Starting phenix.real_space_refine
on Thu May 15 00:43:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ucs_42139/05_2025/8ucs_42139.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ucs_42139/05_2025/8ucs_42139.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ucs_42139/05_2025/8ucs_42139.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ucs_42139/05_2025/8ucs_42139.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ucs_42139/05_2025/8ucs_42139.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ucs_42139/05_2025/8ucs_42139.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.073
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     102      5.16       5
     C    8038      2.51       5
     N    2087      2.21       5
     O    2378      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12605
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 362
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 45, 354
          Classifications: {'peptide': 45}
          Link IDs: {'TRANS': 44}
      Conformer: "B"
        Number of residues, atoms: 45, 354
          Classifications: {'peptide': 45}
          Link IDs: {'TRANS': 44}
          bond proxies already assigned to first conformer: 351
    Chain: "B"
      Number of atoms: 394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 394
          Classifications: {'peptide': 50}
          Link IDs: {'TRANS': 49}
    Chain: "C"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1942
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 8, 'TRANS': 244}
    Chain: "D"
      Number of atoms: 1978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1978
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
    Chain: "E"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1942
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 8, 'TRANS': 244}
    Chain: "F"
      Number of atoms: 1978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1978
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
    Chain: "G"
      Number of atoms: 1943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1943
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 8, 'TRANS': 244}
    Chain: "H"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 688
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "I"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 688
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "J"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 688
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 10.36, per 1000 atoms: 0.82
  Number of scatterers: 12605
  At special positions: 0
  Unit cell: (98.406, 114.345, 127.512, 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     102     16.00
     O    2378      8.00
     N    2087      7.00
     C    8038      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.16
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2996

  Finding SS restraints...
    Secondary structure from input PDB file:
      89 helices and 1 sheets defined
      86.6% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 40
      removed outlier: 3.799A  pdb=" N   PHE A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   PHE A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'B' and resid 17 through 40
      removed outlier: 4.131A  pdb=" N   ALA B  21 " --> pdb=" O   ASP B  17 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   THR B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 60
    Processing helix  chain 'C' and resid 8 through 24
      removed outlier: 3.608A  pdb=" N   VAL C  13 " --> pdb=" O   PRO C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
      removed outlier: 3.571A  pdb=" N   VAL C  32 " --> pdb=" O   ASN C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 54
    Processing helix  chain 'C' and resid 57 through 72
      removed outlier: 3.799A  pdb=" N   LYS C  71 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 95
      removed outlier: 3.609A  pdb=" N   ARG C  93 " --> pdb=" O   ARG C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 98
      No H-bonds generated for 'chain 'C' and resid 96 through 98'
    Processing helix  chain 'C' and resid 99 through 105
      removed outlier: 3.550A  pdb=" N   ASN C 105 " --> pdb=" O   ASP C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 120
    Processing helix  chain 'C' and resid 123 through 174
      Proline residue:  C 157  - end of helix
    Processing helix  chain 'C' and resid 177 through 189
      removed outlier: 3.671A  pdb=" N   GLY C 186 " --> pdb=" O   ALA C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 202
    Processing helix  chain 'C' and resid 202 through 233
      removed outlier: 4.177A  pdb=" N   GLY C 227 " --> pdb=" O   MET C 223 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ALA C 230 " --> pdb=" O   GLU C 226 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN C 232 " --> pdb=" O   VAL C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 245
    Processing helix  chain 'C' and resid 249 through 258
    Processing helix  chain 'D' and resid 6 through 24
    Processing helix  chain 'D' and resid 29 through 34
    Processing helix  chain 'D' and resid 35 through 42
    Processing helix  chain 'D' and resid 42 through 54
    Processing helix  chain 'D' and resid 55 through 70
      removed outlier: 3.608A  pdb=" N   PHE D  70 " --> pdb=" O   ILE D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 95
      removed outlier: 3.662A  pdb=" N   ILE D  81 " --> pdb=" O   ASN D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 121
    Processing helix  chain 'D' and resid 123 through 174
      Proline residue:  D 157  - end of helix
    Processing helix  chain 'D' and resid 177 through 202
      removed outlier: 3.678A  pdb=" N   THR D 192 " --> pdb=" O   ALA D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 233
    Processing helix  chain 'D' and resid 239 through 245
      removed outlier: 3.740A  pdb=" N   VAL D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 246 through 248
      No H-bonds generated for 'chain 'D' and resid 246 through 248'
    Processing helix  chain 'D' and resid 249 through 258
      removed outlier: 4.454A  pdb=" N   GLN D 254 " --> pdb=" O   PRO D 250 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ALA D 255 " --> pdb=" O   PRO D 251 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS D 258 " --> pdb=" O   GLN D 254 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 9 through 24
      removed outlier: 3.742A  pdb=" N   VAL E  13 " --> pdb=" O   PRO E   9 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 34
      removed outlier: 3.764A  pdb=" N   VAL E  32 " --> pdb=" O   ASN E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 54
      removed outlier: 3.514A  pdb=" N   PHE E  40 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 70
      removed outlier: 3.603A  pdb=" N   PHE E  70 " --> pdb=" O   ILE E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 94
    Processing helix  chain 'E' and resid 100 through 105
      removed outlier: 3.543A  pdb=" N   ASN E 104 " --> pdb=" O   GLU E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 110 through 119
    Processing helix  chain 'E' and resid 123 through 174
      Proline residue:  E 157  - end of helix
      removed outlier: 3.521A  pdb=" N   ASN E 174 " --> pdb=" O   GLN E 170 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 189
    Processing helix  chain 'E' and resid 189 through 202
    Processing helix  chain 'E' and resid 202 through 234
    Processing helix  chain 'E' and resid 236 through 246
      removed outlier: 3.649A  pdb=" N   SER E 246 " --> pdb=" O   GLU E 242 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 249 through 258
    Processing helix  chain 'F' and resid 6 through 24
    Processing helix  chain 'F' and resid 29 through 34
    Processing helix  chain 'F' and resid 35 through 54
      removed outlier: 3.618A  pdb=" N   GLY F  44 " --> pdb=" O   PHE F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 55 through 70
    Processing helix  chain 'F' and resid 76 through 95
    Processing helix  chain 'F' and resid 96 through 98
      No H-bonds generated for 'chain 'F' and resid 96 through 98'
    Processing helix  chain 'F' and resid 99 through 105
      removed outlier: 3.548A  pdb=" N   ASN F 105 " --> pdb=" O   ASP F 101 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 108 through 121
    Processing helix  chain 'F' and resid 123 through 174
      Proline residue:  F 157  - end of helix
      removed outlier: 3.580A  pdb=" N   ASN F 174 " --> pdb=" O   GLN F 170 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 179 through 202
      removed outlier: 3.654A  pdb=" N   THR F 192 " --> pdb=" O   ALA F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 234
    Processing helix  chain 'F' and resid 238 through 245
      removed outlier: 3.611A  pdb=" N   GLU F 242 " --> pdb=" O   ARG F 238 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 246 through 248
      No H-bonds generated for 'chain 'F' and resid 246 through 248'
    Processing helix  chain 'F' and resid 249 through 254
      removed outlier: 4.193A  pdb=" N   GLN F 254 " --> pdb=" O   PRO F 250 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 26
      removed outlier: 3.745A  pdb=" N   GLY G  26 " --> pdb=" O   GLY G  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 34
    Processing helix  chain 'G' and resid 35 through 54
    Processing helix  chain 'G' and resid 55 through 72
      removed outlier: 3.581A  pdb=" N   PHE G  70 " --> pdb=" O   ILE G  66 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 76 through 94
    Processing helix  chain 'G' and resid 95 through 98
      removed outlier: 3.589A  pdb=" N   SER G  98 " --> pdb=" O   GLY G  95 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 95 through 98'
    Processing helix  chain 'G' and resid 99 through 105
    Processing helix  chain 'G' and resid 111 through 120
      removed outlier: 3.643A  pdb=" N   VAL G 118 " --> pdb=" O   GLY G 114 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 123 through 174
      Proline residue:  G 157  - end of helix
    Processing helix  chain 'G' and resid 177 through 179
      No H-bonds generated for 'chain 'G' and resid 177 through 179'
    Processing helix  chain 'G' and resid 180 through 189
    Processing helix  chain 'G' and resid 189 through 202
    Processing helix  chain 'G' and resid 202 through 233
    Processing helix  chain 'G' and resid 236 through 246
      removed outlier: 3.884A  pdb=" N   SER G 246 " --> pdb=" O   GLU G 242 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 249 through 260
      removed outlier: 3.520A  pdb=" N   GLN G 254 " --> pdb=" O   PRO G 250 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL G 259 " --> pdb=" O   ALA G 255 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 247 through 255
    Processing helix  chain 'H' and resid 259 through 266
      removed outlier: 3.531A  pdb=" N   ALA H 264 " --> pdb=" O   THR H 260 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 271 through 280
    Processing helix  chain 'H' and resid 283 through 295
    Processing helix  chain 'H' and resid 304 through 320
    Processing helix  chain 'I' and resid 239 through 244
      removed outlier: 4.130A  pdb=" N   ILE I 244 " --> pdb=" O   GLU I 241 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 247 through 256
      removed outlier: 3.539A  pdb=" N   ARG I 253 " --> pdb=" O   VAL I 249 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL I 254 " --> pdb=" O   ALA I 250 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG I 256 " --> pdb=" O   GLN I 252 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 259 through 268
      removed outlier: 3.835A  pdb=" N   LYS I 268 " --> pdb=" O   ALA I 264 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 271 through 281
      removed outlier: 3.665A  pdb=" N   ALA I 275 " --> pdb=" O   SER I 271 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL I 277 " --> pdb=" O   GLU I 273 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN I 281 " --> pdb=" O   VAL I 277 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 283 through 296
    Processing helix  chain 'I' and resid 301 through 319
      removed outlier: 3.573A  pdb=" N   GLN I 310 " --> pdb=" O   GLU I 306 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLY I 311 " --> pdb=" O   LYS I 307 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE I 316 " --> pdb=" O   ILE I 312 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG I 317 " --> pdb=" O   VAL I 313 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 247 through 256
      removed outlier: 3.787A  pdb=" N   GLN J 252 " --> pdb=" O   ASP J 248 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG J 253 " --> pdb=" O   VAL J 249 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 259 through 268
      removed outlier: 3.562A  pdb=" N   LYS J 268 " --> pdb=" O   ALA J 264 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 271 through 279
    Processing helix  chain 'J' and resid 283 through 298
      removed outlier: 3.733A  pdb=" N   SER J 288 " --> pdb=" O   LYS J 284 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU J 292 " --> pdb=" O   SER J 288 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLU J 295 " --> pdb=" O   LYS J 291 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   GLY J 298 " --> pdb=" O   ILE J 294 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 302 through 319
      removed outlier: 4.138A  pdb=" N   GLU J 306 " --> pdb=" O   ILE J 302 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS J 307 " --> pdb=" O   MET J 303 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE J 316 " --> pdb=" O   ILE J 312 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43

    991 hydrogen bonds defined for protein.
    2928 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: 3.67

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4116
        1.34 -     1.46: 2682
        1.46 -     1.58: 5786
        1.58 -     1.70: 0
        1.70 -     1.81: 199
  Bond restraints: 12783
  Sorted by residual:
  bond pdb=" CB  GLU I 292 "
       pdb=" CG  GLU I 292 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" CB  ASP J 293 "
       pdb=" CG  ASP J 293 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.72e-01
  bond pdb=" CB  MET H 303 "
       pdb=" CG  MET H 303 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.62e-01
  bond pdb=" CB  ASP F  86 "
       pdb=" CG  ASP F  86 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.39e-01
  bond pdb=" CB  ASP I 262 "
       pdb=" CG  ASP I 262 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.26e-01
  ... (remaining 12778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 17026
        1.81 -     3.63: 147
        3.63 -     5.44: 43
        5.44 -     7.25: 6
        7.25 -     9.06: 3
  Bond angle restraints: 17225
  Sorted by residual:
  angle pdb=" CA  MET H 303 "
        pdb=" CB  MET H 303 "
        pdb=" CG  MET H 303 "
      ideal   model   delta    sigma   weight residual
     114.10  121.90   -7.80 2.00e+00 2.50e-01 1.52e+01
  angle pdb=" CB  MET H 303 "
        pdb=" CG  MET H 303 "
        pdb=" SD  MET H 303 "
      ideal   model   delta    sigma   weight residual
     112.70  121.76   -9.06 3.00e+00 1.11e-01 9.13e+00
  angle pdb=" N   ILE F   6 "
        pdb=" CA  ILE F   6 "
        pdb=" C   ILE F   6 "
      ideal   model   delta    sigma   weight residual
     113.10  110.36    2.74 9.70e-01 1.06e+00 7.98e+00
  angle pdb=" CA  GLU J 273 "
        pdb=" CB  GLU J 273 "
        pdb=" CG  GLU J 273 "
      ideal   model   delta    sigma   weight residual
     114.10  119.62   -5.52 2.00e+00 2.50e-01 7.62e+00
  angle pdb=" C   ASP E 108 "
        pdb=" N   ASP E 109 "
        pdb=" CA  ASP E 109 "
      ideal   model   delta    sigma   weight residual
     121.54  126.71   -5.17 1.91e+00 2.74e-01 7.33e+00
  ... (remaining 17220 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 6588
       17.83 -    35.66: 852
       35.66 -    53.48: 260
       53.48 -    71.31: 55
       71.31 -    89.14: 19
  Dihedral angle restraints: 7774
    sinusoidal: 3122
      harmonic: 4652
  Sorted by residual:
  dihedral pdb=" CA  GLY C 227 "
           pdb=" C   GLY C 227 "
           pdb=" N   VAL C 228 "
           pdb=" CA  VAL C 228 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.09   18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  VAL D 202 "
           pdb=" C   VAL D 202 "
           pdb=" N   PHE D 203 "
           pdb=" CA  PHE D 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.48  -18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  VAL F 202 "
           pdb=" C   VAL F 202 "
           pdb=" N   PHE F 203 "
           pdb=" CA  PHE F 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.56  -18.44     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 7771 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1473
       0.037 -    0.074: 450
       0.074 -    0.111: 81
       0.111 -    0.148: 7
       0.148 -    0.185: 1
  Chirality restraints: 2012
  Sorted by residual:
  chirality pdb=" CA  THR F   8 "
            pdb=" N   THR F   8 "
            pdb=" C   THR F   8 "
            pdb=" CB  THR F   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CG  LEU E 172 "
            pdb=" CB  LEU E 172 "
            pdb=" CD1 LEU E 172 "
            pdb=" CD2 LEU E 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  ILE C 122 "
            pdb=" N   ILE C 122 "
            pdb=" C   ILE C 122 "
            pdb=" CB  ILE C 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 2009 not shown)

  Planarity restraints: 2184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET H 303 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.28e+00
        pdb=" C   MET H 303 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   MET H 303 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP H 304 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E 236 "   -0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO E 237 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E 237 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 237 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 250 "    0.028 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO C 251 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C 251 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 251 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2181 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2490
        2.77 -     3.30: 12723
        3.30 -     3.83: 22411
        3.83 -     4.37: 26233
        4.37 -     4.90: 43397
  Nonbonded interactions: 107254
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C 238 "
            pdb=" OD2 ASP D 120 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" O   GLY G  95 "
            pdb=" OG  SER G  98 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   GLY F  95 "
            pdb=" OG  SER F  98 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   ARG H 253 "
            pdb=" NH1 ARG H 253 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   GLY D  22 "
            pdb=" OG  SER D  25 "
     model   vdw
     2.281 3.040
  ... (remaining 107249 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 16 through 32 or resid 34 through 60))
  selection = (chain 'B' and (resid 16 through 32 or resid 34 through 60))
}
ncs_group {
  reference = (chain 'C' and resid 8 through 259)
  selection = (chain 'D' and resid 8 through 259)
  selection = (chain 'E' and resid 8 through 259)
  selection = (chain 'F' and resid 8 through 259)
  selection = (chain 'G' and resid 8 through 259)
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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=0.37 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:             4.180
  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:          0.660
  Check model and map are aligned:         0.110
  Set scattering table:                    0.170
  Process input model:                     32.290
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.060
  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:12.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12783  Z= 0.105
  Angle     :  0.485   9.064  17225  Z= 0.253
  Chirality :  0.036   0.185   2012
  Planarity :  0.004   0.051   2184
  Dihedral  : 18.156  89.141   4778
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 28.89 %
    Favored  : 70.74 %
  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:  0.55 (0.20), residues: 1613
  helix:  0.70 (0.14), residues: 1354
  sheet:  None (None), residues: 0
  loop : -0.95 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  21 
 HIS   0.001   0.000   HIS D 142 
 PHE   0.016   0.001   PHE C  59 
 TYR   0.006   0.001   TYR F 256 
 ARG   0.005   0.000   ARG I 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21686 (  991)
  hydrogen bonds       : angle       7.31428 ( 2928)
  covalent geometry    : bond        0.00252 (12783)
  covalent geometry    : angle       0.48520 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 250
  time to evaluate  : 1.490 
Fit side-chains
   revert: symmetry clash
REVERT: D  223 MET cc_start: 0.8604 (ptm) cc_final: 0.8391 (ptt)
REVERT: F  104 ASN cc_start: 0.7700 (m-40) cc_final: 0.7267 (m110)
REVERT: F  108 ASP cc_start: 0.7627 (t70) cc_final: 0.7171 (t70)
  outliers start: 4
  outliers final: 4
  residues processed: 253
  average time/residue: 1.2974
  time to fit residues: 354.8176
Evaluate side-chains
  237 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 233
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain D residue  125 GLU
Chi-restraints excluded: chain F residue   14 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    0.9980
   chunk 119 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 123 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 143 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C  29 ASN
D  29 ASN
F 254 GLN
J 252 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.198374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.128596 restraints weight = 12623.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.98
r_work: 0.3165 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12783  Z= 0.154
  Angle     :  0.553   7.793  17225  Z= 0.301
  Chirality :  0.040   0.167   2012
  Planarity :  0.005   0.049   2184
  Dihedral  :  4.836  52.581   1743
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 24.75 %
    Favored  : 70.52 %
  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:  1.60 (0.21), residues: 1613
  helix:  1.44 (0.14), residues: 1379
  sheet:  None (None), residues: 0
  loop : -0.98 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  19 
 HIS   0.001   0.001   HIS G 142 
 PHE   0.022   0.002   PHE B  48 
 TYR   0.009   0.001   TYR F 110 
 ARG   0.004   0.000   ARG C 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05199 (  991)
  hydrogen bonds       : angle       4.54020 ( 2928)
  covalent geometry    : bond        0.00334 (12783)
  covalent geometry    : angle       0.55328 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 258
  time to evaluate  : 1.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LYS cc_start: 0.7684 (tmtt) cc_final: 0.6965 (mttm)
REVERT: B   56 GLN cc_start: 0.7391 (mt0) cc_final: 0.7178 (mm-40)
REVERT: C   68 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6521 (tm-30)
REVERT: C   72 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.4893 (p0)
REVERT: C  187 LYS cc_start: 0.8397 (mppt) cc_final: 0.7542 (mmtm)
REVERT: D   35 ASP cc_start: 0.9107 (t70) cc_final: 0.8886 (t70)
REVERT: D  223 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8589 (ttt)
REVERT: D  243 LYS cc_start: 0.6672 (ptpt) cc_final: 0.6452 (pttt)
REVERT: F   14 LEU cc_start: 0.8354 (mt) cc_final: 0.8001 (tp)
REVERT: F  108 ASP cc_start: 0.7507 (t70) cc_final: 0.7070 (t70)
REVERT: F  129 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7257 (pt0)
REVERT: G   56 MET cc_start: 0.7603 (tpt) cc_final: 0.7376 (mmp)
REVERT: G  141 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7726 (mtm110)
  outliers start: 64
  outliers final: 19
  residues processed: 293
  average time/residue: 1.3063
  time to fit residues: 413.2178
Evaluate side-chains
  262 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 241
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain B residue   59 MET
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  249 SER
Chi-restraints excluded: chain D residue  223 MET
Chi-restraints excluded: chain E residue   81 ILE
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain I residue  318 ARG
Chi-restraints excluded: chain J residue  239 VAL
Chi-restraints excluded: chain J residue  249 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 137 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0010
   chunk 8 optimal weight:    0.9980
   chunk 135 optimal weight:    6.9990
   chunk 150 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
F 254 GLN
G  68 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.198794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.131136 restraints weight = 15891.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.41
r_work: 0.3181 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12783  Z= 0.137
  Angle     :  0.517   7.454  17225  Z= 0.280
  Chirality :  0.039   0.159   2012
  Planarity :  0.005   0.047   2184
  Dihedral  :  4.469  52.211   1737
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 25.40 %
    Favored  : 70.60 %
  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:  1.93 (0.21), residues: 1613
  helix:  1.69 (0.14), residues: 1381
  sheet:  None (None), residues: 0
  loop : -1.08 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  19 
 HIS   0.001   0.000   HIS G 142 
 PHE   0.021   0.002   PHE B  48 
 TYR   0.009   0.001   TYR E 110 
 ARG   0.004   0.000   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04645 (  991)
  hydrogen bonds       : angle       4.26582 ( 2928)
  covalent geometry    : bond        0.00296 (12783)
  covalent geometry    : angle       0.51660 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 244
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7672 (tp40)
REVERT: B   47 LYS cc_start: 0.7715 (tmtt) cc_final: 0.7055 (mttm)
REVERT: B   56 GLN cc_start: 0.7490 (mt0) cc_final: 0.7241 (mm-40)
REVERT: C   68 GLN cc_start: 0.7068 (tm-30) cc_final: 0.6588 (tm-30)
REVERT: C   72 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.4688 (p0)
REVERT: C  187 LYS cc_start: 0.8470 (mppt) cc_final: 0.7632 (mmtm)
REVERT: D  185 MET cc_start: 0.8913 (tpt) cc_final: 0.8707 (tpt)
REVERT: F   14 LEU cc_start: 0.8445 (mt) cc_final: 0.8137 (tp)
REVERT: G  129 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6711 (mp0)
REVERT: G  141 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7775 (mtm110)
REVERT: J  303 MET cc_start: 0.6325 (ttt) cc_final: 0.6064 (mpt)
  outliers start: 54
  outliers final: 23
  residues processed: 279
  average time/residue: 1.3462
  time to fit residues: 404.7176
Evaluate side-chains
  259 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 233
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  171 MET
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  249 SER
Chi-restraints excluded: chain E residue   10 ILE
Chi-restraints excluded: chain E residue   81 ILE
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  231 ILE
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue  129 GLU
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain J residue  249 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 122 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 70 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0980
   chunk 92 optimal weight:    0.9990
   chunk 152 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
F 254 GLN
G  68 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.200013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.131562 restraints weight = 10761.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.47
r_work: 0.3228 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12783  Z= 0.125
  Angle     :  0.500   7.272  17225  Z= 0.270
  Chirality :  0.038   0.159   2012
  Planarity :  0.004   0.048   2184
  Dihedral  :  4.413  51.723   1737
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.18 %
    Favored  : 70.67 %
  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:  2.14 (0.21), residues: 1613
  helix:  1.84 (0.14), residues: 1380
  sheet:  None (None), residues: 0
  loop : -1.10 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  19 
 HIS   0.001   0.000   HIS G 142 
 PHE   0.021   0.002   PHE B  48 
 TYR   0.010   0.001   TYR F 110 
 ARG   0.004   0.000   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04241 (  991)
  hydrogen bonds       : angle       4.11005 ( 2928)
  covalent geometry    : bond        0.00264 (12783)
  covalent geometry    : angle       0.49973 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 249
  time to evaluate  : 1.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7532 (tp40)
REVERT: B   47 LYS cc_start: 0.7681 (tmtt) cc_final: 0.7055 (mttm)
REVERT: B   55 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7649 (ttm)
REVERT: B   56 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7151 (mm-40)
REVERT: C   68 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6582 (tm-30)
REVERT: C   72 ASP cc_start: 0.5419 (OUTLIER) cc_final: 0.4703 (p0)
REVERT: C  187 LYS cc_start: 0.8405 (mppt) cc_final: 0.7508 (mmtm)
REVERT: C  249 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7827 (m)
REVERT: D   35 ASP cc_start: 0.9074 (t70) cc_final: 0.8864 (t70)
REVERT: D  123 GLU cc_start: 0.7377 (pm20) cc_final: 0.6895 (tp30)
REVERT: F   14 LEU cc_start: 0.8370 (mt) cc_final: 0.8053 (tp)
REVERT: F  108 ASP cc_start: 0.7528 (t70) cc_final: 0.7141 (t70)
REVERT: G  129 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6591 (mp0)
REVERT: G  141 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7645 (mtm110)
REVERT: J  303 MET cc_start: 0.6335 (ttt) cc_final: 0.6053 (mpt)
  outliers start: 56
  outliers final: 25
  residues processed: 283
  average time/residue: 1.4784
  time to fit residues: 453.9273
Evaluate side-chains
  270 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 240
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   55 MET
Chi-restraints excluded: chain B residue   59 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  171 MET
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  249 SER
Chi-restraints excluded: chain E residue   10 ILE
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   81 ILE
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  231 ILE
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  129 GLU
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain I residue  318 ARG
Chi-restraints excluded: chain J residue  239 VAL
Chi-restraints excluded: chain J residue  249 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 104 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 138 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.198035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.128914 restraints weight = 12595.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.02
r_work: 0.3182 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12783  Z= 0.142
  Angle     :  0.515   7.342  17225  Z= 0.279
  Chirality :  0.039   0.166   2012
  Planarity :  0.005   0.050   2184
  Dihedral  :  4.491  54.883   1737
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 24.82 %
    Favored  : 70.74 %
  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:  2.11 (0.21), residues: 1613
  helix:  1.79 (0.14), residues: 1387
  sheet:  None (None), residues: 0
  loop : -0.97 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  19 
 HIS   0.001   0.001   HIS G 142 
 PHE   0.023   0.002   PHE B  48 
 TYR   0.009   0.001   TYR F 110 
 ARG   0.005   0.000   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04493 (  991)
  hydrogen bonds       : angle       4.16140 ( 2928)
  covalent geometry    : bond        0.00314 (12783)
  covalent geometry    : angle       0.51527 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 241
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7541 (tp40)
REVERT: B   47 LYS cc_start: 0.7666 (tmtt) cc_final: 0.6999 (mttm)
REVERT: B   56 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7107 (mm-40)
REVERT: C   68 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6514 (tm-30)
REVERT: C   72 ASP cc_start: 0.5375 (OUTLIER) cc_final: 0.4639 (p0)
REVERT: C  187 LYS cc_start: 0.8440 (mppt) cc_final: 0.7538 (mmtm)
REVERT: D   35 ASP cc_start: 0.9129 (t70) cc_final: 0.8887 (t70)
REVERT: F   14 LEU cc_start: 0.8373 (mt) cc_final: 0.8009 (tp)
REVERT: F   59 PHE cc_start: 0.8469 (t80) cc_final: 0.8257 (t80)
REVERT: F  108 ASP cc_start: 0.7559 (t70) cc_final: 0.7105 (t70)
REVERT: G  129 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6616 (mp0)
REVERT: G  141 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7707 (mtm110)
REVERT: J  303 MET cc_start: 0.6417 (ttt) cc_final: 0.6083 (mpt)
  outliers start: 60
  outliers final: 33
  residues processed: 280
  average time/residue: 1.3539
  time to fit residues: 408.5915
Evaluate side-chains
  272 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 236
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   59 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  171 MET
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  249 SER
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain E residue   10 ILE
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   81 ILE
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  231 ILE
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  129 GLU
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain I residue  318 ARG
Chi-restraints excluded: chain J residue  239 VAL
Chi-restraints excluded: chain J residue  249 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9980
   chunk 86 optimal weight:    0.3980
   chunk 98 optimal weight:    0.9980
   chunk 126 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   chunk 25 optimal weight:    0.3980
   chunk 99 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
F 254 GLN
G  68 GLN
** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.199284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.129383 restraints weight = 12680.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.61
r_work: 0.3234 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12783  Z= 0.125
  Angle     :  0.499   7.307  17225  Z= 0.269
  Chirality :  0.038   0.161   2012
  Planarity :  0.004   0.050   2184
  Dihedral  :  4.412  53.297   1737
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 24.82 %
    Favored  : 70.82 %
  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:  2.24 (0.21), residues: 1613
  helix:  1.89 (0.14), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.01 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  19 
 HIS   0.001   0.000   HIS G 142 
 PHE   0.021   0.002   PHE B  48 
 TYR   0.009   0.001   TYR F 110 
 ARG   0.005   0.000   ARG C  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  991)
  hydrogen bonds       : angle       4.04652 ( 2928)
  covalent geometry    : bond        0.00268 (12783)
  covalent geometry    : angle       0.49869 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 247
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7547 (tp40)
REVERT: B   55 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7705 (ttm)
REVERT: B   56 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7106 (mm-40)
REVERT: C   61 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7148 (ttt180)
REVERT: C   68 GLN cc_start: 0.6958 (tm-30) cc_final: 0.6578 (tm-30)
REVERT: C   92 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7339 (mtt-85)
REVERT: C  187 LYS cc_start: 0.8432 (mppt) cc_final: 0.7555 (mmtm)
REVERT: C  249 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7837 (m)
REVERT: D   35 ASP cc_start: 0.9089 (t70) cc_final: 0.8876 (t70)
REVERT: F   14 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8030 (tp)
REVERT: G  129 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6619 (mp0)
REVERT: G  141 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7678 (mtm110)
REVERT: J  303 MET cc_start: 0.6431 (ttt) cc_final: 0.6102 (mpt)
  outliers start: 59
  outliers final: 33
  residues processed: 283
  average time/residue: 1.2729
  time to fit residues: 389.1528
Evaluate side-chains
  278 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 240
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   55 MET
Chi-restraints excluded: chain B residue   59 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  171 MET
Chi-restraints excluded: chain C residue  175 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  249 SER
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain E residue   10 ILE
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   81 ILE
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue   88 SER
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  231 ILE
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  129 GLU
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain I residue  243 ILE
Chi-restraints excluded: chain I residue  316 ILE
Chi-restraints excluded: chain J residue  239 VAL
Chi-restraints excluded: chain J residue  249 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 157 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0670
   chunk 128 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0170
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.200005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.131614 restraints weight = 12568.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.00
r_work: 0.3196 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12783  Z= 0.121
  Angle     :  0.508  12.632  17225  Z= 0.271
  Chirality :  0.038   0.161   2012
  Planarity :  0.004   0.051   2184
  Dihedral  :  4.364  52.112   1737
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 25.04 %
    Favored  : 70.74 %
  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:  2.32 (0.21), residues: 1613
  helix:  1.95 (0.14), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.01 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  19 
 HIS   0.001   0.000   HIS G 142 
 PHE   0.020   0.002   PHE B  48 
 TYR   0.009   0.001   TYR F 110 
 ARG   0.005   0.000   ARG C 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  991)
  hydrogen bonds       : angle       3.99301 ( 2928)
  covalent geometry    : bond        0.00257 (12783)
  covalent geometry    : angle       0.50751 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 251
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7546 (tp40)
REVERT: B   47 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6912 (mttm)
REVERT: B   55 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7740 (ttm)
REVERT: B   56 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7154 (mm-40)
REVERT: C   61 ARG cc_start: 0.7308 (ttp80) cc_final: 0.7074 (ttt180)
REVERT: C   68 GLN cc_start: 0.6901 (tm-30) cc_final: 0.6461 (tm-30)
REVERT: C   72 ASP cc_start: 0.5319 (OUTLIER) cc_final: 0.4613 (p0)
REVERT: C   92 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7323 (mtt-85)
REVERT: C  187 LYS cc_start: 0.8477 (mppt) cc_final: 0.7580 (mmtm)
REVERT: C  249 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7832 (m)
REVERT: D   35 ASP cc_start: 0.9113 (t70) cc_final: 0.8891 (t70)
REVERT: F   14 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7980 (tp)
REVERT: F  108 ASP cc_start: 0.7575 (t70) cc_final: 0.7131 (t70)
REVERT: F  125 GLU cc_start: 0.7344 (pm20) cc_final: 0.6985 (pm20)
REVERT: G  129 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6607 (mp0)
REVERT: G  141 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7693 (mtm110)
REVERT: H  303 MET cc_start: 0.5867 (tmm) cc_final: 0.5459 (tmm)
REVERT: J  303 MET cc_start: 0.6436 (ttt) cc_final: 0.6100 (mpt)
  outliers start: 57
  outliers final: 34
  residues processed: 289
  average time/residue: 1.2651
  time to fit residues: 395.6569
Evaluate side-chains
  282 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 241
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   55 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  171 MET
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  249 SER
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain E residue   10 ILE
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  228 VAL
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   57 ASP
Chi-restraints excluded: chain F residue   88 SER
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue   69 THR
Chi-restraints excluded: chain G residue  129 GLU
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain I residue  243 ILE
Chi-restraints excluded: chain I residue  268 LYS
Chi-restraints excluded: chain I residue  316 ILE
Chi-restraints excluded: chain J residue  239 VAL
Chi-restraints excluded: chain J residue  249 VAL
Chi-restraints excluded: chain J residue  271 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 116 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 86 optimal weight:    0.7980
   chunk 146 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 138 optimal weight:    0.0670
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 120 optimal weight:    0.0270
   overall best weight:    0.3554

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
D  83 ASN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.201076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.132407 restraints weight = 11831.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.87
r_work: 0.3248 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12783  Z= 0.113
  Angle     :  0.499  11.572  17225  Z= 0.266
  Chirality :  0.037   0.160   2012
  Planarity :  0.004   0.054   2184
  Dihedral  :  4.280  50.316   1737
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 25.76 %
    Favored  : 70.67 %
  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:  2.45 (0.22), residues: 1613
  helix:  2.04 (0.14), residues: 1386
  sheet:  None (None), residues: 0
  loop : -0.98 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  21 
 HIS   0.001   0.000   HIS G 142 
 PHE   0.022   0.002   PHE F  70 
 TYR   0.009   0.001   TYR F 110 
 ARG   0.006   0.000   ARG C 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  991)
  hydrogen bonds       : angle       3.91563 ( 2928)
  covalent geometry    : bond        0.00236 (12783)
  covalent geometry    : angle       0.49894 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 249
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7527 (tp40)
REVERT: B   47 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6827 (mttm)
REVERT: B   55 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7711 (ttm)
REVERT: B   56 GLN cc_start: 0.7402 (mm-40) cc_final: 0.6983 (tp40)
REVERT: C   61 ARG cc_start: 0.7273 (ttp80) cc_final: 0.7057 (ttt180)
REVERT: C   68 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6470 (tm-30)
REVERT: C   72 ASP cc_start: 0.5240 (OUTLIER) cc_final: 0.4560 (p0)
REVERT: C   92 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7295 (mtt-85)
REVERT: C  180 THR cc_start: 0.7838 (m) cc_final: 0.7620 (t)
REVERT: C  187 LYS cc_start: 0.8464 (mppt) cc_final: 0.7572 (mmtm)
REVERT: D    7 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8010 (mp)
REVERT: D   35 ASP cc_start: 0.9089 (t70) cc_final: 0.8886 (t70)
REVERT: D  123 GLU cc_start: 0.7367 (pm20) cc_final: 0.6856 (tp30)
REVERT: F   14 LEU cc_start: 0.8323 (mt) cc_final: 0.7988 (tp)
REVERT: F   59 PHE cc_start: 0.8483 (t80) cc_final: 0.8277 (t80)
REVERT: F  108 ASP cc_start: 0.7592 (t70) cc_final: 0.7138 (t70)
REVERT: F  125 GLU cc_start: 0.7282 (pm20) cc_final: 0.6913 (pm20)
REVERT: F  129 GLU cc_start: 0.7683 (pt0) cc_final: 0.7253 (pp20)
REVERT: F  226 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7140 (mp0)
REVERT: G  141 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7663 (mtm110)
REVERT: H  303 MET cc_start: 0.5856 (tmm) cc_final: 0.5417 (tmm)
REVERT: J  303 MET cc_start: 0.6434 (ttt) cc_final: 0.6111 (mpt)
  outliers start: 48
  outliers final: 24
  residues processed: 282
  average time/residue: 1.2681
  time to fit residues: 386.9429
Evaluate side-chains
  272 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 243
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   55 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain D residue    7 LEU
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  228 VAL
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue   69 THR
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain I residue  243 ILE
Chi-restraints excluded: chain I residue  316 ILE
Chi-restraints excluded: chain J residue  249 VAL
Chi-restraints excluded: chain J residue  271 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0570
   chunk 79 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 11 optimal weight:    0.3980
   chunk 114 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
D  83 ASN
D 174 ASN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.199177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.130048 restraints weight = 12818.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.85
r_work: 0.3183 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12783  Z= 0.132
  Angle     :  0.524  10.782  17225  Z= 0.279
  Chirality :  0.038   0.166   2012
  Planarity :  0.005   0.055   2184
  Dihedral  :  4.386  53.522   1737
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 26.49 %
    Favored  : 70.31 %
  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:  2.34 (0.21), residues: 1613
  helix:  1.96 (0.14), residues: 1386
  sheet:  None (None), residues: 0
  loop : -0.96 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  21 
 HIS   0.001   0.000   HIS G 142 
 PHE   0.021   0.002   PHE B  48 
 TYR   0.010   0.001   TYR F 110 
 ARG   0.013   0.000   ARG D  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  991)
  hydrogen bonds       : angle       4.03155 ( 2928)
  covalent geometry    : bond        0.00289 (12783)
  covalent geometry    : angle       0.52378 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 247
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7614 (tp40)
REVERT: B   47 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6898 (mttm)
REVERT: B   55 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7724 (ttm)
REVERT: B   56 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7161 (mm-40)
REVERT: C   61 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7117 (ttt180)
REVERT: C   68 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6494 (tm-30)
REVERT: C   72 ASP cc_start: 0.5317 (OUTLIER) cc_final: 0.4602 (p0)
REVERT: C   92 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7348 (mtt-85)
REVERT: C  180 THR cc_start: 0.7918 (m) cc_final: 0.7680 (t)
REVERT: C  187 LYS cc_start: 0.8507 (mppt) cc_final: 0.7629 (mmtt)
REVERT: D   31 LYS cc_start: 0.8446 (mtmt) cc_final: 0.7692 (mmtt)
REVERT: D   35 ASP cc_start: 0.9129 (t70) cc_final: 0.8892 (t70)
REVERT: D  123 GLU cc_start: 0.7458 (pm20) cc_final: 0.6966 (tp30)
REVERT: F   14 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8033 (tp)
REVERT: F  108 ASP cc_start: 0.7626 (t70) cc_final: 0.7125 (t70)
REVERT: F  129 GLU cc_start: 0.7783 (pt0) cc_final: 0.7377 (pp20)
REVERT: G  141 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7730 (mtm110)
REVERT: H  303 MET cc_start: 0.5832 (tmm) cc_final: 0.5435 (tmm)
REVERT: J  303 MET cc_start: 0.6443 (ttt) cc_final: 0.6114 (mpt)
  outliers start: 43
  outliers final: 28
  residues processed: 277
  average time/residue: 1.3070
  time to fit residues: 391.6118
Evaluate side-chains
  273 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 240
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   55 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   81 ILE
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  174 ASN
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue   69 THR
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain I residue  243 ILE
Chi-restraints excluded: chain I residue  268 LYS
Chi-restraints excluded: chain I residue  316 ILE
Chi-restraints excluded: chain J residue  249 VAL
Chi-restraints excluded: chain J residue  271 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 120 optimal weight:    0.5980
   chunk 136 optimal weight:    8.9990
   chunk 142 optimal weight:   10.0000
   chunk 34 optimal weight:    0.2980
   chunk 68 optimal weight:    4.9990
   chunk 145 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 13 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
D  83 ASN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.199802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.131298 restraints weight = 10807.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.45
r_work: 0.3262 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12783  Z= 0.125
  Angle     :  0.522  10.677  17225  Z= 0.277
  Chirality :  0.038   0.163   2012
  Planarity :  0.005   0.056   2184
  Dihedral  :  4.354  52.647   1737
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 26.78 %
    Favored  : 70.31 %
  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:  2.39 (0.21), residues: 1613
  helix:  1.99 (0.14), residues: 1386
  sheet:  None (None), residues: 0
  loop : -0.95 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  21 
 HIS   0.001   0.000   HIS G 142 
 PHE   0.022   0.002   PHE F  70 
 TYR   0.010   0.001   TYR F 110 
 ARG   0.012   0.000   ARG D  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04027 (  991)
  hydrogen bonds       : angle       3.99627 ( 2928)
  covalent geometry    : bond        0.00268 (12783)
  covalent geometry    : angle       0.52153 (17225)

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

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

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3226 Ramachandran restraints generated.
    1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 242
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7501 (tp40)
REVERT: B   47 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6917 (mttm)
REVERT: B   55 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7658 (mtt)
REVERT: B   56 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7159 (mm-40)
REVERT: C   61 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7093 (ttt180)
REVERT: C   68 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6528 (tm-30)
REVERT: C   72 ASP cc_start: 0.5325 (OUTLIER) cc_final: 0.4608 (p0)
REVERT: C   92 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7323 (mtt-85)
REVERT: C  180 THR cc_start: 0.7920 (m) cc_final: 0.7673 (t)
REVERT: C  187 LYS cc_start: 0.8436 (mppt) cc_final: 0.7558 (mmtt)
REVERT: D   31 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7669 (mmtt)
REVERT: D  123 GLU cc_start: 0.7341 (pm20) cc_final: 0.6879 (tp30)
REVERT: F   14 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8039 (tp)
REVERT: F  108 ASP cc_start: 0.7581 (t70) cc_final: 0.7136 (t70)
REVERT: F  125 GLU cc_start: 0.7290 (pm20) cc_final: 0.6931 (pm20)
REVERT: F  129 GLU cc_start: 0.7661 (pt0) cc_final: 0.7279 (pp20)
REVERT: F  226 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6974 (mm-30)
REVERT: G  141 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7625 (mtm110)
REVERT: H  303 MET cc_start: 0.5811 (tmm) cc_final: 0.5407 (tmm)
REVERT: J  303 MET cc_start: 0.6436 (ttt) cc_final: 0.6136 (mpt)
  outliers start: 39
  outliers final: 25
  residues processed: 268
  average time/residue: 1.3130
  time to fit residues: 381.3601
Evaluate side-chains
  269 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 239
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   49 GLN
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   55 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  174 ASN
Chi-restraints excluded: chain E residue  245 VAL
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   14 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue   69 THR
Chi-restraints excluded: chain G residue  136 ASP
Chi-restraints excluded: chain G residue  183 SER
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  245 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain I residue  243 ILE
Chi-restraints excluded: chain I residue  268 LYS
Chi-restraints excluded: chain I residue  316 ILE
Chi-restraints excluded: chain J residue  249 VAL
Chi-restraints excluded: chain J residue  271 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 122 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 144 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
C 105 ASN
D  29 ASN
D  83 ASN
D 174 ASN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.198550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.129382 restraints weight = 10897.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.48
r_work: 0.3238 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12783  Z= 0.140
  Angle     :  0.537  10.237  17225  Z= 0.287
  Chirality :  0.039   0.168   2012
  Planarity :  0.005   0.056   2184
  Dihedral  :  4.452  54.824   1737
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 26.56 %
    Favored  : 70.31 %
  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:  2.30 (0.21), residues: 1613
  helix:  1.92 (0.14), residues: 1389
  sheet:  None (None), residues: 0
  loop : -0.91 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  21 
 HIS   0.001   0.001   HIS G 142 
 PHE   0.026   0.002   PHE F  70 
 TYR   0.010   0.001   TYR F 110 
 ARG   0.013   0.000   ARG D  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04294 (  991)
  hydrogen bonds       : angle       4.08027 ( 2928)
  covalent geometry    : bond        0.00311 (12783)
  covalent geometry    : angle       0.53690 (17225)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14697.51 seconds
wall clock time: 252 minutes 49.65 seconds (15169.65 seconds total)