283 ARG cc_start: 0.8551 (tpt-90) cc_final: 0.8319 (tpp-160)
REVERT: B  289 TYR cc_start: 0.8305 (m-80) cc_final: 0.7413 (m-80)
REVERT: B  291 ASP cc_start: 0.6365 (t70) cc_final: 0.6161 (t0)
REVERT: S   34 MET cc_start: 0.8099 (mmm) cc_final: 0.7722 (mmm)
REVERT: S  128 MET cc_start: 0.8529 (mtm) cc_final: 0.8255 (mtt)
REVERT: S  218 MET cc_start: 0.7909 (mtp) cc_final: 0.7574 (ttm)
REVERT: R   24 TYR cc_start: 0.7973 (m-10) cc_final: 0.7705 (m-10)
REVERT: R  230 ILE cc_start: 0.8289 (mm) cc_final: 0.8067 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 208
  average time/residue: 0.3980
  time to fit residues: 89.1167
Evaluate side-chains
  192 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   84 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.0030
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    0.0970
   overall best weight:    0.3166

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 110 ASN
B 142 HIS
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 269 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.112707 restraints weight = 12766.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.93
r_work: 0.3407 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8594  Z= 0.112
  Angle     :  0.534   6.206  11745  Z= 0.282
  Chirality :  0.042   0.143   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  4.156  23.999   1229
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.20 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.26), residues: 1133
  helix:  2.06 (0.26), residues: 392
  sheet:  0.21 (0.30), residues: 266
  loop : -0.64 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  49 
 TYR   0.018   0.001   TYR S 178 
 PHE   0.019   0.001   PHE S  68 
 TRP   0.014   0.001   TRP R  83 
 HIS   0.004   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8592)
  covalent geometry    : angle       0.53339 (11741)
  SS BOND              : bond        0.00404 (    2)
  SS BOND              : angle       1.16227 (    4)
  hydrogen bonds       : bond        0.03512 (  442)
  hydrogen bonds       : angle       4.73321 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 208
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  227 ASP cc_start: 0.7881 (t0) cc_final: 0.7558 (t0)
REVERT: A  257 ASN cc_start: 0.8153 (t0) cc_final: 0.7924 (t0)
REVERT: A  265 LYS cc_start: 0.8223 (ttmm) cc_final: 0.8021 (ttmt)
REVERT: B   68 ARG cc_start: 0.8035 (tpt-90) cc_final: 0.7822 (tpt90)
REVERT: B  155 ASN cc_start: 0.8158 (t0) cc_final: 0.7934 (t0)
REVERT: B  158 VAL cc_start: 0.8301 (p) cc_final: 0.8058 (t)
REVERT: B  175 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7927 (mm-40)
REVERT: B  285 LEU cc_start: 0.8231 (tt) cc_final: 0.7924 (tp)
REVERT: B  291 ASP cc_start: 0.6505 (t70) cc_final: 0.6290 (t0)
REVERT: B  303 ASP cc_start: 0.7600 (m-30) cc_final: 0.7400 (m-30)
REVERT: S   34 MET cc_start: 0.8157 (mmm) cc_final: 0.7802 (mmm)
REVERT: S  115 THR cc_start: 0.7747 (p) cc_final: 0.7543 (p)
REVERT: S  180 MET cc_start: 0.7992 (ttp) cc_final: 0.7725 (ttp)
REVERT: R   66 TYR cc_start: 0.8255 (t80) cc_final: 0.7810 (t80)
REVERT: R   70 LEU cc_start: 0.8724 (tp) cc_final: 0.8512 (tm)
REVERT: R   76 TYR cc_start: 0.7811 (t80) cc_final: 0.7344 (t80)
REVERT: R  125 PHE cc_start: 0.8620 (m-80) cc_final: 0.8286 (m-80)
REVERT: R  251 TYR cc_start: 0.8452 (t80) cc_final: 0.7920 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 211
  average time/residue: 0.3899
  time to fit residues: 88.9039
Evaluate side-chains
  208 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 200
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain R residue   28 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0970
   chunk 62 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 40 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 244 ASN
A 352 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 121 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.110498 restraints weight = 12676.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.91
r_work: 0.3369 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8594  Z= 0.136
  Angle     :  0.537   6.649  11745  Z= 0.282
  Chirality :  0.042   0.154   1367
  Planarity :  0.004   0.052   1496
  Dihedral  :  4.037  24.269   1227
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.07 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1133
  helix:  2.05 (0.26), residues: 394
  sheet:  0.14 (0.30), residues: 268
  loop : -0.70 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  49 
 TYR   0.017   0.001   TYR R 102 
 PHE   0.023   0.002   PHE R 274 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8592)
  covalent geometry    : angle       0.53684 (11741)
  SS BOND              : bond        0.00449 (    2)
  SS BOND              : angle       0.93931 (    4)
  hydrogen bonds       : bond        0.03580 (  442)
  hydrogen bonds       : angle       4.61593 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 209
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.7865 (t0) cc_final: 0.7567 (t0)
REVERT: A  257 ASN cc_start: 0.8207 (t0) cc_final: 0.7980 (t0)
REVERT: A  265 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7999 (ttmt)
REVERT: B   68 ARG cc_start: 0.8164 (tpt-90) cc_final: 0.7925 (tpt90)
REVERT: B  175 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7963 (mm-40)
REVERT: B  239 ASN cc_start: 0.8428 (m-40) cc_final: 0.8206 (m110)
REVERT: B  285 LEU cc_start: 0.8234 (tt) cc_final: 0.7962 (tp)
REVERT: B  291 ASP cc_start: 0.6564 (t70) cc_final: 0.6263 (t70)
REVERT: S   34 MET cc_start: 0.8237 (mmm) cc_final: 0.7801 (mmm)
REVERT: S  115 THR cc_start: 0.7785 (p) cc_final: 0.7566 (p)
REVERT: S  128 MET cc_start: 0.8728 (mtt) cc_final: 0.8484 (mtt)
REVERT: S  143 VAL cc_start: 0.8671 (p) cc_final: 0.8361 (m)
REVERT: S  160 THR cc_start: 0.8512 (p) cc_final: 0.8076 (p)
REVERT: S  180 MET cc_start: 0.7963 (ttp) cc_final: 0.7753 (ttp)
REVERT: R  124 ARG cc_start: 0.8490 (mtp180) cc_final: 0.8214 (mtp180)
REVERT: R  125 PHE cc_start: 0.8650 (m-80) cc_final: 0.8102 (m-80)
REVERT: R  163 TYR cc_start: 0.8322 (m-10) cc_final: 0.8041 (m-10)
REVERT: R  172 PHE cc_start: 0.8072 (m-80) cc_final: 0.7801 (m-10)
REVERT: R  251 TYR cc_start: 0.8492 (t80) cc_final: 0.7892 (t80)
REVERT: R  264 VAL cc_start: 0.8697 (p) cc_final: 0.8496 (p)
REVERT: R  265 PHE cc_start: 0.8756 (t80) cc_final: 0.8482 (t80)
  outliers start: 23
  outliers final: 14
  residues processed: 215
  average time/residue: 0.3691
  time to fit residues: 86.1458
Evaluate side-chains
  212 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 198
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  202 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0010
   chunk 105 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0970
   chunk 81 optimal weight:    8.9990
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
B  88 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 155 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 295 ASN
B 340 ASN
R 121 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.125047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.110751 restraints weight = 12881.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.92
r_work: 0.3373 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8594  Z= 0.122
  Angle     :  0.516   6.134  11745  Z= 0.271
  Chirality :  0.041   0.137   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  3.908  24.095   1227
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.44 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.25), residues: 1133
  helix:  2.13 (0.26), residues: 395
  sheet:  0.01 (0.30), residues: 268
  loop : -0.62 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  49 
 TYR   0.015   0.001   TYR R 102 
 PHE   0.013   0.001   PHE S  68 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8592)
  covalent geometry    : angle       0.51548 (11741)
  SS BOND              : bond        0.00409 (    2)
  SS BOND              : angle       0.95549 (    4)
  hydrogen bonds       : bond        0.03406 (  442)
  hydrogen bonds       : angle       4.51082 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  227 ASP cc_start: 0.7845 (t0) cc_final: 0.7571 (t0)
REVERT: A  257 ASN cc_start: 0.8202 (t0) cc_final: 0.7998 (t0)
REVERT: A  265 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7874 (ttmt)
REVERT: B  175 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7978 (mm-40)
REVERT: B  285 LEU cc_start: 0.8232 (tt) cc_final: 0.8002 (tp)
REVERT: B  289 TYR cc_start: 0.8302 (m-80) cc_final: 0.7352 (m-80)
REVERT: B  291 ASP cc_start: 0.6591 (t70) cc_final: 0.6256 (t70)
REVERT: S   34 MET cc_start: 0.8227 (mmm) cc_final: 0.7856 (mmm)
REVERT: S  128 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8368 (mtt)
REVERT: S  143 VAL cc_start: 0.8678 (p) cc_final: 0.8379 (m)
REVERT: S  160 THR cc_start: 0.8608 (p) cc_final: 0.8201 (p)
REVERT: S  163 TYR cc_start: 0.8116 (m-80) cc_final: 0.7874 (m-80)
REVERT: S  180 MET cc_start: 0.7970 (ttp) cc_final: 0.7746 (ttp)
REVERT: R   76 TYR cc_start: 0.8055 (t80) cc_final: 0.7197 (t80)
REVERT: R  125 PHE cc_start: 0.8656 (m-80) cc_final: 0.8269 (m-80)
REVERT: R  172 PHE cc_start: 0.7979 (m-80) cc_final: 0.7778 (m-10)
REVERT: R  251 TYR cc_start: 0.8408 (t80) cc_final: 0.7778 (t80)
REVERT: R  264 VAL cc_start: 0.8713 (p) cc_final: 0.8487 (p)
REVERT: R  265 PHE cc_start: 0.8765 (t80) cc_final: 0.8462 (t80)
  outliers start: 25
  outliers final: 15
  residues processed: 208
  average time/residue: 0.3663
  time to fit residues: 82.5786
Evaluate side-chains
  209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   70 LEU
Chi-restraints excluded: chain R residue  202 ARG
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  245 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0170
   chunk 78 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.7222

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
A 322 HIS
B  88 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 239 ASN
B 295 ASN
R 121 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.124139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.109771 restraints weight = 12819.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.93
r_work: 0.3353 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8594  Z= 0.142
  Angle     :  0.525   6.067  11745  Z= 0.277
  Chirality :  0.042   0.133   1367
  Planarity :  0.004   0.051   1496
  Dihedral  :  3.950  24.243   1227
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.81 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.25), residues: 1133
  helix:  2.15 (0.26), residues: 396
  sheet: -0.04 (0.29), residues: 278
  loop : -0.60 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.019   0.001   TYR R 102 
 PHE   0.012   0.001   PHE S  68 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8592)
  covalent geometry    : angle       0.52467 (11741)
  SS BOND              : bond        0.00460 (    2)
  SS BOND              : angle       0.94633 (    4)
  hydrogen bonds       : bond        0.03491 (  442)
  hydrogen bonds       : angle       4.47673 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.7867 (t0) cc_final: 0.7622 (t0)
REVERT: A  265 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7788 (ttmt)
REVERT: B  285 LEU cc_start: 0.8257 (tt) cc_final: 0.8025 (tp)
REVERT: B  289 TYR cc_start: 0.8318 (m-80) cc_final: 0.7399 (m-80)
REVERT: B  291 ASP cc_start: 0.6701 (t70) cc_final: 0.6357 (t70)
REVERT: S   34 MET cc_start: 0.8269 (mmm) cc_final: 0.7926 (mmm)
REVERT: S  143 VAL cc_start: 0.8678 (p) cc_final: 0.8388 (m)
REVERT: S  160 THR cc_start: 0.8592 (p) cc_final: 0.8183 (p)
REVERT: S  180 MET cc_start: 0.8001 (ttp) cc_final: 0.7749 (ttp)
REVERT: S  216 TYR cc_start: 0.8011 (m-80) cc_final: 0.7804 (m-80)
REVERT: R  125 PHE cc_start: 0.8680 (m-80) cc_final: 0.8286 (m-80)
REVERT: R  247 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7534 (mtp180)
REVERT: R  264 VAL cc_start: 0.8697 (p) cc_final: 0.8484 (p)
  outliers start: 28
  outliers final: 14
  residues processed: 198
  average time/residue: 0.3720
  time to fit residues: 79.8353
Evaluate side-chains
  197 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 183
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 94 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0060
   chunk 83 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
B  88 ASN
B 225 HIS
B 340 ASN
R 121 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.123779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.109503 restraints weight = 12682.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.90
r_work: 0.3350 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8594  Z= 0.147
  Angle     :  0.542   7.252  11745  Z= 0.285
  Chirality :  0.042   0.140   1367
  Planarity :  0.004   0.051   1496
  Dihedral  :  3.971  24.210   1227
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.68 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.25), residues: 1133
  helix:  2.17 (0.26), residues: 396
  sheet: -0.05 (0.29), residues: 277
  loop : -0.56 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  49 
 TYR   0.023   0.001   TYR R 102 
 PHE   0.013   0.001   PHE A 328 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8592)
  covalent geometry    : angle       0.54168 (11741)
  SS BOND              : bond        0.00586 (    2)
  SS BOND              : angle       0.94062 (    4)
  hydrogen bonds       : bond        0.03523 (  442)
  hydrogen bonds       : angle       4.49955 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: A  208 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7932 (mmtp)
REVERT: A  227 ASP cc_start: 0.7888 (t0) cc_final: 0.7668 (t0)
REVERT: A  257 ASN cc_start: 0.8194 (t0) cc_final: 0.7974 (t0)
REVERT: A  258 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7974 (mtpm)
REVERT: A  265 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7823 (ttmt)
REVERT: B  291 ASP cc_start: 0.6712 (t70) cc_final: 0.6358 (t70)
REVERT: S   34 MET cc_start: 0.8237 (mmm) cc_final: 0.7917 (mmm)
REVERT: S  128 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8432 (mtt)
REVERT: S  143 VAL cc_start: 0.8694 (p) cc_final: 0.8408 (m)
REVERT: S  160 THR cc_start: 0.8602 (p) cc_final: 0.8179 (p)
REVERT: S  163 TYR cc_start: 0.8047 (m-80) cc_final: 0.7807 (m-80)
REVERT: S  180 MET cc_start: 0.8033 (ttp) cc_final: 0.7765 (ttp)
REVERT: R   76 TYR cc_start: 0.8048 (t80) cc_final: 0.7291 (t80)
REVERT: R  125 PHE cc_start: 0.8693 (m-80) cc_final: 0.8299 (m-80)
REVERT: R  264 VAL cc_start: 0.8710 (p) cc_final: 0.8495 (p)
  outliers start: 29
  outliers final: 16
  residues processed: 197
  average time/residue: 0.3637
  time to fit residues: 77.8472
Evaluate side-chains
  203 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0370
   chunk 68 optimal weight:   10.0000
   chunk 102 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
B 340 ASN
R 121 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.124255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.109957 restraints weight = 12839.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.93
r_work: 0.3362 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8594  Z= 0.127
  Angle     :  0.531   6.505  11745  Z= 0.280
  Chirality :  0.042   0.142   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  3.916  24.184   1227
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.17 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.26), residues: 1133
  helix:  2.23 (0.26), residues: 395
  sheet:  0.00 (0.30), residues: 280
  loop : -0.50 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.023   0.001   TYR R 102 
 PHE   0.033   0.001   PHE R 265 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.008   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8592)
  covalent geometry    : angle       0.53069 (11741)
  SS BOND              : bond        0.00506 (    2)
  SS BOND              : angle       0.90813 (    4)
  hydrogen bonds       : bond        0.03390 (  442)
  hydrogen bonds       : angle       4.43954 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7734 (mt-10)
REVERT: A  227 ASP cc_start: 0.7889 (t0) cc_final: 0.7655 (t0)
REVERT: A  257 ASN cc_start: 0.8161 (t0) cc_final: 0.7862 (t0)
REVERT: B  291 ASP cc_start: 0.6671 (t70) cc_final: 0.6302 (t70)
REVERT: S   34 MET cc_start: 0.8201 (mmm) cc_final: 0.7893 (mmm)
REVERT: S   83 MET cc_start: 0.6828 (mmm) cc_final: 0.6330 (mmm)
REVERT: S  128 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8430 (mtt)
REVERT: S  143 VAL cc_start: 0.8698 (p) cc_final: 0.8415 (m)
REVERT: S  160 THR cc_start: 0.8610 (p) cc_final: 0.8148 (p)
REVERT: S  163 TYR cc_start: 0.8023 (m-80) cc_final: 0.7807 (m-80)
REVERT: S  180 MET cc_start: 0.7981 (ttp) cc_final: 0.7700 (ttp)
REVERT: R   76 TYR cc_start: 0.8032 (t80) cc_final: 0.7324 (t80)
REVERT: R  125 PHE cc_start: 0.8672 (m-80) cc_final: 0.8287 (m-80)
REVERT: R  264 VAL cc_start: 0.8683 (p) cc_final: 0.8450 (p)
  outliers start: 25
  outliers final: 15
  residues processed: 191
  average time/residue: 0.4001
  time to fit residues: 82.7355
Evaluate side-chains
  200 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 98 optimal weight:    0.0670
   chunk 27 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0670
   chunk 52 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
A 357 ASN
R 121 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.124248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.109986 restraints weight = 12584.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.91
r_work: 0.3365 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8594  Z= 0.129
  Angle     :  0.537   8.004  11745  Z= 0.282
  Chirality :  0.042   0.156   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  3.909  24.418   1227
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.67 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1133
  helix:  2.22 (0.26), residues: 395
  sheet:  0.03 (0.31), residues: 256
  loop : -0.47 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.028   0.001   TYR R 102 
 PHE   0.025   0.002   PHE R 265 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.007   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8592)
  covalent geometry    : angle       0.53689 (11741)
  SS BOND              : bond        0.00472 (    2)
  SS BOND              : angle       0.90793 (    4)
  hydrogen bonds       : bond        0.03370 (  442)
  hydrogen bonds       : angle       4.43573 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7719 (mt-10)
REVERT: A  227 ASP cc_start: 0.7862 (t0) cc_final: 0.7641 (t0)
REVERT: A  257 ASN cc_start: 0.8187 (t0) cc_final: 0.7881 (t0)
REVERT: B  291 ASP cc_start: 0.6693 (t70) cc_final: 0.6305 (t70)
REVERT: S   34 MET cc_start: 0.8192 (mmm) cc_final: 0.7889 (mmm)
REVERT: S  128 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8450 (mtt)
REVERT: S  143 VAL cc_start: 0.8678 (p) cc_final: 0.8397 (m)
REVERT: S  160 THR cc_start: 0.8638 (p) cc_final: 0.8170 (p)
REVERT: S  163 TYR cc_start: 0.8020 (m-80) cc_final: 0.7795 (m-80)
REVERT: S  180 MET cc_start: 0.7995 (ttp) cc_final: 0.7715 (ttp)
REVERT: R   76 TYR cc_start: 0.8009 (t80) cc_final: 0.7325 (t80)
REVERT: R  125 PHE cc_start: 0.8671 (m-80) cc_final: 0.8259 (m-80)
REVERT: R  264 VAL cc_start: 0.8656 (p) cc_final: 0.8424 (p)
  outliers start: 20
  outliers final: 15
  residues processed: 195
  average time/residue: 0.3577
  time to fit residues: 76.0053
Evaluate side-chains
  199 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 106 optimal weight:    0.3980
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.124311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.110037 restraints weight = 12776.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.92
r_work: 0.3362 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8594  Z= 0.138
  Angle     :  0.553   9.093  11745  Z= 0.288
  Chirality :  0.042   0.139   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  3.935  24.337   1227
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.42 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.26), residues: 1133
  helix:  2.19 (0.26), residues: 395
  sheet: -0.07 (0.29), residues: 285
  loop : -0.40 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  49 
 TYR   0.032   0.001   TYR R 102 
 PHE   0.023   0.002   PHE R 265 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8592)
  covalent geometry    : angle       0.55270 (11741)
  SS BOND              : bond        0.00482 (    2)
  SS BOND              : angle       0.91768 (    4)
  hydrogen bonds       : bond        0.03427 (  442)
  hydrogen bonds       : angle       4.48064 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7740 (mt-10)
REVERT: A  227 ASP cc_start: 0.7870 (t0) cc_final: 0.7649 (t0)
REVERT: A  257 ASN cc_start: 0.8201 (t0) cc_final: 0.7879 (t0)
REVERT: B  291 ASP cc_start: 0.6702 (t70) cc_final: 0.6313 (t70)
REVERT: S    5 VAL cc_start: 0.7905 (t) cc_final: 0.7658 (p)
REVERT: S   34 MET cc_start: 0.8184 (mmm) cc_final: 0.7890 (mmm)
REVERT: S  128 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8464 (mtt)
REVERT: S  143 VAL cc_start: 0.8687 (p) cc_final: 0.8389 (m)
REVERT: S  160 THR cc_start: 0.8618 (p) cc_final: 0.8199 (p)
REVERT: S  163 TYR cc_start: 0.8023 (m-80) cc_final: 0.7793 (m-80)
REVERT: S  180 MET cc_start: 0.8010 (ttp) cc_final: 0.7749 (ttp)
REVERT: R   76 TYR cc_start: 0.7972 (t80) cc_final: 0.7397 (t80)
REVERT: R  125 PHE cc_start: 0.8670 (m-80) cc_final: 0.8259 (m-80)
REVERT: R  264 VAL cc_start: 0.8654 (p) cc_final: 0.8420 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 192
  average time/residue: 0.3713
  time to fit residues: 77.3556
Evaluate side-chains
  201 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.123461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.109251 restraints weight = 12672.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.91
r_work: 0.3350 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8594  Z= 0.162
  Angle     :  0.567   8.461  11745  Z= 0.297
  Chirality :  0.043   0.180   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  4.032  24.413   1227
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.42 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.25), residues: 1133
  helix:  2.05 (0.26), residues: 398
  sheet: -0.03 (0.30), residues: 266
  loop : -0.41 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  49 
 TYR   0.034   0.002   TYR R 102 
 PHE   0.025   0.002   PHE A 328 
 TRP   0.010   0.001   TRP A 209 
 HIS   0.006   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8592)
  covalent geometry    : angle       0.56704 (11741)
  SS BOND              : bond        0.00496 (    2)
  SS BOND              : angle       0.97919 (    4)
  hydrogen bonds       : bond        0.03600 (  442)
  hydrogen bonds       : angle       4.58151 ( 1245)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7655 (mt-10)
REVERT: A  227 ASP cc_start: 0.7847 (t0) cc_final: 0.7630 (t0)
REVERT: A  257 ASN cc_start: 0.8194 (t0) cc_final: 0.7934 (t0)
REVERT: B  291 ASP cc_start: 0.6752 (t70) cc_final: 0.6366 (t70)
REVERT: S   34 MET cc_start: 0.8213 (mmm) cc_final: 0.7848 (mmm)
REVERT: S  128 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8466 (mtt)
REVERT: S  143 VAL cc_start: 0.8683 (p) cc_final: 0.8402 (m)
REVERT: S  160 THR cc_start: 0.8610 (p) cc_final: 0.8200 (p)
REVERT: S  163 TYR cc_start: 0.8026 (m-80) cc_final: 0.7775 (m-80)
REVERT: S  180 MET cc_start: 0.8021 (ttp) cc_final: 0.7749 (ttp)
REVERT: R   76 TYR cc_start: 0.7989 (t80) cc_final: 0.7522 (t80)
REVERT: R  125 PHE cc_start: 0.8685 (m-80) cc_final: 0.8264 (m-80)
REVERT: R  264 VAL cc_start: 0.8661 (p) cc_final: 0.8425 (p)
  outliers start: 18
  outliers final: 14
  residues processed: 200
  average time/residue: 0.3462
  time to fit residues: 75.3879
Evaluate side-chains
  207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 192
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0770
   chunk 88 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8138

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.123390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.109202 restraints weight = 12725.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.90
r_work: 0.3352 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8594  Z= 0.157
  Angle     :  0.568   8.995  11745  Z= 0.298
  Chirality :  0.043   0.137   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  4.043  24.352   1227
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 22.67 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.25), residues: 1133
  helix:  2.07 (0.26), residues: 397
  sheet: -0.09 (0.29), residues: 279
  loop : -0.36 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  49 
 TYR   0.037   0.001   TYR R 102 
 PHE   0.022   0.002   PHE R 265 
 TRP   0.010   0.001   TRP A 209 
 HIS   0.005   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8592)
  covalent geometry    : angle       0.56769 (11741)
  SS BOND              : bond        0.00497 (    2)
  SS BOND              : angle       1.19754 (    4)
  hydrogen bonds       : bond        0.03575 (  442)
  hydrogen bonds       : angle       4.56007 ( 1245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2829.68 seconds
wall clock time: 48 minutes 54.12 seconds (2934.12 seconds total)