Starting phenix.real_space_refine
on Thu Feb  5 15:39:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nqj_49659/02_2026/9nqj_49659_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nqj_49659/02_2026/9nqj_49659.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nqj_49659/02_2026/9nqj_49659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nqj_49659/02_2026/9nqj_49659.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nqj_49659/02_2026/9nqj_49659_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nqj_49659/02_2026/9nqj_49659_neut.cif"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 10116 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     V       2      8.30       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      48      5.16       5
     C    6647      2.51       5
     N    1732      2.21       5
     O    1831      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10266
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2876
          Classifications: {'peptide': 371}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 350}
    Chain: "B"
      Number of atoms: 2879
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 371, 2876
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 20, 'TRANS': 350}
      Conformer: "B"
        Number of residues, atoms: 371, 2876
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 20, 'TRANS': 350}
          bond proxies already assigned to first conformer: 2921
    Chain: "F"
      Number of atoms: 2341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2341
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 14, 'TRANS': 287}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 2104
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 272, 2093
          Classifications: {'peptide': 272}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 256}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 272, 2093
          Classifications: {'peptide': 272}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 256}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2134
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 65
          Unusual residues: {' MG': 1, 'ADP': 2, 'VO4': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER G 103 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER G 103 " occ=0.50
  Time building chain proxies: 3.27, per 1000 atoms: 0.32
  Number of scatterers: 10266
  At special positions: 0
  Unit cell: (80.948, 87.556, 135.464, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     V       2     22.97
     S      48     16.00
     P       4     15.00
     Mg      2     11.99
     O    1831      8.00
     N    1732      7.00
     C    6647      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 469.6 milliseconds
  

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      48.6% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 91 through 104
      removed outlier: 4.940A  pdb=" N   GLY A  99 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   LEU A 100 " --> pdb=" O   MET A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 121
      removed outlier: 3.525A  pdb=" N   VAL A 120 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 134
    Processing helix  chain 'A' and resid 135 through 150
      removed outlier: 3.854A  pdb=" N   THR A 147 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 184
    Processing helix  chain 'A' and resid 193 through 201
    Processing helix  chain 'A' and resid 217 through 224
    Processing helix  chain 'A' and resid 227 through 234
    Processing helix  chain 'A' and resid 287 through 290
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'B' and resid 41 through 51
    Processing helix  chain 'B' and resid 91 through 103
      removed outlier: 5.049A  pdb=" N   GLY B  99 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   LEU B 100 " --> pdb=" O   MET B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 121
    Processing helix  chain 'B' and resid 135 through 150
    Processing helix  chain 'B' and resid 165 through 184
    Processing helix  chain 'B' and resid 193 through 200
    Processing helix  chain 'B' and resid 217 through 224
    Processing helix  chain 'B' and resid 227 through 234
    Processing helix  chain 'B' and resid 286 through 290
    Processing helix  chain 'B' and resid 348 through 352
      removed outlier: 3.839A  pdb=" N   CYS B 352 " --> pdb=" O   PRO B 349 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 19 through 37
      removed outlier: 3.616A  pdb=" N   GLY F  24 " --> pdb=" O   LEU F  20 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU F  30 " --> pdb=" O   LEU F  26 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL F  32 " --> pdb=" O   GLY F  28 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU F  33 " --> pdb=" O   TYR F  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 39 through 59
    Processing helix  chain 'F' and resid 62 through 79
      Proline residue:  F  70  - end of helix
    Processing helix  chain 'F' and resid 79 through 90
    Processing helix  chain 'F' and resid 261 through 269
    Processing helix  chain 'F' and resid 270 through 272
      No H-bonds generated for 'chain 'F' and resid 270 through 272'
    Processing helix  chain 'F' and resid 273 through 308
      removed outlier: 3.573A  pdb=" N   ALA F 279 " --> pdb=" O   LYS F 275 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 313 through 323
    Processing helix  chain 'F' and resid 324 through 326
      No H-bonds generated for 'chain 'F' and resid 324 through 326'
    Processing helix  chain 'F' and resid 331 through 340
    Processing helix  chain 'F' and resid 364 through 393
      Proline residue:  F 382  - end of helix
    Processing helix  chain 'F' and resid 396 through 406
      removed outlier: 4.322A  pdb=" N   TYR F 400 " --> pdb=" O   PRO F 396 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 409 through 439
      removed outlier: 4.858A  pdb=" N   LEU F 419 " --> pdb=" O   PHE F 415 " (cutoff:3.500A)
      Proline residue:  F 420  - end of helix
      removed outlier: 3.789A  pdb=" N   LYS F 424 " --> pdb=" O   PRO F 420 " (cutoff:3.500A)
      Proline residue:  F 425  - end of helix
      Proline residue:  F 428  - end of helix
    Processing helix  chain 'F' and resid 483 through 503
    Processing helix  chain 'G' and resid 8 through 29
      removed outlier: 3.527A  pdb=" N   ARG G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 33 through 38
      removed outlier: 3.914A  pdb=" N   ILE G  37 " --> pdb=" O   MET G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 42 through 44
      No H-bonds generated for 'chain 'G' and resid 42 through 44'
    Processing helix  chain 'G' and resid 68 through 69
      No H-bonds generated for 'chain 'G' and resid 68 through 69'
    Processing helix  chain 'G' and resid 83 through 113
    Processing helix  chain 'G' and resid 117 through 130
      removed outlier: 4.241A  pdb=" N   MET G 130 " --> pdb=" O   LEU G 126 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 132 through 148
      removed outlier: 3.592A  pdb=" N   SER G 136 " --> pdb=" O   PRO G 132 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   VAL G 138 " --> pdb=" O   VAL G 134 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY G 148 " --> pdb=" O   PHE G 144 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 171 through 184
    Processing helix  chain 'G' and resid 186 through 195
    Processing helix  chain 'G' and resid 198 through 206
    Processing helix  chain 'G' and resid 206 through 228
      removed outlier: 3.564A  pdb=" N   LEU G 210 " --> pdb=" O   VAL G 206 " (cutoff:3.500A)
      Proline residue:  G 213  - end of helix
    Processing helix  chain 'G' and resid 244 through 253
    Processing helix  chain 'G' and resid 262 through 283
      removed outlier: 3.931A  pdb=" N   ALA G 266 " --> pdb=" O   ASP G 262 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA G 267 " --> pdb=" O   PHE G 263 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU G 272 " --> pdb=" O   VAL G 268 " (cutoff:3.500A)
      Proline residue:  G 273  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 26
      removed outlier: 6.380A  pdb=" N   LYS A  11 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   LYS A  20 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   VAL A   9 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE A  22 " --> pdb=" O   GLN A   7 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN A   7 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LEU A  24 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   GLN A   5 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80
      removed outlier: 6.051A  pdb=" N   PHE A 155 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   VAL A 190 " --> pdb=" O   PHE A 155 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU A 157 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLN A 214 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268
      removed outlier: 6.853A  pdb=" N   GLN A 255 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292
      removed outlier: 3.634A  pdb=" N   ILE A 345 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   HIS A 317 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   VAL A 307 " --> pdb=" O   GLN A 315 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLN A 315 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   GLN A 309 " --> pdb=" O   GLU A 313 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   GLU A 313 " --> pdb=" O   GLN A 309 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 22
      removed outlier: 4.188A  pdb=" N   VAL B  16 " --> pdb=" O   TRP B  13 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL B  18 " --> pdb=" O   LYS B  11 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LYS B  11 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   LYS B  20 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL B   9 " --> pdb=" O   LYS B  20 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE B  22 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLN B   7 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL B   9 " --> pdb=" O   SER B  57 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   SER B  57 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 79
      removed outlier: 6.757A  pdb=" N   GLY B  78 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   ASP B 158 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   PHE B 155 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL B 190 " --> pdb=" O   PHE B 155 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LEU B 157 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   PHE B  31 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL B 205 " --> pdb=" O   PHE B  31 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL B  33 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   LEU B 207 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL B  35 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ILE B 204 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   VAL B 215 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL B 206 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 268
      removed outlier: 7.301A  pdb=" N   GLN B 255 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS B 245 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B 244 " --> pdb=" O   MET B 281 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LEU B 354 " --> pdb=" O   CYS B 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 292
      removed outlier: 3.507A  pdb=" N   LEU B 291 " --> pdb=" O   GLY B 346 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 332
      removed outlier: 7.163A  pdb=" N   GLU B 313 " --> pdb=" O   GLN B 309 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   GLN B 309 " --> pdb=" O   GLU B 313 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   GLN B 315 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   VAL B 307 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   HIS B 317 " --> pdb=" O   GLN B 305 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU B 303 " --> pdb=" O   GLN B 319 " (cutoff:3.500A)

    504 hydrogen bonds defined for protein.
    1456 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 3335
        1.36 -     1.49: 2579
        1.49 -     1.63: 4477
        1.63 -     1.77: 0
        1.77 -     1.91: 94
  Bond restraints: 10485
  Sorted by residual:
  bond pdb=" C4  ADP A1504 "
       pdb=" C5  ADP A1504 "
    ideal  model  delta    sigma   weight residual
    1.490  1.379  0.111 2.00e-02 2.50e+03 3.06e+01
  bond pdb=" C4  ADP A1502 "
       pdb=" C5  ADP A1502 "
    ideal  model  delta    sigma   weight residual
    1.490  1.379  0.111 2.00e-02 2.50e+03 3.06e+01
  bond pdb=" C5  ADP A1504 "
       pdb=" C6  ADP A1504 "
    ideal  model  delta    sigma   weight residual
    1.490  1.406  0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" C5  ADP A1502 "
       pdb=" C6  ADP A1502 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" N   PRO B 348 "
       pdb=" CA  PRO B 348 "
    ideal  model  delta    sigma   weight residual
    1.465  1.413  0.052 2.03e-02 2.43e+03 6.61e+00
  ... (remaining 10480 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 14043
        2.45 -     4.91: 179
        4.91 -     7.36: 37
        7.36 -     9.82: 16
        9.82 -    12.27: 4
  Bond angle restraints: 14279
  Sorted by residual:
  angle pdb=" CA  PRO B 348 "
        pdb=" N   PRO B 348 "
        pdb=" CD  PRO B 348 "
      ideal   model   delta    sigma   weight residual
     112.00   99.73   12.27 1.40e+00 5.10e-01 7.69e+01
  angle pdb=" CA  PRO G  78 "
        pdb=" N   PRO G  78 "
        pdb=" CD  PRO G  78 "
      ideal   model   delta    sigma   weight residual
     112.00  103.18    8.82 1.40e+00 5.10e-01 3.97e+01
  angle pdb=" CB  ARG G 283 "
        pdb=" CG  ARG G 283 "
        pdb=" CD  ARG G 283 "
      ideal   model   delta    sigma   weight residual
     111.30  119.73   -8.43 2.30e+00 1.89e-01 1.34e+01
  angle pdb=" CA  LEU F 497 "
        pdb=" CB  LEU F 497 "
        pdb=" CG  LEU F 497 "
      ideal   model   delta    sigma   weight residual
     116.30  128.31  -12.01 3.50e+00 8.16e-02 1.18e+01
  angle pdb=" PA  ADP A1504 "
        pdb=" O3A ADP A1504 "
        pdb=" PB  ADP A1504 "
      ideal   model   delta    sigma   weight residual
     120.50  130.15   -9.65 3.00e+00 1.11e-01 1.03e+01
  ... (remaining 14274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.09: 5843
       28.09 -    56.17: 348
       56.17 -    84.26: 48
       84.26 -   112.34: 4
      112.34 -   140.43: 2
  Dihedral angle restraints: 6245
    sinusoidal: 2462
      harmonic: 3783
  Sorted by residual:
  dihedral pdb=" O2A ADP A1502 "
           pdb=" O3A ADP A1502 "
           pdb=" PA  ADP A1502 "
           pdb=" PB  ADP A1502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   80.43 -140.43     1      2.00e+01 2.50e-03 4.25e+01
  dihedral pdb=" O2A ADP A1504 "
           pdb=" O3A ADP A1504 "
           pdb=" PA  ADP A1504 "
           pdb=" PB  ADP A1504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   80.39 -140.39     1      2.00e+01 2.50e-03 4.25e+01
  dihedral pdb=" CA  PRO F 460 "
           pdb=" C   PRO F 460 "
           pdb=" N   ALA F 461 "
           pdb=" CA  ALA F 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.68   23.32     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 6242 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1432
       0.064 -    0.128: 238
       0.128 -    0.191: 9
       0.191 -    0.255: 1
       0.255 -    0.319: 1
  Chirality restraints: 1681
  Sorted by residual:
  chirality pdb=" CG  LEU F 447 "
            pdb=" CB  LEU F 447 "
            pdb=" CD1 LEU F 447 "
            pdb=" CD2 LEU F 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.27   -0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" CB  ILE F 331 "
            pdb=" CA  ILE F 331 "
            pdb=" CG1 ILE F 331 "
            pdb=" CG2 ILE F 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  ILE F 444 "
            pdb=" CA  ILE F 444 "
            pdb=" CG1 ILE F 444 "
            pdb=" CG2 ILE F 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.24e-01
  ... (remaining 1678 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 347 "   -0.113 5.00e-02 4.00e+02   1.62e-01 4.20e+01
        pdb=" N   PRO B 348 "    0.280 5.00e-02 4.00e+02
        pdb=" CA  PRO B 348 "   -0.089 5.00e-02 4.00e+02
        pdb=" CD  PRO B 348 "   -0.078 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO G  77 "   -0.084 5.00e-02 4.00e+02   1.21e-01 2.33e+01
        pdb=" N   PRO G  78 "    0.208 5.00e-02 4.00e+02
        pdb=" CA  PRO G  78 "   -0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO G  78 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  75 "   -0.057 5.00e-02 4.00e+02   8.64e-02 1.19e+01
        pdb=" N   PRO G  76 "    0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO G  76 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO G  76 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.21: 14
        2.21 -     2.88: 3928
        2.88 -     3.55: 15224
        3.55 -     4.23: 23019
        4.23 -     4.90: 41091
  Nonbonded interactions: 83276
  Sorted by model distance:
  nonbonded pdb="MG    MG A1501 "
            pdb=" O4  VO4 A1503 "
     model   vdw
     1.533 2.170
  nonbonded pdb=" OG  SER A  43 "
            pdb="MG    MG A1501 "
     model   vdw
     1.828 2.170
  nonbonded pdb=" OG  SER B  43 "
            pdb="MG    MG B 401 "
     model   vdw
     1.974 2.170
  nonbonded pdb=" O4  VO4 A1505 "
            pdb="MG    MG B 401 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" OD1 ASN F 376 "
            pdb=" OH  TYR F 463 "
     model   vdw
     2.094 3.040
  ... (remaining 83271 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 2 through 52 or resid 54 through 1501))
  selection = (chain 'B' and (resid 2 through 52 or resid 54 through 401))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.810
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
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      :  0.010   0.743  10488  Z= 0.927
  Angle     :  0.789  12.274  14279  Z= 0.389
  Chirality :  0.046   0.319   1681
  Planarity :  0.007   0.162   1804
  Dihedral  : 17.540 140.425   3813
  Min Nonbonded Distance : 1.533

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.76 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 25.05 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.23), residues: 1307
  helix:  0.76 (0.21), residues: 627
  sheet: -0.32 (0.50), residues: 118
  loop : -1.70 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 324 
 TYR   0.041   0.002   TYR F 472 
 PHE   0.023   0.001   PHE F 287 
 TRP   0.029   0.002   TRP G 284 
 HIS   0.005   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10485)
  covalent geometry    : angle       0.78875 (14279)
  hydrogen bonds       : bond        0.13417 (  504)
  hydrogen bonds       : angle       5.68983 ( 1456)
  Misc. bond           : bond        0.53470 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 167
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: F   34 MET cc_start: 0.6626 (mmp) cc_final: 0.6408 (mmm)
REVERT: F  325 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6724 (m-10)
REVERT: G   13 LEU cc_start: 0.8558 (tp) cc_final: 0.8149 (tt)
REVERT: G  159 HIS cc_start: 0.7808 (t70) cc_final: 0.7591 (t-90)
REVERT: G  247 VAL cc_start: 0.9347 (t) cc_final: 0.9051 (t)
REVERT: G  250 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8531 (tm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1250
  time to fit residues: 27.9251
Evaluate side-chains
  120 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  325 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
B 317 HIS
F  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.093898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.062466 restraints weight = 42034.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 4.46
r_work: 0.2601 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.066  10488  Z= 0.392
  Angle     :  0.838  10.441  14279  Z= 0.411
  Chirality :  0.050   0.284   1681
  Planarity :  0.006   0.098   1804
  Dihedral  :  8.027 137.404   1441
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.07 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 23.58 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.23), residues: 1307
  helix:  0.76 (0.21), residues: 621
  sheet: -0.94 (0.44), residues: 132
  loop : -1.63 (0.25), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G 112 
 TYR   0.024   0.002   TYR B 222 
 PHE   0.029   0.002   PHE G 164 
 TRP   0.019   0.002   TRP G 284 
 HIS   0.007   0.001   HIS G 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00914 (10485)
  covalent geometry    : angle       0.83762 (14279)
  hydrogen bonds       : bond        0.05113 (  504)
  hydrogen bonds       : angle       5.25373 ( 1456)
  Misc. bond           : bond        0.00088 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7572 (ttp-170)
REVERT: A  158 ASP cc_start: 0.9032 (t0) cc_final: 0.8766 (t0)
REVERT: A  281 MET cc_start: 0.9172 (mmm) cc_final: 0.8851 (mtp)
REVERT: B  239 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8403 (ttp)
REVERT: F   34 MET cc_start: 0.6914 (mmp) cc_final: 0.6276 (mmm)
REVERT: F  379 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9022 (tt)
REVERT: F  424 LYS cc_start: 0.9283 (tttp) cc_final: 0.8912 (tppt)
REVERT: F  447 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6928 (mm)
REVERT: G    5 GLN cc_start: 0.7883 (pp30) cc_final: 0.7281 (mm-40)
REVERT: G   13 LEU cc_start: 0.8371 (tp) cc_final: 0.8000 (tt)
REVERT: G   69 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8125 (mm-40)
REVERT: G  190 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8862 (mt-10)
REVERT: G  238 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7085 (ptt-90)
REVERT: G  250 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8786 (tm-30)
  outliers start: 35
  outliers final: 17
  residues processed: 149
  average time/residue: 0.1108
  time to fit residues: 22.7308
Evaluate side-chains
  133 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  372 LEU
Chi-restraints excluded: chain F residue  375 VAL
Chi-restraints excluded: chain F residue  379 LEU
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue   21 LEU
Chi-restraints excluded: chain G residue  121 LEU
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  174 VAL
Chi-restraints excluded: chain G residue  217 VAL
Chi-restraints excluded: chain G residue  262 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 107 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   chunk 81 optimal weight:    0.0010
   chunk 84 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
F 469 ASN
G 157 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.098198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.066882 restraints weight = 44924.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 4.35
r_work: 0.2709 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10488  Z= 0.130
  Angle     :  0.680  13.335  14279  Z= 0.325
  Chirality :  0.045   0.300   1681
  Planarity :  0.005   0.075   1804
  Dihedral  :  7.626 127.315   1441
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.15 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 24.68 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.23), residues: 1307
  helix:  1.05 (0.21), residues: 619
  sheet: -0.52 (0.39), residues: 174
  loop : -1.71 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 112 
 TYR   0.023   0.001   TYR G 243 
 PHE   0.020   0.001   PHE G 164 
 TRP   0.007   0.001   TRP G 260 
 HIS   0.004   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10485)
  covalent geometry    : angle       0.68049 (14279)
  hydrogen bonds       : bond        0.03975 (  504)
  hydrogen bonds       : angle       4.78535 ( 1456)
  Misc. bond           : bond        0.00077 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7972 (ttp-170)
REVERT: A  158 ASP cc_start: 0.8991 (t0) cc_final: 0.8720 (t70)
REVERT: F  266 ARG cc_start: 0.9012 (tpt90) cc_final: 0.8749 (tpm170)
REVERT: F  271 GLU cc_start: 0.9047 (tp30) cc_final: 0.8533 (mm-30)
REVERT: F  447 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7074 (mm)
REVERT: F  482 GLN cc_start: 0.8202 (mm110) cc_final: 0.6884 (tt0)
REVERT: G    5 GLN cc_start: 0.7873 (pp30) cc_final: 0.7424 (pp30)
REVERT: G   13 LEU cc_start: 0.8411 (tp) cc_final: 0.8011 (tt)
REVERT: G   19 LEU cc_start: 0.8889 (mp) cc_final: 0.8334 (tt)
REVERT: G  157 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8547 (t160)
REVERT: G  159 HIS cc_start: 0.7581 (t70) cc_final: 0.7353 (t70)
REVERT: G  190 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8714 (mt-10)
REVERT: G  243 TYR cc_start: 0.7320 (p90) cc_final: 0.6792 (p90)
REVERT: G  250 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8700 (tm-30)
  outliers start: 24
  outliers final: 8
  residues processed: 143
  average time/residue: 0.1120
  time to fit residues: 21.5781
Evaluate side-chains
  130 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain F residue  286 VAL
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  157 ASN
Chi-restraints excluded: chain G residue  217 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   chunk 128 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0040
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
G 157 ASN
G 282 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.099102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.068401 restraints weight = 34117.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 3.78
r_work: 0.2754 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10488  Z= 0.129
  Angle     :  0.666  14.218  14279  Z= 0.314
  Chirality :  0.045   0.239   1681
  Planarity :  0.005   0.062   1804
  Dihedral  :  7.344 119.016   1441
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.15 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 25.05 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.24), residues: 1307
  helix:  1.20 (0.21), residues: 626
  sheet: -0.59 (0.38), residues: 184
  loop : -1.60 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 112 
 TYR   0.023   0.001   TYR G 243 
 PHE   0.017   0.001   PHE G 164 
 TRP   0.007   0.001   TRP G 260 
 HIS   0.005   0.001   HIS G 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10485)
  covalent geometry    : angle       0.66645 (14279)
  hydrogen bonds       : bond        0.03681 (  504)
  hydrogen bonds       : angle       4.59364 ( 1456)
  Misc. bond           : bond        0.00077 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7883 (ttp-170)
REVERT: A  158 ASP cc_start: 0.8891 (t0) cc_final: 0.8634 (t70)
REVERT: B  329 TYR cc_start: 0.9004 (t80) cc_final: 0.8710 (t80)
REVERT: F  262 LYS cc_start: 0.9261 (ptpt) cc_final: 0.9059 (tptp)
REVERT: F  393 LYS cc_start: 0.8748 (mptt) cc_final: 0.8323 (mmtp)
REVERT: F  418 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.8972 (p)
REVERT: F  424 LYS cc_start: 0.9339 (tttp) cc_final: 0.8942 (tppt)
REVERT: F  447 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6866 (mm)
REVERT: F  482 GLN cc_start: 0.8097 (mm110) cc_final: 0.6806 (tt0)
REVERT: G   13 LEU cc_start: 0.8342 (tp) cc_final: 0.7974 (tt)
REVERT: G   19 LEU cc_start: 0.8855 (mp) cc_final: 0.8295 (tt)
REVERT: G  157 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.7967 (t160)
REVERT: G  190 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8657 (mt-10)
REVERT: G  250 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8681 (tm-30)
REVERT: G  282 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8410 (tp40)
  outliers start: 22
  outliers final: 13
  residues processed: 139
  average time/residue: 0.1170
  time to fit residues: 22.0337
Evaluate side-chains
  137 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain F residue  316 VAL
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  330 PHE
Chi-restraints excluded: chain F residue  418 THR
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain G residue   21 LEU
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  157 ASN
Chi-restraints excluded: chain G residue  198 THR
Chi-restraints excluded: chain G residue  262 ASP
Chi-restraints excluded: chain G residue  282 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 121 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
G 157 ASN
G 282 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.067647 restraints weight = 33000.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 3.69
r_work: 0.2743 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10488  Z= 0.161
  Angle     :  0.671  14.013  14279  Z= 0.317
  Chirality :  0.045   0.228   1681
  Planarity :  0.005   0.056   1804
  Dihedral  :  7.279 116.455   1441
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.38 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 25.14 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.24), residues: 1307
  helix:  1.21 (0.21), residues: 627
  sheet: -0.52 (0.38), residues: 184
  loop : -1.58 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 324 
 TYR   0.023   0.001   TYR G 243 
 PHE   0.018   0.001   PHE G 128 
 TRP   0.007   0.001   TRP G 284 
 HIS   0.002   0.001   HIS G 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10485)
  covalent geometry    : angle       0.67092 (14279)
  hydrogen bonds       : bond        0.03757 (  504)
  hydrogen bonds       : angle       4.55878 ( 1456)
  Misc. bond           : bond        0.00081 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8831 (mmt) cc_final: 0.8596 (mmm)
REVERT: A  113 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7906 (ttp-170)
REVERT: A  158 ASP cc_start: 0.8888 (t0) cc_final: 0.8610 (t70)
REVERT: B  329 TYR cc_start: 0.9011 (t80) cc_final: 0.8765 (t80)
REVERT: F  262 LYS cc_start: 0.9247 (ptpt) cc_final: 0.9045 (tptp)
REVERT: F  418 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.8991 (p)
REVERT: F  424 LYS cc_start: 0.9340 (tttp) cc_final: 0.8948 (tppt)
REVERT: F  447 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6831 (mm)
REVERT: F  482 GLN cc_start: 0.8084 (mm110) cc_final: 0.6780 (tt0)
REVERT: G   13 LEU cc_start: 0.8355 (tp) cc_final: 0.7967 (tt)
REVERT: G   19 LEU cc_start: 0.8864 (mp) cc_final: 0.8287 (tt)
REVERT: G  190 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8688 (mt-10)
REVERT: G  250 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8693 (tm-30)
  outliers start: 29
  outliers final: 17
  residues processed: 144
  average time/residue: 0.1155
  time to fit residues: 22.8315
Evaluate side-chains
  135 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  316 VAL
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  418 THR
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain G residue   21 LEU
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  198 THR
Chi-restraints excluded: chain G residue  217 VAL
Chi-restraints excluded: chain G residue  262 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 114 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0870
   chunk 98 optimal weight:    8.9990
   chunk 111 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 126 optimal weight:    3.9990
   chunk 122 optimal weight:    0.4980
   overall best weight:    1.0762

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

Flipped N/Q/H residues before XYZ refinement:
** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.097802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.067301 restraints weight = 38880.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 4.05
r_work: 0.2728 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10488  Z= 0.144
  Angle     :  0.675  14.581  14279  Z= 0.318
  Chirality :  0.044   0.225   1681
  Planarity :  0.004   0.054   1804
  Dihedral  :  7.180 112.856   1441
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.07 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.05 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.24), residues: 1307
  helix:  1.27 (0.21), residues: 627
  sheet: -0.49 (0.38), residues: 184
  loop : -1.53 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 324 
 TYR   0.025   0.001   TYR G 243 
 PHE   0.017   0.001   PHE G 164 
 TRP   0.007   0.001   TRP G 284 
 HIS   0.003   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10485)
  covalent geometry    : angle       0.67460 (14279)
  hydrogen bonds       : bond        0.03635 (  504)
  hydrogen bonds       : angle       4.50327 ( 1456)
  Misc. bond           : bond        0.00079 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8818 (mmt) cc_final: 0.8582 (mmm)
REVERT: A  113 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7911 (ttp-170)
REVERT: A  158 ASP cc_start: 0.8849 (t0) cc_final: 0.8594 (t70)
REVERT: B  187 MET cc_start: 0.8591 (mtp) cc_final: 0.8350 (mtt)
REVERT: B  329 TYR cc_start: 0.9027 (t80) cc_final: 0.8774 (t80)
REVERT: F  271 GLU cc_start: 0.9038 (tp30) cc_final: 0.8603 (pm20)
REVERT: F  418 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.8980 (p)
REVERT: F  424 LYS cc_start: 0.9342 (tttp) cc_final: 0.8946 (tppt)
REVERT: F  447 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6764 (mm)
REVERT: F  482 GLN cc_start: 0.8073 (mm110) cc_final: 0.6783 (tt0)
REVERT: G   13 LEU cc_start: 0.8354 (tp) cc_final: 0.7978 (tt)
REVERT: G   19 LEU cc_start: 0.8875 (mp) cc_final: 0.8300 (tt)
REVERT: G  182 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9230 (mm-30)
REVERT: G  190 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8686 (mt-10)
REVERT: G  250 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8687 (tm-30)
REVERT: G  252 TYR cc_start: 0.7918 (t80) cc_final: 0.7627 (t80)
  outliers start: 32
  outliers final: 21
  residues processed: 149
  average time/residue: 0.1131
  time to fit residues: 23.1836
Evaluate side-chains
  136 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  327 VAL
Chi-restraints excluded: chain F residue  418 THR
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain F residue  457 THR
Chi-restraints excluded: chain G residue    4 VAL
Chi-restraints excluded: chain G residue   21 LEU
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  198 THR
Chi-restraints excluded: chain G residue  217 VAL
Chi-restraints excluded: chain G residue  262 ASP
Chi-restraints excluded: chain G residue  272 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 97 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0870
   chunk 19 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.7164

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

Flipped N/Q/H residues before XYZ refinement:
** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.066027 restraints weight = 40634.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 4.11
r_work: 0.2695 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10488  Z= 0.189
  Angle     :  0.705  14.610  14279  Z= 0.333
  Chirality :  0.045   0.217   1681
  Planarity :  0.005   0.053   1804
  Dihedral  :  7.200 112.340   1441
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.22 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 25.32 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.24), residues: 1307
  helix:  1.28 (0.21), residues: 628
  sheet: -0.56 (0.38), residues: 184
  loop : -1.49 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 263 
 TYR   0.024   0.001   TYR G 243 
 PHE   0.020   0.001   PHE G 128 
 TRP   0.009   0.001   TRP G 284 
 HIS   0.003   0.001   HIS G 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (10485)
  covalent geometry    : angle       0.70475 (14279)
  hydrogen bonds       : bond        0.03829 (  504)
  hydrogen bonds       : angle       4.55059 ( 1456)
  Misc. bond           : bond        0.00091 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7905 (ttp-170)
REVERT: A  116 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8557 (tm-30)
REVERT: A  158 ASP cc_start: 0.8889 (t0) cc_final: 0.8621 (t70)
REVERT: B  187 MET cc_start: 0.8658 (mtp) cc_final: 0.8407 (mtt)
REVERT: B  329 TYR cc_start: 0.9025 (t80) cc_final: 0.8812 (t80)
REVERT: F  418 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.8981 (p)
REVERT: F  424 LYS cc_start: 0.9350 (tttp) cc_final: 0.8956 (tppt)
REVERT: F  447 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6578 (mm)
REVERT: F  482 GLN cc_start: 0.8069 (mm110) cc_final: 0.6758 (tt0)
REVERT: F  486 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8268 (mm)
REVERT: G    3 MET cc_start: 0.7253 (ttm) cc_final: 0.6843 (ttm)
REVERT: G   13 LEU cc_start: 0.8375 (tp) cc_final: 0.7986 (tt)
REVERT: G   19 LEU cc_start: 0.8871 (mp) cc_final: 0.8303 (tt)
REVERT: G  121 LEU cc_start: 0.9123 (mt) cc_final: 0.8570 (mt)
REVERT: G  190 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8639 (mt-10)
REVERT: G  250 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8702 (tm-30)
REVERT: G  252 TYR cc_start: 0.7946 (t80) cc_final: 0.7664 (t80)
REVERT: G  282 GLN cc_start: 0.8864 (tp40) cc_final: 0.8354 (tp40)
  outliers start: 33
  outliers final: 23
  residues processed: 149
  average time/residue: 0.1086
  time to fit residues: 22.1720
Evaluate side-chains
  144 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  285 VAL
Chi-restraints excluded: chain F residue  286 VAL
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  327 VAL
Chi-restraints excluded: chain F residue  418 THR
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain F residue  457 THR
Chi-restraints excluded: chain F residue  486 LEU
Chi-restraints excluded: chain G residue    4 VAL
Chi-restraints excluded: chain G residue   21 LEU
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  198 THR
Chi-restraints excluded: chain G residue  217 VAL
Chi-restraints excluded: chain G residue  262 ASP
Chi-restraints excluded: chain G residue  272 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 75 optimal weight:   30.0000
   chunk 73 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 123 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.064733 restraints weight = 49998.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 4.89
r_work: 0.2639 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2644
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2644 r_free = 0.2644    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2644
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10488  Z= 0.222
  Angle     :  0.735  15.396  14279  Z= 0.346
  Chirality :  0.046   0.221   1681
  Planarity :  0.005   0.053   1804
  Dihedral  :  7.310 112.830   1441
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.53 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 25.23 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.24), residues: 1307
  helix:  1.33 (0.21), residues: 617
  sheet: -0.67 (0.38), residues: 184
  loop : -1.48 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 263 
 TYR   0.025   0.002   TYR G 243 
 PHE   0.021   0.001   PHE G 128 
 TRP   0.011   0.001   TRP G 284 
 HIS   0.003   0.001   HIS G 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (10485)
  covalent geometry    : angle       0.73462 (14279)
  hydrogen bonds       : bond        0.04091 (  504)
  hydrogen bonds       : angle       4.65102 ( 1456)
  Misc. bond           : bond        0.00099 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7936 (ttp-170)
REVERT: A  116 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8563 (tm-30)
REVERT: A  158 ASP cc_start: 0.8991 (t0) cc_final: 0.8753 (t70)
REVERT: B  187 MET cc_start: 0.8752 (mtp) cc_final: 0.8462 (mtt)
REVERT: F   25 LEU cc_start: 0.8707 (mm) cc_final: 0.8441 (pp)
REVERT: F  262 LYS cc_start: 0.9245 (ptpt) cc_final: 0.9010 (tptp)
REVERT: F  271 GLU cc_start: 0.8958 (tp30) cc_final: 0.8599 (pm20)
REVERT: F  418 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.8991 (p)
REVERT: F  424 LYS cc_start: 0.9361 (tttp) cc_final: 0.8967 (tppt)
REVERT: F  447 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6548 (mm)
REVERT: F  482 GLN cc_start: 0.8092 (mm110) cc_final: 0.6799 (tt0)
REVERT: G    3 MET cc_start: 0.7317 (ttm) cc_final: 0.6864 (ttm)
REVERT: G   19 LEU cc_start: 0.8887 (mp) cc_final: 0.8318 (tt)
REVERT: G  190 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8629 (mt-10)
REVERT: G  250 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8722 (tm-30)
REVERT: G  252 TYR cc_start: 0.8059 (t80) cc_final: 0.7815 (t80)
REVERT: G  282 GLN cc_start: 0.8923 (tp40) cc_final: 0.8446 (tp40)
  outliers start: 34
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1131
  time to fit residues: 22.6509
Evaluate side-chains
  142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  285 VAL
Chi-restraints excluded: chain F residue  286 VAL
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  327 VAL
Chi-restraints excluded: chain F residue  379 LEU
Chi-restraints excluded: chain F residue  418 THR
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain F residue  457 THR
Chi-restraints excluded: chain G residue    4 VAL
Chi-restraints excluded: chain G residue   21 LEU
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  198 THR
Chi-restraints excluded: chain G residue  217 VAL
Chi-restraints excluded: chain G residue  262 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 118 optimal weight:    6.9990
   chunk 114 optimal weight:    8.9990
   chunk 80 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 88 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0020
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.098972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.067477 restraints weight = 47063.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 4.45
r_work: 0.2717 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10488  Z= 0.124
  Angle     :  0.691  15.684  14279  Z= 0.322
  Chirality :  0.044   0.222   1681
  Planarity :  0.004   0.051   1804
  Dihedral  :  7.101 109.577   1441
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.07 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 25.96 %
    Favored  : 71.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.24), residues: 1307
  helix:  1.45 (0.22), residues: 611
  sheet: -0.54 (0.38), residues: 184
  loop : -1.35 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 263 
 TYR   0.019   0.001   TYR G 243 
 PHE   0.022   0.001   PHE G 128 
 TRP   0.007   0.001   TRP G 260 
 HIS   0.003   0.000   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10485)
  covalent geometry    : angle       0.69147 (14279)
  hydrogen bonds       : bond        0.03560 (  504)
  hydrogen bonds       : angle       4.49395 ( 1456)
  Misc. bond           : bond        0.00069 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8810 (mmt) cc_final: 0.8605 (mmm)
REVERT: A  113 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7945 (ttp-170)
REVERT: A  116 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8591 (tm-30)
REVERT: A  158 ASP cc_start: 0.8907 (t0) cc_final: 0.8656 (t70)
REVERT: B  187 MET cc_start: 0.8661 (mtp) cc_final: 0.8410 (mtm)
REVERT: F   25 LEU cc_start: 0.8694 (mm) cc_final: 0.8452 (pp)
REVERT: F  271 GLU cc_start: 0.8902 (tp30) cc_final: 0.8598 (pm20)
REVERT: F  330 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7186 (m-80)
REVERT: F  393 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7880 (mmmt)
REVERT: F  418 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.8975 (p)
REVERT: F  424 LYS cc_start: 0.9368 (tttp) cc_final: 0.8975 (tppt)
REVERT: F  482 GLN cc_start: 0.8384 (mm110) cc_final: 0.7191 (tt0)
REVERT: G    3 MET cc_start: 0.7167 (ttm) cc_final: 0.6716 (ttm)
REVERT: G   19 LEU cc_start: 0.8896 (mp) cc_final: 0.8367 (tt)
REVERT: G  121 LEU cc_start: 0.9137 (mt) cc_final: 0.8588 (mt)
REVERT: G  178 LYS cc_start: 0.8705 (tttm) cc_final: 0.8384 (tttp)
REVERT: G  182 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9196 (mm-30)
REVERT: G  190 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8607 (mt-10)
REVERT: G  250 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8668 (tm-30)
REVERT: G  252 TYR cc_start: 0.8060 (t80) cc_final: 0.7798 (t80)
REVERT: G  269 MET cc_start: 0.8560 (mmp) cc_final: 0.8333 (mmp)
REVERT: G  282 GLN cc_start: 0.8830 (tp40) cc_final: 0.8452 (tp40)
  outliers start: 28
  outliers final: 22
  residues processed: 145
  average time/residue: 0.1082
  time to fit residues: 21.5471
Evaluate side-chains
  143 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  286 VAL
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  327 VAL
Chi-restraints excluded: chain F residue  330 PHE
Chi-restraints excluded: chain F residue  379 LEU
Chi-restraints excluded: chain F residue  393 LYS
Chi-restraints excluded: chain F residue  418 THR
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain F residue  457 THR
Chi-restraints excluded: chain G residue    4 VAL
Chi-restraints excluded: chain G residue   32 LEU
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  198 THR
Chi-restraints excluded: chain G residue  217 VAL
Chi-restraints excluded: chain G residue  262 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
F 307 GLN
** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.065723 restraints weight = 51699.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 5.02
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10488  Z= 0.185
  Angle     :  0.729  16.117  14279  Z= 0.340
  Chirality :  0.045   0.204   1681
  Planarity :  0.005   0.052   1804
  Dihedral  :  7.129 111.182   1441
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.30 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 26.05 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.24), residues: 1307
  helix:  1.48 (0.22), residues: 607
  sheet: -0.59 (0.38), residues: 184
  loop : -1.38 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 263 
 TYR   0.023   0.002   TYR G 243 
 PHE   0.022   0.001   PHE G 128 
 TRP   0.009   0.001   TRP G 284 
 HIS   0.002   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (10485)
  covalent geometry    : angle       0.72908 (14279)
  hydrogen bonds       : bond        0.03865 (  504)
  hydrogen bonds       : angle       4.54485 ( 1456)
  Misc. bond           : bond        0.00091 (    3)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7859 (ttp-170)
REVERT: A  116 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8391 (tm-30)
REVERT: A  158 ASP cc_start: 0.8632 (t0) cc_final: 0.8319 (t70)
REVERT: B  187 MET cc_start: 0.8224 (mtp) cc_final: 0.7927 (mtm)
REVERT: F   25 LEU cc_start: 0.8671 (mm) cc_final: 0.8441 (pp)
REVERT: F  271 GLU cc_start: 0.8968 (tp30) cc_final: 0.8645 (pm20)
REVERT: F  330 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7126 (m-80)
REVERT: F  393 LYS cc_start: 0.8728 (mptt) cc_final: 0.7970 (mmmt)
REVERT: F  418 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8891 (p)
REVERT: F  424 LYS cc_start: 0.9276 (tttp) cc_final: 0.8940 (tppt)
REVERT: F  447 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6231 (mm)
REVERT: F  482 GLN cc_start: 0.8327 (mm110) cc_final: 0.7079 (tt0)
REVERT: G    3 MET cc_start: 0.6664 (ttm) cc_final: 0.6123 (ttm)
REVERT: G   19 LEU cc_start: 0.8860 (mp) cc_final: 0.8303 (tt)
REVERT: G  121 LEU cc_start: 0.9054 (mt) cc_final: 0.8537 (mt)
REVERT: G  178 LYS cc_start: 0.8732 (tttm) cc_final: 0.8428 (tttm)
REVERT: G  182 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9108 (mm-30)
REVERT: G  190 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8326 (mt-10)
REVERT: G  250 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8647 (tm-30)
REVERT: G  252 TYR cc_start: 0.7919 (t80) cc_final: 0.7639 (t80)
REVERT: G  282 GLN cc_start: 0.8796 (tp40) cc_final: 0.8377 (tp40)
  outliers start: 30
  outliers final: 25
  residues processed: 143
  average time/residue: 0.1073
  time to fit residues: 20.9925
Evaluate side-chains
  146 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain F residue  278 LEU
Chi-restraints excluded: chain F residue  286 VAL
Chi-restraints excluded: chain F residue  307 GLN
Chi-restraints excluded: chain F residue  325 TYR
Chi-restraints excluded: chain F residue  327 VAL
Chi-restraints excluded: chain F residue  330 PHE
Chi-restraints excluded: chain F residue  379 LEU
Chi-restraints excluded: chain F residue  418 THR
Chi-restraints excluded: chain F residue  447 LEU
Chi-restraints excluded: chain F residue  454 ARG
Chi-restraints excluded: chain F residue  457 THR
Chi-restraints excluded: chain G residue    4 VAL
Chi-restraints excluded: chain G residue   32 LEU
Chi-restraints excluded: chain G residue   44 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  151 ILE
Chi-restraints excluded: chain G residue  198 THR
Chi-restraints excluded: chain G residue  217 VAL
Chi-restraints excluded: chain G residue  262 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 114 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0980
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 121 optimal weight:    0.9980
   chunk 75 optimal weight:   30.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.097611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.067583 restraints weight = 33455.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 3.74
r_work: 0.2734 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10488  Z= 0.137
  Angle     :  0.722  16.126  14279  Z= 0.337
  Chirality :  0.045   0.199   1681
  Planarity :  0.005   0.051   1804
  Dihedral  :  7.119 110.629   1441
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.38 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 26.05 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.24), residues: 1307
  helix:  1.51 (0.22), residues: 606
  sheet: -0.54 (0.38), residues: 184
  loop : -1.36 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 263 
 TYR   0.021   0.001   TYR G 243 
 PHE   0.024   0.001   PHE G 128 
 TRP   0.007   0.001   TRP G 284 
 HIS   0.003   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10485)
  covalent geometry    : angle       0.72152 (14279)
  hydrogen bonds       : bond        0.03789 (  504)
  hydrogen bonds       : angle       4.50500 ( 1456)
  Misc. bond           : bond        0.00078 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2397.04 seconds
wall clock time: 41 minutes 44.43 seconds (2504.43 seconds total)