Starting phenix.real_space_refine
on Sun Jun  8 05:59:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ije_60629/06_2025/9ije_60629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ije_60629/06_2025/9ije_60629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ije_60629/06_2025/9ije_60629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ije_60629/06_2025/9ije_60629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ije_60629/06_2025/9ije_60629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ije_60629/06_2025/9ije_60629.cif"
  }
  resolution = 2.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.113
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      61      5.16       5
     C    5931      2.51       5
     N    1617      2.21       5
     O    1731      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9340
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 2539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2539
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 61
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 67
    Chain: "N"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 950
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1754
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 1886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1886
          Classifications: {'peptide': 252}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 14, 'TRANS': 237}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1804
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 6, 'TRANS': 217}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "C"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 393
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 14
          Unusual residues: {'ALE': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 5.83, per 1000 atoms: 0.62
  Number of scatterers: 9340
  At special positions: 0
  Unit cell: (89.8475, 123.405, 126.652, 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      61     16.00
     O    1731      8.00
     N    1617      7.00
     C    5931      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 159 " - pdb=" SG  CYS D 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.59
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 16 sheets defined
      36.1% alpha, 24.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 4.110A  pdb=" N   THR D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 43 through 65
    Processing helix  chain 'R' and resid 71 through 90
      removed outlier: 4.179A  pdb=" N   PHE R  75 " --> pdb=" O   MET R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 90 through 101
    Processing helix  chain 'R' and resid 106 through 141
      removed outlier: 3.508A  pdb=" N   GLU R 111 " --> pdb=" O   ALA R 107 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 144 through 149
    Processing helix  chain 'R' and resid 150 through 175
      Proline residue:  R 172  - end of helix
    Processing helix  chain 'R' and resid 203 through 213
    Processing helix  chain 'R' and resid 213 through 243
    Processing helix  chain 'R' and resid 290 through 317
      removed outlier: 3.754A  pdb=" N   PHE R 301 " --> pdb=" O   ILE R 297 " (cutoff:3.500A)
      Proline residue:  R 307  - end of helix
    Processing helix  chain 'R' and resid 319 through 323
    Processing helix  chain 'R' and resid 324 through 337
    Processing helix  chain 'R' and resid 337 through 347
      Proline residue:  R 343  - end of helix
    Processing helix  chain 'R' and resid 349 through 362
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.703A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 217
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.756A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.285A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.508A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 340
      removed outlier: 3.653A  pdb=" N   PHE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
    Processing helix  chain 'C' and resid 11 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.581A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.801A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.803A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.640A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.676A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.755A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.675A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12
      removed outlier: 6.861A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12
      removed outlier: 4.338A  pdb=" N   PHE D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 148
      removed outlier: 6.483A  pdb=" N   VAL D 147 " --> pdb=" O   GLU D 246 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'D' and resid 194 through 195
      removed outlier: 6.544A  pdb=" N   TRP D 176 " --> pdb=" O   LEU D 188 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   TYR D 190 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LEU D 174 " --> pdb=" O   TYR D 190 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 210 through 212
      removed outlier: 9.436A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1344 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 2.99 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1496
        1.30 -     1.43: 2563
        1.43 -     1.56: 5387
        1.56 -     1.69: 2
        1.69 -     1.82: 87
  Bond restraints: 9535
  Sorted by residual:
  bond pdb=" C3  ALE R 401 "
       pdb=" O1  ALE R 401 "
    ideal  model  delta    sigma   weight residual
    1.353  1.505 -0.152 2.00e-02 2.50e+03 5.81e+01
  bond pdb=" C   ASP R 117 "
       pdb=" O   ASP R 117 "
    ideal  model  delta    sigma   weight residual
    1.236  1.172  0.065 1.15e-02 7.56e+03 3.17e+01
  bond pdb=" CA  SER B 227 "
       pdb=" CB  SER B 227 "
    ideal  model  delta    sigma   weight residual
    1.535  1.480  0.055 1.32e-02 5.74e+03 1.71e+01
  bond pdb=" CA  SER B 245 "
       pdb=" CB  SER B 245 "
    ideal  model  delta    sigma   weight residual
    1.534  1.479  0.056 1.45e-02 4.76e+03 1.48e+01
  bond pdb=" C4  ALE R 401 "
       pdb=" O2  ALE R 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.416 -0.065 2.00e-02 2.50e+03 1.06e+01
  ... (remaining 9530 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 12590
        1.93 -     3.85: 316
        3.85 -     5.78: 40
        5.78 -     7.70: 12
        7.70 -     9.63: 2
  Bond angle restraints: 12960
  Sorted by residual:
  angle pdb=" CA  ASP R 117 "
        pdb=" CB  ASP R 117 "
        pdb=" CG  ASP R 117 "
      ideal   model   delta    sigma   weight residual
     112.60  119.24   -6.64 1.00e+00 1.00e+00 4.41e+01
  angle pdb=" CA  GLY R 318 "
        pdb=" C   GLY R 318 "
        pdb=" O   GLY R 318 "
      ideal   model   delta    sigma   weight residual
     122.23  118.03    4.20 6.90e-01 2.10e+00 3.71e+01
  angle pdb=" CA  GLY A 345 "
        pdb=" C   GLY A 345 "
        pdb=" N   ARG A 346 "
      ideal   model   delta    sigma   weight residual
     118.46  124.96   -6.50 1.15e+00 7.56e-01 3.19e+01
  angle pdb=" C   THR C  52 "
        pdb=" CA  THR C  52 "
        pdb=" CB  THR C  52 "
      ideal   model   delta    sigma   weight residual
     110.17  104.68    5.49 9.90e-01 1.02e+00 3.07e+01
  angle pdb=" CA  ASP B 247 "
        pdb=" CB  ASP B 247 "
        pdb=" CG  ASP B 247 "
      ideal   model   delta    sigma   weight residual
     112.60  117.90   -5.30 1.00e+00 1.00e+00 2.81e+01
  ... (remaining 12955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 4962
       17.71 -    35.42: 496
       35.42 -    53.13: 135
       53.13 -    70.83: 34
       70.83 -    88.54: 8
  Dihedral angle restraints: 5635
    sinusoidal: 2095
      harmonic: 3540
  Sorted by residual:
  dihedral pdb=" CA  GLU D 234 "
           pdb=" C   GLU D 234 "
           pdb=" N   TYR D 235 "
           pdb=" CA  TYR D 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.56  -23.44     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  LEU A 281 "
           pdb=" C   LEU A 281 "
           pdb=" N   ASN A 282 "
           pdb=" CA  ASN A 282 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.70  -23.30     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -118.58   32.58     1      1.00e+01 1.00e-02 1.51e+01
  ... (remaining 5632 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 1443
       0.114 -    0.228: 41
       0.228 -    0.342: 3
       0.342 -    0.456: 0
       0.456 -    0.570: 1
  Chirality restraints: 1488
  Sorted by residual:
  chirality pdb=" C7  ALE R 401 "
            pdb=" C1  ALE R 401 "
            pdb=" C8  ALE R 401 "
            pdb=" O3  ALE R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.28    2.85   -0.57 2.00e-01 2.50e+01 8.13e+00
  chirality pdb=" CA  THR C  52 "
            pdb=" N   THR C  52 "
            pdb=" C   THR C  52 "
            pdb=" CB  THR C  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.79   -0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  VAL R 323 "
            pdb=" N   VAL R 323 "
            pdb=" C   VAL R 323 "
            pdb=" CB  VAL R 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1485 not shown)

  Planarity restraints: 1648
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  74 "   -0.064 5.00e-02 4.00e+02   9.47e-02 1.44e+01
        pdb=" N   PRO D  75 "    0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO D  75 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO D  75 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  92 "    0.056 5.00e-02 4.00e+02   8.49e-02 1.15e+01
        pdb=" N   PRO R  93 "   -0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO R  93 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R  93 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 244 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   GLY B 244 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLY B 244 "    0.018 2.00e-02 2.50e+03
        pdb=" N   SER B 245 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1645 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1729
        2.77 -     3.30: 8515
        3.30 -     3.84: 15752
        3.84 -     4.37: 18931
        4.37 -     4.90: 33135
  Nonbonded interactions: 78062
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" N   GLU A 304 "
            pdb=" OE1 GLU A 304 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   TYR R 204 "
            pdb=" OG  SER R 208 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" NZ  LYS D 163 "
            pdb=" OE2 GLU D 234 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OG  SER D  52 "
            pdb=" OE2 GLU A  21 "
     model   vdw
     2.305 3.040
  ... (remaining 78057 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:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.700
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
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      :  0.005   0.152   9539  Z= 0.300
  Angle     :  0.695   9.626  12968  Z= 0.447
  Chirality :  0.050   0.570   1488
  Planarity :  0.006   0.105   1648
  Dihedral  : 15.986  88.544   3345
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.61 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.24), residues: 1207
  helix:  1.79 (0.25), residues: 393
  sheet:  0.85 (0.28), residues: 301
  loop : -0.12 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 113 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.012   0.001   PHE R 309 
 TYR   0.025   0.002   TYR D 235 
 ARG   0.015   0.001   ARG D 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17047 (  481)
  hydrogen bonds       : angle       6.49754 ( 1344)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       1.03436 (    8)
  covalent geometry    : bond        0.00480 ( 9535)
  covalent geometry    : angle       0.69508 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 1.184 
Fit side-chains
REVERT: B  189 SER cc_start: 0.9143 (t) cc_final: 0.8916 (p)
REVERT: N   83 MET cc_start: 0.8606 (mtp) cc_final: 0.8304 (mtm)
REVERT: D   63 THR cc_start: 0.8665 (p) cc_final: 0.8401 (t)
REVERT: D  160 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6949 (ttp80)
REVERT: D  186 GLN cc_start: 0.8194 (pt0) cc_final: 0.7839 (pt0)
REVERT: D  234 GLU cc_start: 0.8051 (mp0) cc_final: 0.7661 (mp0)
REVERT: R  155 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6157 (mmm160)
REVERT: R  333 TRP cc_start: 0.8128 (m100) cc_final: 0.7204 (m-10)
REVERT: R  358 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6412 (ttp-110)
REVERT: A  254 ASN cc_start: 0.8682 (t0) cc_final: 0.8429 (m-40)
REVERT: C   42 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.5931 (mp0)
  outliers start: 21
  outliers final: 12
  residues processed: 165
  average time/residue: 1.8537
  time to fit residues: 324.1964
Evaluate side-chains
  147 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  223 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   57 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0010
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 109 optimal weight:   20.0000
   overall best weight:    0.9390

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
N 120 GLN
D   3 GLN
D  77 ASN
D 142 GLN
D 179 GLN
D 183 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
A 239 ASN
A 380 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.126828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.097733 restraints weight = 11774.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.27
r_work: 0.3098 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9539  Z= 0.118
  Angle     :  0.513   6.798  12968  Z= 0.276
  Chirality :  0.042   0.198   1488
  Planarity :  0.005   0.067   1648
  Dihedral  :  5.786  54.283   1360
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.22 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.24), residues: 1207
  helix:  2.45 (0.25), residues: 392
  sheet:  0.89 (0.28), residues: 300
  loop :  0.02 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.017   0.001   TYR D 235 
 ARG   0.005   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  481)
  hydrogen bonds       : angle       4.58603 ( 1344)
  SS BOND              : bond        0.00254 (    4)
  SS BOND              : angle       0.67639 (    8)
  covalent geometry    : bond        0.00262 ( 9535)
  covalent geometry    : angle       0.51330 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5979 (tp30)
REVERT: B  189 SER cc_start: 0.9072 (t) cc_final: 0.8613 (p)
REVERT: B  217 MET cc_start: 0.8047 (pp-130) cc_final: 0.7754 (pp-130)
REVERT: B  314 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8165 (ttt180)
REVERT: N    1 GLN cc_start: 0.7430 (pm20) cc_final: 0.7217 (pm20)
REVERT: N   83 MET cc_start: 0.8775 (mtp) cc_final: 0.8352 (mtm)
REVERT: D   18 ARG cc_start: 0.7062 (tpp-160) cc_final: 0.6665 (tpp-160)
REVERT: D  180 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7433 (mtt180)
REVERT: D  186 GLN cc_start: 0.8367 (pt0) cc_final: 0.8148 (pt0)
REVERT: D  234 GLU cc_start: 0.8177 (mp0) cc_final: 0.7851 (mp0)
REVERT: D  235 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6564 (m-80)
REVERT: R  148 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7949 (mp)
REVERT: R  333 TRP cc_start: 0.8134 (m100) cc_final: 0.6982 (m-10)
REVERT: C   21 MET cc_start: 0.7107 (tpp) cc_final: 0.6751 (tpt)
REVERT: C   42 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6878 (mp0)
REVERT: C   58 GLU cc_start: 0.8113 (pt0) cc_final: 0.7586 (pm20)
  outliers start: 31
  outliers final: 11
  residues processed: 163
  average time/residue: 1.3398
  time to fit residues: 231.9716
Evaluate side-chains
  150 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue  148 LEU
Chi-restraints excluded: chain R residue  207 LEU
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   42 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 85 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 117 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 293 ASN
N 120 GLN
D   3 GLN
D  77 ASN
D 183 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.126087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.097431 restraints weight = 11917.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.19
r_work: 0.3084 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9539  Z= 0.125
  Angle     :  0.513   6.545  12968  Z= 0.274
  Chirality :  0.042   0.205   1488
  Planarity :  0.005   0.061   1648
  Dihedral  :  5.542  55.479   1345
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.25 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.24), residues: 1207
  helix:  2.53 (0.25), residues: 388
  sheet:  0.82 (0.28), residues: 298
  loop :  0.00 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.018   0.001   TYR D 235 
 ARG   0.006   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  481)
  hydrogen bonds       : angle       4.43217 ( 1344)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       0.73408 (    8)
  covalent geometry    : bond        0.00286 ( 9535)
  covalent geometry    : angle       0.51299 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
REVERT: B  189 SER cc_start: 0.8978 (t) cc_final: 0.8436 (p)
REVERT: B  217 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7522 (pp-130)
REVERT: B  314 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8106 (ttt180)
REVERT: N    1 GLN cc_start: 0.7471 (pm20) cc_final: 0.7081 (pm20)
REVERT: N   83 MET cc_start: 0.8559 (mtp) cc_final: 0.8129 (mtm)
REVERT: D  160 ARG cc_start: 0.7441 (mtp-110) cc_final: 0.6921 (ttp-110)
REVERT: D  234 GLU cc_start: 0.8137 (mp0) cc_final: 0.7728 (mp0)
REVERT: D  235 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6086 (t80)
REVERT: R  298 MET cc_start: 0.7232 (mmm) cc_final: 0.7003 (mmp)
REVERT: R  333 TRP cc_start: 0.8007 (m100) cc_final: 0.6812 (m-10)
REVERT: C   21 MET cc_start: 0.7015 (tpp) cc_final: 0.6604 (tpt)
REVERT: C   42 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6760 (mp0)
  outliers start: 32
  outliers final: 16
  residues processed: 153
  average time/residue: 1.3627
  time to fit residues: 221.5744
Evaluate side-chains
  149 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  223 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   42 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 112 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
N 120 GLN
D   3 GLN
D  77 ASN
D 183 GLN
D 186 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.123505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.094882 restraints weight = 11857.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.16
r_work: 0.3049 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9539  Z= 0.176
  Angle     :  0.563   7.043  12968  Z= 0.301
  Chirality :  0.044   0.225   1488
  Planarity :  0.005   0.058   1648
  Dihedral  :  5.657  53.897   1345
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.02 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.24), residues: 1207
  helix:  2.34 (0.26), residues: 382
  sheet:  0.72 (0.28), residues: 300
  loop : -0.12 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.014   0.002   PHE R 309 
 TYR   0.018   0.002   TYR D 235 
 ARG   0.006   0.001   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04685 (  481)
  hydrogen bonds       : angle       4.61289 ( 1344)
  SS BOND              : bond        0.00355 (    4)
  SS BOND              : angle       0.94644 (    8)
  covalent geometry    : bond        0.00414 ( 9535)
  covalent geometry    : angle       0.56219 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  189 SER cc_start: 0.8985 (t) cc_final: 0.8410 (p)
REVERT: B  217 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7562 (pp-130)
REVERT: B  234 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.6692 (t80)
REVERT: B  314 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8127 (ttt180)
REVERT: N    1 GLN cc_start: 0.7451 (pm20) cc_final: 0.7120 (pm20)
REVERT: N   83 MET cc_start: 0.8515 (mtp) cc_final: 0.8240 (mtm)
REVERT: D  160 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6935 (ttp-110)
REVERT: D  235 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6081 (t80)
REVERT: R  333 TRP cc_start: 0.8090 (m100) cc_final: 0.6863 (m-10)
REVERT: C   21 MET cc_start: 0.7105 (tpp) cc_final: 0.6665 (tpt)
  outliers start: 35
  outliers final: 21
  residues processed: 161
  average time/residue: 1.3657
  time to fit residues: 233.8035
Evaluate side-chains
  159 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  223 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   42 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0040
   overall best weight:    1.5398

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 293 ASN
N 120 GLN
D   3 GLN
D 183 GLN
D 186 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.095998 restraints weight = 11905.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.16
r_work: 0.3064 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9539  Z= 0.147
  Angle     :  0.532   6.679  12968  Z= 0.284
  Chirality :  0.042   0.213   1488
  Planarity :  0.005   0.062   1648
  Dihedral  :  5.494  53.661   1345
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 19.71 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.24), residues: 1207
  helix:  2.41 (0.26), residues: 388
  sheet:  0.72 (0.28), residues: 300
  loop : -0.12 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.018   0.002   TYR D 235 
 ARG   0.008   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04252 (  481)
  hydrogen bonds       : angle       4.45745 ( 1344)
  SS BOND              : bond        0.00340 (    4)
  SS BOND              : angle       0.85422 (    8)
  covalent geometry    : bond        0.00343 ( 9535)
  covalent geometry    : angle       0.53164 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 137
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  189 SER cc_start: 0.8991 (t) cc_final: 0.8389 (p)
REVERT: B  217 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7526 (pp-130)
REVERT: B  234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.6812 (t80)
REVERT: B  314 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8094 (ttt180)
REVERT: N    1 GLN cc_start: 0.7443 (pm20) cc_final: 0.7060 (pm20)
REVERT: N   80 TYR cc_start: 0.8646 (m-80) cc_final: 0.8342 (m-80)
REVERT: N   83 MET cc_start: 0.8515 (mtp) cc_final: 0.8252 (mtm)
REVERT: D  160 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6929 (ttp-110)
REVERT: D  234 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7896 (mp0)
REVERT: D  235 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.6098 (t80)
REVERT: R  151 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7052 (ttmm)
REVERT: R  333 TRP cc_start: 0.8080 (m100) cc_final: 0.6905 (m-10)
REVERT: C   21 MET cc_start: 0.7108 (tpp) cc_final: 0.6665 (tpt)
REVERT: C   46 LYS cc_start: 0.8224 (tppp) cc_final: 0.7416 (ptpp)
  outliers start: 40
  outliers final: 25
  residues processed: 168
  average time/residue: 1.3119
  time to fit residues: 234.4246
Evaluate side-chains
  166 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  151 LYS
Chi-restraints excluded: chain R residue  223 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 108 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 293 ASN
N 120 GLN
D   3 GLN
D  77 ASN
D 169 ASN
D 183 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.096177 restraints weight = 11799.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.17
r_work: 0.3067 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9539  Z= 0.136
  Angle     :  0.525   6.478  12968  Z= 0.280
  Chirality :  0.042   0.199   1488
  Planarity :  0.005   0.063   1648
  Dihedral  :  5.429  53.347   1345
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.33 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.24), residues: 1207
  helix:  2.48 (0.26), residues: 388
  sheet:  0.76 (0.28), residues: 300
  loop : -0.11 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.016   0.002   TYR D 235 
 ARG   0.009   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  481)
  hydrogen bonds       : angle       4.42146 ( 1344)
  SS BOND              : bond        0.00321 (    4)
  SS BOND              : angle       0.88317 (    8)
  covalent geometry    : bond        0.00316 ( 9535)
  covalent geometry    : angle       0.52476 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 141
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  189 SER cc_start: 0.8985 (t) cc_final: 0.8369 (p)
REVERT: B  217 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7536 (pp-130)
REVERT: B  234 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.6737 (t80)
REVERT: B  314 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8365 (ttt180)
REVERT: N    1 GLN cc_start: 0.7511 (pm20) cc_final: 0.7126 (pm20)
REVERT: N   83 MET cc_start: 0.8491 (mtp) cc_final: 0.8202 (mtm)
REVERT: D  160 ARG cc_start: 0.7311 (mtp-110) cc_final: 0.6899 (ttp-110)
REVERT: D  235 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.6001 (t80)
REVERT: R  151 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7041 (ttmm)
REVERT: R  333 TRP cc_start: 0.8059 (m100) cc_final: 0.6863 (m-10)
REVERT: C   21 MET cc_start: 0.7128 (tpp) cc_final: 0.6645 (tpt)
REVERT: C   46 LYS cc_start: 0.8248 (tppp) cc_final: 0.7420 (ptpp)
  outliers start: 38
  outliers final: 30
  residues processed: 165
  average time/residue: 1.2796
  time to fit residues: 225.1322
Evaluate side-chains
  172 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  151 LYS
Chi-restraints excluded: chain R residue  223 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  297 ILE
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 8 optimal weight:    0.0070
   chunk 32 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 57 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 120 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
N 120 GLN
D   3 GLN
D 183 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.098200 restraints weight = 12031.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.27
r_work: 0.3107 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9539  Z= 0.099
  Angle     :  0.485   6.641  12968  Z= 0.258
  Chirality :  0.040   0.176   1488
  Planarity :  0.005   0.061   1648
  Dihedral  :  4.993  52.738   1345
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.74 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.24), residues: 1207
  helix:  2.74 (0.26), residues: 388
  sheet:  0.81 (0.28), residues: 301
  loop : -0.06 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.002   0.001   HIS A 347 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.015   0.001   TYR D 235 
 ARG   0.011   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03476 (  481)
  hydrogen bonds       : angle       4.15678 ( 1344)
  SS BOND              : bond        0.00244 (    4)
  SS BOND              : angle       0.78969 (    8)
  covalent geometry    : bond        0.00218 ( 9535)
  covalent geometry    : angle       0.48432 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 141
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8557 (pp-130) cc_final: 0.8179 (pp-130)
REVERT: B  217 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7565 (pp-130)
REVERT: B  234 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.6917 (t80)
REVERT: N    1 GLN cc_start: 0.7502 (pm20) cc_final: 0.7163 (pm20)
REVERT: N   80 TYR cc_start: 0.8554 (m-80) cc_final: 0.8193 (m-80)
REVERT: N   83 MET cc_start: 0.8737 (mtp) cc_final: 0.8478 (mtm)
REVERT: D   89 GLU cc_start: 0.8240 (mp0) cc_final: 0.7860 (pp20)
REVERT: D  160 ARG cc_start: 0.7365 (mtp-110) cc_final: 0.6971 (ttp-110)
REVERT: D  235 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5977 (t80)
REVERT: R  117 ASP cc_start: 0.8914 (t0) cc_final: 0.8695 (t0)
REVERT: R  151 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7112 (ttmm)
REVERT: R  298 MET cc_start: 0.7439 (mmm) cc_final: 0.7235 (mmp)
REVERT: R  333 TRP cc_start: 0.8137 (m100) cc_final: 0.7008 (m-10)
REVERT: A   25 MET cc_start: 0.7619 (mmm) cc_final: 0.7236 (mtp)
REVERT: C   42 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6831 (mp0)
REVERT: C   46 LYS cc_start: 0.8271 (tppp) cc_final: 0.7509 (ptpp)
  outliers start: 36
  outliers final: 23
  residues processed: 164
  average time/residue: 1.3829
  time to fit residues: 240.9091
Evaluate side-chains
  164 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue  151 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 45 optimal weight:    0.2980
   chunk 115 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 117 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 64 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
N  77 ASN
N 120 GLN
D   3 GLN
D  77 ASN
D 183 GLN
A 236 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.125299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.096653 restraints weight = 12038.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.23
r_work: 0.3078 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9539  Z= 0.125
  Angle     :  0.512   6.933  12968  Z= 0.272
  Chirality :  0.041   0.185   1488
  Planarity :  0.005   0.062   1648
  Dihedral  :  5.247  52.085   1345
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 20.63 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.24), residues: 1207
  helix:  2.63 (0.26), residues: 388
  sheet:  0.83 (0.28), residues: 299
  loop : -0.04 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.014   0.001   TYR D 235 
 ARG   0.012   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03921 (  481)
  hydrogen bonds       : angle       4.29101 ( 1344)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       0.84076 (    8)
  covalent geometry    : bond        0.00287 ( 9535)
  covalent geometry    : angle       0.51169 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 139
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.6802 (t80)
REVERT: N    1 GLN cc_start: 0.7450 (pm20) cc_final: 0.7079 (pm20)
REVERT: N   80 TYR cc_start: 0.8613 (m-80) cc_final: 0.8237 (m-80)
REVERT: N   83 MET cc_start: 0.8552 (mtp) cc_final: 0.8239 (mtm)
REVERT: D   89 GLU cc_start: 0.8223 (mp0) cc_final: 0.7827 (pp20)
REVERT: D  160 ARG cc_start: 0.7300 (mtp-110) cc_final: 0.6893 (ttp-110)
REVERT: D  235 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.5986 (t80)
REVERT: R  151 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7064 (ttmm)
REVERT: R  298 MET cc_start: 0.7312 (mmm) cc_final: 0.7095 (mmp)
REVERT: R  333 TRP cc_start: 0.8086 (m100) cc_final: 0.6900 (m-10)
REVERT: A   25 MET cc_start: 0.7495 (mmm) cc_final: 0.7050 (mtp)
REVERT: A  346 ARG cc_start: 0.7076 (ptp-110) cc_final: 0.6198 (ptp-110)
REVERT: C   21 MET cc_start: 0.7145 (tpp) cc_final: 0.6661 (tpt)
REVERT: C   42 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6703 (mp0)
REVERT: C   46 LYS cc_start: 0.8234 (tppp) cc_final: 0.7455 (ptpp)
  outliers start: 40
  outliers final: 27
  residues processed: 165
  average time/residue: 1.2662
  time to fit residues: 222.5561
Evaluate side-chains
  168 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  151 LYS
Chi-restraints excluded: chain R residue  223 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0270
   chunk 63 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.0044

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
N  77 ASN
N 120 GLN
D   3 GLN
D 183 GLN
A 236 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.125836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.097375 restraints weight = 11818.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.21
r_work: 0.3090 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9539  Z= 0.117
  Angle     :  0.508   7.184  12968  Z= 0.269
  Chirality :  0.041   0.188   1488
  Planarity :  0.005   0.060   1648
  Dihedral  :  5.173  51.989   1345
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.84 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.24), residues: 1207
  helix:  2.67 (0.26), residues: 388
  sheet:  0.75 (0.28), residues: 302
  loop :  0.01 (0.28), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.015   0.001   TYR D 235 
 ARG   0.013   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  481)
  hydrogen bonds       : angle       4.24712 ( 1344)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       0.77391 (    8)
  covalent geometry    : bond        0.00266 ( 9535)
  covalent geometry    : angle       0.50791 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.6793 (t80)
REVERT: N    1 GLN cc_start: 0.7413 (pm20) cc_final: 0.7048 (pm20)
REVERT: N   80 TYR cc_start: 0.8613 (m-80) cc_final: 0.8176 (m-80)
REVERT: N   83 MET cc_start: 0.8579 (mtp) cc_final: 0.8243 (mtm)
REVERT: D   89 GLU cc_start: 0.8199 (mp0) cc_final: 0.7741 (pp20)
REVERT: D  160 ARG cc_start: 0.7293 (mtp-110) cc_final: 0.6886 (ttp-110)
REVERT: D  234 GLU cc_start: 0.8112 (mp0) cc_final: 0.7691 (mp0)
REVERT: D  235 TYR cc_start: 0.6430 (OUTLIER) cc_final: 0.5925 (t80)
REVERT: R  148 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8016 (mp)
REVERT: R  151 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7049 (ttmm)
REVERT: R  298 MET cc_start: 0.7266 (mmm) cc_final: 0.7057 (mmp)
REVERT: R  333 TRP cc_start: 0.8065 (m100) cc_final: 0.6932 (m-10)
REVERT: A   25 MET cc_start: 0.7495 (mmm) cc_final: 0.7049 (mtp)
REVERT: A  346 ARG cc_start: 0.7060 (ptp-110) cc_final: 0.6171 (ptp-110)
REVERT: C   42 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6698 (mp0)
REVERT: C   46 LYS cc_start: 0.8223 (tppp) cc_final: 0.7461 (ptpp)
  outliers start: 36
  outliers final: 29
  residues processed: 165
  average time/residue: 1.2755
  time to fit residues: 224.1546
Evaluate side-chains
  171 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  148 LEU
Chi-restraints excluded: chain R residue  151 LYS
Chi-restraints excluded: chain R residue  223 VAL
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 113 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0370
   chunk 110 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
N  77 ASN
N 120 GLN
D  77 ASN
D 183 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.127518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.098994 restraints weight = 12115.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.28
r_work: 0.3115 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9539  Z= 0.099
  Angle     :  0.488   7.272  12968  Z= 0.258
  Chirality :  0.040   0.168   1488
  Planarity :  0.005   0.060   1648
  Dihedral  :  4.881  51.228   1345
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.55 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1207
  helix:  2.83 (0.26), residues: 388
  sheet:  0.76 (0.28), residues: 304
  loop :  0.04 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.002   0.001   HIS A 347 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.013   0.001   TYR D 235 
 ARG   0.013   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  481)
  hydrogen bonds       : angle       4.08258 ( 1344)
  SS BOND              : bond        0.00221 (    4)
  SS BOND              : angle       0.61900 (    8)
  covalent geometry    : bond        0.00219 ( 9535)
  covalent geometry    : angle       0.48802 (12960)

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

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

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2414 Ramachandran restraints generated.
    1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.6913 (t80)
REVERT: N    1 GLN cc_start: 0.7505 (pm20) cc_final: 0.7163 (pm20)
REVERT: N   80 TYR cc_start: 0.8619 (m-80) cc_final: 0.8254 (m-80)
REVERT: N   83 MET cc_start: 0.8742 (mtp) cc_final: 0.8469 (mtm)
REVERT: D   89 GLU cc_start: 0.8235 (mp0) cc_final: 0.7790 (pp20)
REVERT: D  160 ARG cc_start: 0.7401 (mtp-110) cc_final: 0.7008 (ttp-110)
REVERT: D  235 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5800 (t80)
REVERT: R  148 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8212 (mp)
REVERT: R  151 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7114 (ttmm)
REVERT: R  298 MET cc_start: 0.7430 (mmm) cc_final: 0.7224 (mmp)
REVERT: R  333 TRP cc_start: 0.8119 (m100) cc_final: 0.6997 (m-10)
REVERT: A   25 MET cc_start: 0.7585 (mmm) cc_final: 0.7168 (mtp)
REVERT: A  346 ARG cc_start: 0.7206 (ptp-110) cc_final: 0.6376 (ptp-110)
REVERT: C   21 MET cc_start: 0.7240 (tpp) cc_final: 0.6731 (tpt)
REVERT: C   42 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6861 (mp0)
REVERT: C   46 LYS cc_start: 0.8243 (tppp) cc_final: 0.7500 (ptpp)
  outliers start: 31
  outliers final: 25
  residues processed: 164
  average time/residue: 1.3113
  time to fit residues: 228.8512
Evaluate side-chains
  169 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  148 LEU
Chi-restraints excluded: chain R residue  151 LYS
Chi-restraints excluded: chain R residue  313 VAL
Chi-restraints excluded: chain R residue  354 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 117 optimal weight:    7.9990
   chunk 42 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0000
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
N  77 ASN
N 120 GLN
D 183 GLN
A  35 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.100010 restraints weight = 12006.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.28
r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9539  Z= 0.095
  Angle     :  0.483   7.268  12968  Z= 0.254
  Chirality :  0.040   0.164   1488
  Planarity :  0.005   0.060   1648
  Dihedral  :  4.523  48.530   1343
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.86 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.24), residues: 1207
  helix:  2.94 (0.26), residues: 388
  sheet:  0.81 (0.28), residues: 303
  loop :  0.06 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.002   0.001   HIS A 347 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.014   0.001   TYR D 235 
 ARG   0.013   0.000   ARG R 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03281 (  481)
  hydrogen bonds       : angle       4.00516 ( 1344)
  SS BOND              : bond        0.00218 (    4)
  SS BOND              : angle       0.61273 (    8)
  covalent geometry    : bond        0.00210 ( 9535)
  covalent geometry    : angle       0.48319 (12960)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9233.12 seconds
wall clock time: 158 minutes 27.14 seconds (9507.14 seconds total)