Starting phenix.real_space_refine
on Wed Aug  5 00:14:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w35_65591/08_2026/9w35_65591_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w35_65591/08_2026/9w35_65591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w35_65591/08_2026/9w35_65591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w35_65591/08_2026/9w35_65591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w35_65591/08_2026/9w35_65591_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w35_65591/08_2026/9w35_65591_trim.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       8      5.16       5
     C    4692      2.51       5
     N    1381      2.21       5
     O    1405      1.98       5
     F      12      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7498
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1302
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 215}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 437
          Unresolved non-hydrogen angles: 551
          Unresolved non-hydrogen dihedrals: 348
          Unresolved non-hydrogen chiralities: 44
          Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 12, 'TYR:plan': 2, 'HIS:plan': 4, 'PHE:plan': 4, 'GLN:plan1': 9, 'ASN:plan1': 2, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 232
    Chain: "A"
      Number of atoms: 2376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 2376
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 217}
          Link IDs: {'PTRANS': 15, 'TRANS': 385}
          Chain breaks: 1
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 733
          Unresolved non-hydrogen angles: 945
          Unresolved non-hydrogen dihedrals: 580
          Unresolved non-hydrogen chiralities: 100
          Planarities with less than four sites: {'PHE:plan': 7, 'ARG:plan': 10, 'ASN:plan1': 11, 'ASP:plan': 17, 'GLU:plan': 7, 'GLN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 3, 'TYR:plan': 6}
          Unresolved non-hydrogen planarities: 327
    Chain: "B"
      Number of atoms: 2362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 2362
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 223}
          Link IDs: {'PTRANS': 15, 'TRANS': 385}
          Chain breaks: 1
          Unresolved chain link angles: 11
          Unresolved non-hydrogen bonds: 752
          Unresolved non-hydrogen angles: 972
          Unresolved non-hydrogen dihedrals: 598
          Unresolved non-hydrogen chiralities: 101
          Planarities with less than four sites: {'ARG:plan': 11, 'ASN:plan1': 12, 'ASP:plan': 17, 'GLU:plan': 7, 'GLN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'PHE:plan': 7}
          Unresolved non-hydrogen planarities: 335
    Chain: "D"
      Number of atoms: 1346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1346
          Classifications: {'peptide': 223}
          Incomplete info: {'truncation_to_alanine': 109}
          Link IDs: {'PTRANS': 6, 'TRANS': 216}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 398
          Unresolved non-hydrogen angles: 501
          Unresolved non-hydrogen dihedrals: 320
          Unresolved non-hydrogen chiralities: 37
          Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 12, 'HIS:plan': 1, 'PHE:plan': 4, 'GLN:plan1': 8, 'ASN:plan1': 2, 'ARG:plan': 7, 'TYR:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 217
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'R6Q': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'R6Q': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.03, per 1000 atoms: 0.27
  Number of scatterers: 7498
  At special positions: 0
  Unit cell: (90.143, 66.16, 140.59, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     F      12      9.00
     O    1405      8.00
     N    1381      7.00
     C    4692      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 414.8 milliseconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2298

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 14 sheets defined
      58.9% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'C' and resid 47 through 56
    Processing helix  chain 'C' and resid 77 through 88
    Processing helix  chain 'C' and resid 103 through 114
      Proline residue:  C 111  - end of helix
    Processing helix  chain 'C' and resid 119 through 134
      removed outlier: 3.808A  pdb=" N   ALA C 125 " --> pdb=" O   LYS C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 3.545A  pdb=" N   MET C 140 " --> pdb=" O   SER C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 147
    Processing helix  chain 'C' and resid 148 through 163
      removed outlier: 4.498A  pdb=" N   THR C 163 " --> pdb=" O   ARG C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 176
      removed outlier: 4.438A  pdb=" N   ASN C 176 " --> pdb=" O   PRO C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 197
    Processing helix  chain 'C' and resid 206 through 213
    Processing helix  chain 'A' and resid 4 through 15
    Processing helix  chain 'A' and resid 20 through 62
      removed outlier: 4.078A  pdb=" N   SER A  24 " --> pdb=" O   ASN A  20 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   LEU A  60 " --> pdb=" O   LYS A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 87
      removed outlier: 3.544A  pdb=" N   LEU A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   HIS A  87 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 108
    Processing helix  chain 'A' and resid 118 through 125
    Processing helix  chain 'A' and resid 136 through 140
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 197 through 200
      removed outlier: 3.595A  pdb=" N   SER A 200 " --> pdb=" O   GLU A 197 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 197 through 200'
    Processing helix  chain 'A' and resid 206 through 215
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 232 through 243
    Processing helix  chain 'A' and resid 253 through 297
      removed outlier: 5.429A  pdb=" N   ASN A 259 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 308
    Processing helix  chain 'A' and resid 310 through 342
    Processing helix  chain 'A' and resid 343 through 356
    Processing helix  chain 'A' and resid 373 through 401
      removed outlier: 3.507A  pdb=" N   VAL A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      Proline residue:  A 395  - end of helix
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'B' and resid 4 through 15
    Processing helix  chain 'B' and resid 20 through 63
      removed outlier: 3.864A  pdb=" N   SER B  24 " --> pdb=" O   ASN B  20 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   VAL B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   LEU B  60 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 87
      removed outlier: 3.640A  pdb=" N   LEU B  80 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   HIS B  87 " --> pdb=" O   ARG B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 126
    Processing helix  chain 'B' and resid 127 through 132
      removed outlier: 3.672A  pdb=" N   HIS B 131 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'B' and resid 150 through 158
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.542A  pdb=" N   ASP B 199 " --> pdb=" O   ALA B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 214
    Processing helix  chain 'B' and resid 229 through 231
      No H-bonds generated for 'chain 'B' and resid 229 through 231'
    Processing helix  chain 'B' and resid 232 through 243
    Processing helix  chain 'B' and resid 253 through 258
    Processing helix  chain 'B' and resid 261 through 297
    Processing helix  chain 'B' and resid 297 through 308
    Processing helix  chain 'B' and resid 310 through 342
    Processing helix  chain 'B' and resid 343 through 355
    Processing helix  chain 'B' and resid 373 through 401
      removed outlier: 3.944A  pdb=" N   TYR B 394 " --> pdb=" O   LEU B 390 " (cutoff:3.500A)
      Proline residue:  B 395  - end of helix
    Processing helix  chain 'B' and resid 403 through 408
    Processing helix  chain 'D' and resid 47 through 56
    Processing helix  chain 'D' and resid 77 through 89
    Processing helix  chain 'D' and resid 103 through 114
      Proline residue:  D 111  - end of helix
    Processing helix  chain 'D' and resid 119 through 134
      removed outlier: 3.852A  pdb=" N   ALA D 125 " --> pdb=" O   LYS D 121 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL D 134 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 139
      removed outlier: 4.564A  pdb=" N   HIS D 138 " --> pdb=" O   GLY D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 147
    Processing helix  chain 'D' and resid 148 through 163
      removed outlier: 4.550A  pdb=" N   THR D 163 " --> pdb=" O   ARG D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 197
    Processing helix  chain 'D' and resid 206 through 212
      removed outlier: 3.649A  pdb=" N   ALA D 210 " --> pdb=" O   ASP D 206 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 6 through 8
    Processing sheet with id=AA2, first strand: chain 'C' and resid 13 through 14
    Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 204
      removed outlier: 6.186A  pdb=" N   ILE C  40 " --> pdb=" O   THR C 204 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER C  39 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 89 through 92
      removed outlier: 3.508A  pdb=" N   LEU C 169 " --> pdb=" O   GLY C  90 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   VAL C  92 " --> pdb=" O   LEU C 169 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 205
      removed outlier: 3.781A  pdb=" N   GLY A 203 " --> pdb=" O   MET A 113 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ALA A  66 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 103
      removed outlier: 3.879A  pdb=" N   VAL A 168 " --> pdb=" O   MET A 102 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 96
      removed outlier: 3.600A  pdb=" N   PHE B  96 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ALA B  66 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 149
    Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 167
      removed outlier: 3.771A  pdb=" N   PHE B 186 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 30 through 32
      removed outlier: 3.889A  pdb=" N   LEU D   6 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 14
      removed outlier: 6.772A  pdb=" N   LYS D  13 " --> pdb=" O   VAL D  24 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 39 through 41
    Processing sheet with id=AB4, first strand: chain 'D' and resid 90 through 92
      removed outlier: 6.749A  pdb=" N   GLY D  90 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'D' and resid 218 through 219
      removed outlier: 3.961A  pdb=" N   HIS D 218 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)

    534 hydrogen bonds defined for protein.
    1527 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: 1.05

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1318
        1.31 -     1.43: 1890
        1.43 -     1.55: 4355
        1.55 -     1.68: 20
        1.68 -     1.80: 16
  Bond restraints: 7599
  Sorted by residual:
  bond pdb=" C03 R6Q B 502 "
       pdb=" C04 R6Q B 502 "
    ideal  model  delta    sigma   weight residual
    1.386  1.190  0.196 2.00e-02 2.50e+03 9.63e+01
  bond pdb=" C03 R6Q A 501 "
       pdb=" C04 R6Q A 501 "
    ideal  model  delta    sigma   weight residual
    1.386  1.191  0.195 2.00e-02 2.50e+03 9.51e+01
  bond pdb=" C03 R6Q B 501 "
       pdb=" C04 R6Q B 501 "
    ideal  model  delta    sigma   weight residual
    1.386  1.193  0.193 2.00e-02 2.50e+03 9.34e+01
  bond pdb=" C03 R6Q A 502 "
       pdb=" C04 R6Q A 502 "
    ideal  model  delta    sigma   weight residual
    1.386  1.193  0.193 2.00e-02 2.50e+03 9.31e+01
  bond pdb=" C04 R6Q B 502 "
       pdb=" C05 R6Q B 502 "
    ideal  model  delta    sigma   weight residual
    1.389  1.209  0.180 2.00e-02 2.50e+03 8.07e+01
  ... (remaining 7594 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 10366
        2.97 -     5.93: 90
        5.93 -     8.90: 6
        8.90 -    11.87: 5
       11.87 -    14.84: 13
  Bond angle restraints: 10480
  Sorted by residual:
  angle pdb=" C03 R6Q A 501 "
        pdb=" C04 R6Q A 501 "
        pdb=" C05 R6Q A 501 "
      ideal   model   delta    sigma   weight residual
     119.42  134.26  -14.84 3.00e+00 1.11e-01 2.45e+01
  angle pdb=" C03 R6Q B 501 "
        pdb=" C04 R6Q B 501 "
        pdb=" C05 R6Q B 501 "
      ideal   model   delta    sigma   weight residual
     119.42  134.15  -14.73 3.00e+00 1.11e-01 2.41e+01
  angle pdb=" C03 R6Q A 502 "
        pdb=" C04 R6Q A 502 "
        pdb=" C05 R6Q A 502 "
      ideal   model   delta    sigma   weight residual
     119.42  134.09  -14.67 3.00e+00 1.11e-01 2.39e+01
  angle pdb=" C03 R6Q B 502 "
        pdb=" C04 R6Q B 502 "
        pdb=" C05 R6Q B 502 "
      ideal   model   delta    sigma   weight residual
     119.42  134.05  -14.63 3.00e+00 1.11e-01 2.38e+01
  angle pdb=" C08 R6Q B 501 "
        pdb=" O09 R6Q B 501 "
        pdb=" C10 R6Q B 501 "
      ideal   model   delta    sigma   weight residual
     121.54  107.81   13.73 3.00e+00 1.11e-01 2.10e+01
  ... (remaining 10475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.66: 4165
       25.66 -    51.33: 174
       51.33 -    76.99: 19
       76.99 -   102.65: 6
      102.65 -   128.31: 4
  Dihedral angle restraints: 4368
    sinusoidal: 809
      harmonic: 3559
  Sorted by residual:
  dihedral pdb=" CA  GLY B 258 "
           pdb=" C   GLY B 258 "
           pdb=" N   ASN B 259 "
           pdb=" CA  ASN B 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.23   23.77     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" C10 R6Q A 502 "
           pdb=" C14 R6Q A 502 "
           pdb=" C15 R6Q A 502 "
           pdb=" N13 R6Q A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.48   71.83 -128.31     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" C10 R6Q B 501 "
           pdb=" C14 R6Q B 501 "
           pdb=" C15 R6Q B 501 "
           pdb=" N13 R6Q B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.48   70.97 -127.45     1      3.00e+01 1.11e-03 1.72e+01
  ... (remaining 4365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 614
       0.024 -    0.048: 413
       0.048 -    0.072: 163
       0.072 -    0.095: 62
       0.095 -    0.119: 62
  Chirality restraints: 1314
  Sorted by residual:
  chirality pdb=" CA  VAL B 194 "
            pdb=" N   VAL B 194 "
            pdb=" C   VAL B 194 "
            pdb=" CB  VAL B 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.56e-01
  chirality pdb=" CA  PRO B  78 "
            pdb=" N   PRO B  78 "
            pdb=" C   PRO B  78 "
            pdb=" CB  PRO B  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.53e-01
  chirality pdb=" CA  ILE B 205 "
            pdb=" N   ILE B 205 "
            pdb=" C   ILE B 205 "
            pdb=" CB  ILE B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.43e-01
  ... (remaining 1311 not shown)

  Planarity restraints: 1402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 261 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   PHE B 261 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   PHE B 261 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN B 262 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 254 "   -0.012 2.00e-02 2.50e+03   2.41e-02 5.78e+00
        pdb=" C   THR A 254 "    0.042 2.00e-02 2.50e+03
        pdb=" O   THR A 254 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR A 255 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  57 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.79e+00
        pdb=" C   ASN A  57 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ASN A  57 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A  58 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1399 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 171
        2.68 -     3.24: 8002
        3.24 -     3.79: 11423
        3.79 -     4.35: 13395
        4.35 -     4.90: 22980
  Nonbonded interactions: 55971
  Sorted by model distance:
  nonbonded pdb=" F27 R6Q B 501 "
            pdb=" F25 R6Q B 502 "
     model   vdw
     2.128 2.940
  nonbonded pdb=" OD1 ASP D 178 "
            pdb=" N   THR D 181 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OD1 ASP C 178 "
            pdb=" N   THR C 181 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" N   ALA C   8 "
            pdb=" O   LEU C  30 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   THR D 163 "
            pdb=" OG1 THR D 163 "
     model   vdw
     2.322 3.040
  ... (remaining 55966 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 1 through 7 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 8 through 14 or (resid 15 through 20 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 21 through 22 or (resid 23 through 2 \ 
4 and (name N or name CA or name C or name O or name CB )) or resid 25 through 3 \ 
0 or (resid 31 and (name N or name CA or name C or name O or name CB )) or resid \ 
 32 through 35 or (resid 36 and (name N or name CA or name C or name O or name C \ 
B )) or resid 37 through 41 or (resid 42 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 43 through 48 or (resid 49 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 50 through 62 or (resid 63 through 69 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 70 through 77 or \ 
 (resid 78 through 91 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 92 through 118 or (resid 119 through 134 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 135 through 169 or (resid 170 through 189 and \ 
 (name N or name CA or name C or name O or name CB )) or (resid 190 through 194  \ 
and (name N or name CA or name C or name O or name CB )) or resid 195 through 20 \ 
4 or (resid 205 through 211 and (name N or name CA or name C or name O or name C \ 
B )) or resid 212 through 223 or (resid 224 through 230 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 231 through 250 or (resid 251 through  \ 
253 and (name N or name CA or name C or name O or name CB )) or resid 254 throug \ 
h 272 or (resid 273 through 276 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 277 through 287 or (resid 288 through 293 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 294 through 320 or (resid 321 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 322 through 324 or \ 
 (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 
6 through 341 or (resid 342 and (name N or name CA or name C or name O or name C \ 
B )) or resid 343 or (resid 344 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 345 through 349 or (resid 350 through 352 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 353 or (resid 354 through 355 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 356 through 365 or \ 
 (resid 366 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 
7 through 371 or (resid 372 through 380 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 381 through 382 or (resid 383 through 388 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 389 through 400 or (resid  \ 
401 through 403 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 404 through 502))
  selection = (chain 'B' and ((resid 1 through 7 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 8 through 16 or (resid 17 through 20 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 25 through 34 or (resid \ 
 35 through 36 and (name N or name CA or name C or name O or name CB )) or resid \ 
 37 through 56 or (resid 57 through 60 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 61 through 165 or (resid 166 through 189 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 190 through 200 or (resid 20 \ 
1 and (name N or name CA or name C or name O or name CB )) or resid 202 through  \ 
203 or (resid 204 through 211 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 212 through 216 or (resid 217 through 218 and (name N or name CA \ 
 or name C or name O or name CB )) or (resid 219 through 230 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 231 through 248 or (resid 249 thr \ 
ough 253 and (name N or name CA or name C or name O or name CB )) or resid 254 t \ 
hrough 255 or (resid 256 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 257 through 259 or (resid 260 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 261 through 264 or (resid 265 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 266 through 277 or (resid 278 through \ 
 284 and (name N or name CA or name C or name O or name CB )) or resid 285 throu \ 
gh 291 or (resid 292 through 293 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 294 through 296 or (resid 297 through 298 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 299 through 313 or (resid 314 thr \ 
ough 315 and (name N or name CA or name C or name O or name CB )) or resid 316 t \ 
hrough 326 or (resid 327 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 328 through 347 or (resid 348 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 349 through 358 or (resid 359 through 362 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 363 through 373 or (resid \ 
 374 through 380 and (name N or name CA or name C or name O or name CB )) or res \ 
id 381 through 386 or (resid 387 through 388 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 389 or (resid 390 through 393 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 394 through 502))
}
ncs_group {
  reference = (chain 'C' and (resid 5 through 64 or (resid 65 through 66 and (name N or name C \ 
A or name C or name O or name CB )) or resid 67 through 70 or (resid 71 through  \ 
76 and (name N or name CA or name C or name O or name CB )) or resid 77 through  \ 
87 or (resid 88 through 89 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 90 through 101 or (resid 102 through 104 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 105 through 114 or (resid 115 through 12 \ 
1 and (name N or name CA or name C or name O or name CB )) or resid 122 through  \ 
136 or (resid 137 through 141 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 142 through 147 or (resid 148 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 149 through 156 or (resid 157 through 158 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 159 through 160 or ( \ 
resid 161 through 164 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 165 through 223 or (resid 224 through 225 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 226))
  selection = (chain 'D' and (resid 5 or (resid 6 through 12 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 13 through 25 or (resid 26 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 27 through 43 or (resid 44 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 45 through 53 or (res \ 
id 54 through 55 and (name N or name CA or name C or name O or name CB )) or res \ 
id 56 through 59 or (resid 60 through 63 and (name N or name CA or name C or nam \ 
e O or name CB )) or (resid 64 through 66 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 67 through 72 or (resid 73 through 76 and (name N or \ 
 name CA or name C or name O or name CB )) or (resid 77 through 81 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 82 through 83 or (resid 84  \ 
through 85 and (name N or name CA or name C or name O or name CB )) or resid 86  \ 
or (resid 87 through 89 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 90 through 102 or (resid 103 through 104 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 105 through 109 or (resid 110 through 113 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 114 through 122 \ 
 or (resid 123 through 125 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 126 through 137 or (resid 138 through 141 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 142 through 162 or (resid 163 through 1 \ 
64 and (name N or name CA or name C or name O or name CB )) or resid 165 through \ 
 167 or (resid 168 through 172 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 173 or (resid 174 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 175 through 204 or (resid 205 through 206 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 207 through 217 or (resid 218 t \ 
hrough 221 and (name N or name CA or name C or name O or name CB )) or (resid 22 \ 
2 through 225 and (name N or name CA or name C or name O or name CB )) or resid  \ 
226))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.860
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
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      :  0.012   0.196   7599  Z= 0.614
  Angle     :  0.866  14.837  10480  Z= 0.434
  Chirality :  0.042   0.119   1314
  Planarity :  0.003   0.033   1402
  Dihedral  : 15.777 128.313   2070
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.80 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 33.25 %
    Favored  : 66.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.70 (0.25), residues: 1235
  helix:  1.32 (0.21), residues: 656
  sheet: -3.54 (0.37), residues: 151
  loop : -2.11 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 224 
 TYR   0.016   0.001   TYR A 394 
 PHE   0.024   0.002   PHE B 318 
 TRP   0.012   0.001   TRP B 374 
 HIS   0.005   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01224 /  0.61 ( 7599)
  covalent geometry    : angle       0.86611 /  0.43 (10480)
  hydrogen bonds       : bond        0.13949 /  9.71 (  534)
  hydrogen bonds       : angle       6.21368 /  4.52 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9317 (mt) cc_final: 0.8987 (mp)
REVERT: D   87 GLN cc_start: 0.8684 (tp40) cc_final: 0.8082 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 125
  average time/residue: 0.0699
  time to fit residues: 12.7005
Evaluate side-chains
  123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain B residue  348 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 123 optimal weight:   20.0000
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.131941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109699 restraints weight = 12839.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.112024 restraints weight = 7017.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.113596 restraints weight = 4787.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.114358 restraints weight = 3792.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.114772 restraints weight = 3336.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.0919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7599  Z= 0.159
  Angle     :  0.519   5.546  10480  Z= 0.287
  Chirality :  0.042   0.140   1314
  Planarity :  0.003   0.026   1402
  Dihedral  :  9.048 103.398   1348
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.59 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 29.29 %
    Favored  : 67.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1235
  helix:  1.84 (0.20), residues: 650
  sheet: -3.31 (0.38), residues: 148
  loop : -1.94 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 398 
 TYR   0.015   0.001   TYR A 394 
 PHE   0.015   0.001   PHE A 318 
 TRP   0.018   0.002   TRP B 374 
 HIS   0.004   0.001   HIS D  96 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.16 ( 7599)
  covalent geometry    : angle       0.51873 /  0.29 (10480)
  hydrogen bonds       : bond        0.04869 /  3.49 (  534)
  hydrogen bonds       : angle       5.02457 /  3.63 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9283 (mt) cc_final: 0.8980 (mp)
REVERT: A  342 LEU cc_start: 0.9018 (mt) cc_final: 0.8806 (mt)
REVERT: D   87 GLN cc_start: 0.8581 (tp40) cc_final: 0.8176 (tm-30)
REVERT: D  110 MET cc_start: 0.8938 (tpp) cc_final: 0.8609 (tpp)
  outliers start: 11
  outliers final: 7
  residues processed: 138
  average time/residue: 0.0634
  time to fit residues: 12.7593
Evaluate side-chains
  130 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  379 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 47 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0970
   chunk 115 optimal weight:    0.0020
   chunk 80 optimal weight:    8.9990
   overall best weight:    3.0192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
D 226 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.129861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.107123 restraints weight = 12872.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.109439 restraints weight = 7165.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.110949 restraints weight = 4909.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111630 restraints weight = 3894.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111630 restraints weight = 3453.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7599  Z= 0.196
  Angle     :  0.544   5.985  10480  Z= 0.296
  Chirality :  0.043   0.140   1314
  Planarity :  0.003   0.027   1402
  Dihedral  :  9.005  99.756   1345
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.32 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 29.29 %
    Favored  : 67.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.17 (0.25), residues: 1235
  helix:  1.71 (0.20), residues: 658
  sheet: -3.09 (0.40), residues: 146
  loop : -1.92 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 224 
 TYR   0.015   0.001   TYR A 394 
 PHE   0.019   0.002   PHE A 318 
 TRP   0.011   0.001   TRP B 374 
 HIS   0.005   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.20 ( 7599)
  covalent geometry    : angle       0.54355 /  0.30 (10480)
  hydrogen bonds       : bond        0.05008 /  3.60 (  534)
  hydrogen bonds       : angle       4.84095 /  3.48 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9298 (mt) cc_final: 0.9008 (mp)
REVERT: A  342 LEU cc_start: 0.9003 (mt) cc_final: 0.8789 (mt)
REVERT: B  266 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7774 (mmt)
REVERT: B  270 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7840 (mp)
REVERT: D   87 GLN cc_start: 0.8582 (tp40) cc_final: 0.8231 (tm-30)
REVERT: D  110 MET cc_start: 0.8970 (tpp) cc_final: 0.8638 (tpp)
  outliers start: 11
  outliers final: 9
  residues processed: 134
  average time/residue: 0.0638
  time to fit residues: 12.3244
Evaluate side-chains
  133 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  379 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 79 optimal weight:    0.8980
   chunk 75 optimal weight:   20.0000
   chunk 61 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   chunk 85 optimal weight:   40.0000
   chunk 80 optimal weight:    9.9990
   chunk 83 optimal weight:   30.0000
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.130343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107393 restraints weight = 13221.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109763 restraints weight = 7279.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111299 restraints weight = 4952.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.112098 restraints weight = 3896.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.112481 restraints weight = 3421.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7599  Z= 0.176
  Angle     :  0.523   6.256  10480  Z= 0.284
  Chirality :  0.042   0.144   1314
  Planarity :  0.003   0.026   1402
  Dihedral  :  8.737  99.321   1345
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.67 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.23 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.25), residues: 1235
  helix:  1.81 (0.20), residues: 659
  sheet: -2.83 (0.44), residues: 134
  loop : -1.84 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 139 
 TYR   0.014   0.001   TYR A 394 
 PHE   0.017   0.002   PHE A 318 
 TRP   0.010   0.001   TRP B 374 
 HIS   0.004   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.18 ( 7599)
  covalent geometry    : angle       0.52266 /  0.28 (10480)
  hydrogen bonds       : bond        0.04737 /  3.42 (  534)
  hydrogen bonds       : angle       4.72110 /  3.38 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9248 (mt) cc_final: 0.8996 (mp)
REVERT: B  266 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7785 (mmt)
REVERT: B  270 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7827 (mp)
REVERT: D   87 GLN cc_start: 0.8586 (tp40) cc_final: 0.8246 (tm-30)
REVERT: D  110 MET cc_start: 0.8968 (tpp) cc_final: 0.8638 (tpp)
  outliers start: 17
  outliers final: 14
  residues processed: 135
  average time/residue: 0.0645
  time to fit residues: 12.6228
Evaluate side-chains
  134 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain D residue    5 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 67 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 30 optimal weight:   30.0000
   chunk 17 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 114 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0770
   overall best weight:    1.1140

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
B  57 ASN
B 257 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.133699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111154 restraints weight = 12895.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.113436 restraints weight = 7293.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.114936 restraints weight = 5066.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.115658 restraints weight = 4032.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.116299 restraints weight = 3563.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7599  Z= 0.106
  Angle     :  0.461   7.280  10480  Z= 0.247
  Chirality :  0.041   0.142   1314
  Planarity :  0.002   0.026   1402
  Dihedral  :  8.193  95.896   1345
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 30.08 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.42 (0.25), residues: 1235
  helix:  2.22 (0.20), residues: 659
  sheet: -2.81 (0.43), residues: 139
  loop : -1.75 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 139 
 TYR   0.014   0.001   TYR A 394 
 PHE   0.012   0.001   PHE B 318 
 TRP   0.010   0.001   TRP B 374 
 HIS   0.002   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00192 /  0.11 ( 7599)
  covalent geometry    : angle       0.46131 /  0.25 (10480)
  hydrogen bonds       : bond        0.03965 /  2.87 (  534)
  hydrogen bonds       : angle       4.39582 /  3.13 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9186 (mt) cc_final: 0.8965 (mp)
REVERT: B  266 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7733 (mmt)
REVERT: D   87 GLN cc_start: 0.8515 (tp40) cc_final: 0.8284 (tm-30)
REVERT: D  110 MET cc_start: 0.8908 (tpp) cc_final: 0.8555 (tpp)
  outliers start: 10
  outliers final: 7
  residues processed: 129
  average time/residue: 0.0585
  time to fit residues: 10.9940
Evaluate side-chains
  123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain D residue    5 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 112 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   chunk 109 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0870
   chunk 64 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 88 optimal weight:    6.9990
   chunk 116 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.9360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
B 265 GLN
D 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.135019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.112384 restraints weight = 12924.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114711 restraints weight = 7334.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.116263 restraints weight = 5068.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117011 restraints weight = 4029.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.117583 restraints weight = 3546.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7599  Z= 0.100
  Angle     :  0.453   7.683  10480  Z= 0.241
  Chirality :  0.041   0.139   1314
  Planarity :  0.002   0.026   1402
  Dihedral  :  7.260  91.938   1345
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 30.34 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.69 (0.25), residues: 1235
  helix:  2.48 (0.20), residues: 664
  sheet: -2.71 (0.43), residues: 139
  loop : -1.75 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 139 
 TYR   0.013   0.001   TYR A 394 
 PHE   0.012   0.001   PHE B 318 
 TRP   0.009   0.001   TRP B 374 
 HIS   0.003   0.001   HIS D 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00182 /  0.10 ( 7599)
  covalent geometry    : angle       0.45325 /  0.24 (10480)
  hydrogen bonds       : bond        0.03715 /  2.69 (  534)
  hydrogen bonds       : angle       4.19811 /  2.99 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9198 (mt) cc_final: 0.8986 (mp)
REVERT: B  323 THR cc_start: 0.8950 (m) cc_final: 0.8633 (m)
REVERT: D   87 GLN cc_start: 0.8504 (tp40) cc_final: 0.8281 (tm-30)
REVERT: D  110 MET cc_start: 0.8928 (tpp) cc_final: 0.8536 (tpp)
  outliers start: 12
  outliers final: 7
  residues processed: 128
  average time/residue: 0.0646
  time to fit residues: 11.9876
Evaluate side-chains
  126 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain B residue    2 PHE
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain D residue    5 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:   30.0000
   chunk 44 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 111 optimal weight:    0.0270
   chunk 14 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   overall best weight:    4.9444

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
B  57 ASN
B 353 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.127706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.104790 restraints weight = 13076.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107021 restraints weight = 7326.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.108534 restraints weight = 5024.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.109418 restraints weight = 3976.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.109798 restraints weight = 3461.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   7599  Z= 0.305
  Angle     :  0.642   8.072  10480  Z= 0.349
  Chirality :  0.045   0.159   1314
  Planarity :  0.003   0.031   1402
  Dihedral  :  7.406  91.034   1345
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.64 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 29.55 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.19 (0.24), residues: 1235
  helix:  1.45 (0.20), residues: 670
  sheet: -2.59 (0.45), residues: 130
  loop : -1.86 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 224 
 TYR   0.014   0.002   TYR C  88 
 PHE   0.025   0.002   PHE A 318 
 TRP   0.005   0.001   TRP A 253 
 HIS   0.008   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00655 /  0.31 ( 7599)
  covalent geometry    : angle       0.64198 /  0.35 (10480)
  hydrogen bonds       : bond        0.05581 /  4.02 (  534)
  hydrogen bonds       : angle       4.84903 /  3.48 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9292 (mt) cc_final: 0.9064 (mp)
REVERT: D   83 PHE cc_start: 0.8428 (m-10) cc_final: 0.8206 (m-10)
REVERT: D   87 GLN cc_start: 0.8592 (tp40) cc_final: 0.8323 (tm-30)
REVERT: D  110 MET cc_start: 0.9050 (tpp) cc_final: 0.8677 (tpp)
REVERT: D  226 ASN cc_start: 0.7960 (m-40) cc_final: 0.7731 (m110)
  outliers start: 12
  outliers final: 9
  residues processed: 129
  average time/residue: 0.0535
  time to fit residues: 10.2235
Evaluate side-chains
  123 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain D residue    5 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 83 optimal weight:   30.0000
   chunk 67 optimal weight:    1.9990
   chunk 79 optimal weight:   20.0000
   chunk 104 optimal weight:    3.9990
   chunk 78 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 108 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
B  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.130182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.107943 restraints weight = 12970.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.110281 restraints weight = 7198.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.111806 restraints weight = 4905.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.112535 restraints weight = 3884.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.112967 restraints weight = 3418.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7599  Z= 0.231
  Angle     :  0.561   8.106  10480  Z= 0.308
  Chirality :  0.044   0.143   1314
  Planarity :  0.003   0.028   1402
  Dihedral  :  6.846  91.285   1345
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.67 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 28.76 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.21 (0.25), residues: 1235
  helix:  1.49 (0.20), residues: 672
  sheet: -2.88 (0.41), residues: 147
  loop : -1.80 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 224 
 TYR   0.012   0.001   TYR A 394 
 PHE   0.020   0.002   PHE A 318 
 TRP   0.005   0.001   TRP B 374 
 HIS   0.006   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00488 /  0.23 ( 7599)
  covalent geometry    : angle       0.56065 /  0.31 (10480)
  hydrogen bonds       : bond        0.05085 /  3.67 (  534)
  hydrogen bonds       : angle       4.75904 /  3.40 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9256 (mt) cc_final: 0.9026 (mp)
REVERT: D   83 PHE cc_start: 0.8413 (m-10) cc_final: 0.8197 (m-10)
REVERT: D   87 GLN cc_start: 0.8546 (tp40) cc_final: 0.8328 (tm-30)
REVERT: D  110 MET cc_start: 0.9000 (tpp) cc_final: 0.8644 (tpp)
REVERT: D  226 ASN cc_start: 0.7935 (m-40) cc_final: 0.7708 (m110)
  outliers start: 15
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0558
  time to fit residues: 10.3693
Evaluate side-chains
  131 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   54 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 79 optimal weight:   30.0000
   chunk 77 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
B  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.131681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.109527 restraints weight = 12745.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.111847 restraints weight = 7105.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113321 restraints weight = 4813.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.114113 restraints weight = 3822.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.114702 restraints weight = 3352.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7599  Z= 0.170
  Angle     :  0.502   6.703  10480  Z= 0.277
  Chirality :  0.042   0.141   1314
  Planarity :  0.003   0.027   1402
  Dihedral  :  6.567  89.768   1345
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 28.23 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.08 (0.25), residues: 1235
  helix:  1.80 (0.20), residues: 667
  sheet: -2.81 (0.42), residues: 147
  loop : -1.76 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  53 
 TYR   0.013   0.001   TYR A 394 
 PHE   0.016   0.002   PHE B 318 
 TRP   0.008   0.001   TRP B 374 
 HIS   0.004   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.17 ( 7599)
  covalent geometry    : angle       0.50184 /  0.28 (10480)
  hydrogen bonds       : bond        0.04613 /  3.33 (  534)
  hydrogen bonds       : angle       4.57948 /  3.27 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9247 (mt) cc_final: 0.9021 (mp)
REVERT: D   83 PHE cc_start: 0.8412 (m-10) cc_final: 0.8193 (m-10)
REVERT: D   87 GLN cc_start: 0.8542 (tp40) cc_final: 0.8317 (tm-30)
REVERT: D  110 MET cc_start: 0.8965 (tpp) cc_final: 0.8600 (tpp)
REVERT: D  226 ASN cc_start: 0.7940 (m-40) cc_final: 0.7451 (m110)
  outliers start: 14
  outliers final: 13
  residues processed: 125
  average time/residue: 0.0585
  time to fit residues: 10.5793
Evaluate side-chains
  128 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 38 optimal weight:   20.0000
   chunk 8 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0770
   chunk 109 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 30 optimal weight:   30.0000
   chunk 89 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    2.3744

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
B  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.132257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.109998 restraints weight = 12797.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.112373 restraints weight = 7145.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.113832 restraints weight = 4868.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114748 restraints weight = 3872.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.115160 restraints weight = 3370.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7599  Z= 0.159
  Angle     :  0.491   6.715  10480  Z= 0.271
  Chirality :  0.042   0.140   1314
  Planarity :  0.003   0.027   1402
  Dihedral  :  6.351  84.162   1345
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 27.97 %
    Favored  : 68.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.23 (0.25), residues: 1235
  helix:  1.92 (0.20), residues: 667
  sheet: -2.60 (0.45), residues: 139
  loop : -1.77 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 224 
 TYR   0.013   0.001   TYR A 394 
 PHE   0.016   0.001   PHE B 318 
 TRP   0.008   0.001   TRP B 374 
 HIS   0.004   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.16 ( 7599)
  covalent geometry    : angle       0.49150 /  0.27 (10480)
  hydrogen bonds       : bond        0.04467 /  3.23 (  534)
  hydrogen bonds       : angle       4.49742 /  3.21 ( 1527)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   23 ILE cc_start: 0.9246 (mt) cc_final: 0.9020 (mp)
REVERT: D   83 PHE cc_start: 0.8407 (m-10) cc_final: 0.8190 (m-10)
REVERT: D   87 GLN cc_start: 0.8534 (tp40) cc_final: 0.8322 (tm-30)
REVERT: D  110 MET cc_start: 0.8945 (tpp) cc_final: 0.8592 (tpp)
REVERT: D  226 ASN cc_start: 0.7899 (m-40) cc_final: 0.7467 (m-40)
  outliers start: 14
  outliers final: 13
  residues processed: 126
  average time/residue: 0.0629
  time to fit residues: 11.4147
Evaluate side-chains
  129 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   chunk 96 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 102 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 79 optimal weight:   30.0000
   chunk 75 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0970
   overall best weight:    4.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 ASN
B  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.128996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.106789 restraints weight = 12924.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.109058 restraints weight = 7239.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110522 restraints weight = 4967.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111401 restraints weight = 3945.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.111987 restraints weight = 3430.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7599  Z= 0.274
  Angle     :  0.609   8.256  10480  Z= 0.334
  Chirality :  0.045   0.147   1314
  Planarity :  0.003   0.029   1402
  Dihedral  :  6.520  65.386   1345
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.80 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 27.97 %
    Favored  : 67.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.31 (0.25), residues: 1235
  helix:  1.36 (0.20), residues: 672
  sheet: -2.81 (0.42), residues: 147
  loop : -1.78 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 224 
 TYR   0.014   0.002   TYR B 363 
 PHE   0.025   0.002   PHE A 318 
 TRP   0.003   0.001   TRP A 253 
 HIS   0.007   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00584 /  0.27 ( 7599)
  covalent geometry    : angle       0.60941 /  0.33 (10480)
  hydrogen bonds       : bond        0.05431 /  3.92 (  534)
  hydrogen bonds       : angle       4.84734 /  3.47 ( 1527)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1053.13 seconds
wall clock time: 18 minutes 39.37 seconds (1119.37 seconds total)