Starting phenix.real_space_refine
on Wed Mar  4 11:12:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjg_33226/03_2026/7xjg_33226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjg_33226/03_2026/7xjg_33226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjg_33226/03_2026/7xjg_33226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjg_33226/03_2026/7xjg_33226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjg_33226/03_2026/7xjg_33226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjg_33226/03_2026/7xjg_33226.cif"
  }
  resolution = 2.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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: 6
    Type Number    sf(0)   Gaussians
     P     216      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    7594      2.51       5
     N    2367      2.21       5
     O    2954      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13167
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2518
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 12, 'TRANS': 301}
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1096
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 2, 'TRANS': 129}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 933
          Classifications: {'DNA': 45}
          Link IDs: {'rna3p': 44}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1225
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 15, 'rna3p': 42}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
    Chain: "B"
      Number of atoms: 2518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2518
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 12, 'TRANS': 301}
    Chain: "G"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1225
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 15, 'rna3p': 42}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 176
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
    Chain: "J"
      Number of atoms: 2490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2490
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 6, 'TRANS': 299}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.91, per 1000 atoms: 0.22
  Number of scatterers: 13167
  At special positions: 0
  Unit cell: (96.9, 122.4, 161.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      34     16.00
     P     216     15.00
     Mg      2     11.99
     O    2954      8.00
     N    2367      7.00
     C    7594      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: 1.09
  Conformation dependent library (CDL) restraints added in 446.5 milliseconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 10 sheets defined
      60.1% alpha, 9.8% beta
      68 base pairs and 120 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
      removed outlier: 3.576A  pdb=" N   PHE A  10 " --> pdb=" O   TYR A   6 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A  15 " --> pdb=" O   ARG A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 31
      removed outlier: 3.748A  pdb=" N   MET A  26 " --> pdb=" O   ASN A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 43
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 69 through 83
      removed outlier: 3.616A  pdb=" N   LEU A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 108 through 110
      No H-bonds generated for 'chain 'A' and resid 108 through 110'
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.616A  pdb=" N   LEU A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 140
      removed outlier: 3.946A  pdb=" N   VAL A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   GLY A 140 " --> pdb=" O   PHE A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 154
      removed outlier: 3.557A  pdb=" N   SER A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 174
    Processing helix  chain 'A' and resid 174 through 186
    Processing helix  chain 'A' and resid 205 through 220
      removed outlier: 3.550A  pdb=" N   VAL A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER A 218 " --> pdb=" O   ASP A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 224
      removed outlier: 3.598A  pdb=" N   GLY A 224 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 221 through 224'
    Processing helix  chain 'A' and resid 256 through 272
    Processing helix  chain 'A' and resid 277 through 292
    Processing helix  chain 'A' and resid 292 through 311
    Processing helix  chain 'C' and resid 6 through 18
      removed outlier: 3.726A  pdb=" N   GLN C  11 " --> pdb=" O   ASP C   7 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLN C  12 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 213
      Proline residue:  C 208  - end of helix
    Processing helix  chain 'C' and resid 217 through 230
      removed outlier: 3.509A  pdb=" N   LEU C 221 " --> pdb=" O   ASN C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 250
    Processing helix  chain 'C' and resid 263 through 274
    Processing helix  chain 'C' and resid 275 through 292
      removed outlier: 3.585A  pdb=" N   LEU C 279 " --> pdb=" O   ASP C 275 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG C 292 " --> pdb=" O   ASN C 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 3.888A  pdb=" N   LEU B  15 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 31
      removed outlier: 3.510A  pdb=" N   MET B  26 " --> pdb=" O   ASN B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 44
    Processing helix  chain 'B' and resid 69 through 83
      removed outlier: 3.749A  pdb=" N   LEU B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 87
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 108 through 110
      No H-bonds generated for 'chain 'B' and resid 108 through 110'
    Processing helix  chain 'B' and resid 123 through 127
    Processing helix  chain 'B' and resid 128 through 139
      removed outlier: 3.848A  pdb=" N   VAL B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU B 139 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 154
    Processing helix  chain 'B' and resid 165 through 174
    Processing helix  chain 'B' and resid 175 through 186
    Processing helix  chain 'B' and resid 205 through 220
      removed outlier: 3.600A  pdb=" N   VAL B 209 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASP B 214 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER B 218 " --> pdb=" O   ASP B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 224
    Processing helix  chain 'B' and resid 257 through 273
    Processing helix  chain 'B' and resid 277 through 292
    Processing helix  chain 'B' and resid 292 through 310
      removed outlier: 3.778A  pdb=" N   LYS B 308 " --> pdb=" O   SER B 304 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LYS B 309 " --> pdb=" O   LYS B 305 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 6 through 14
    Processing helix  chain 'J' and resid 45 through 55
      removed outlier: 3.759A  pdb=" N   LEU J  49 " --> pdb=" O   TRP J  45 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS J  55 " --> pdb=" O   GLN J  51 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 79 through 91
    Processing helix  chain 'J' and resid 100 through 111
    Processing helix  chain 'J' and resid 125 through 129
    Processing helix  chain 'J' and resid 133 through 138
    Processing helix  chain 'J' and resid 138 through 147
    Processing helix  chain 'J' and resid 155 through 162
      removed outlier: 3.768A  pdb=" N   LEU J 159 " --> pdb=" O   SER J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 167 through 172
      removed outlier: 3.742A  pdb=" N   ARG J 171 " --> pdb=" O   ILE J 167 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 173 through 190
    Processing helix  chain 'J' and resid 202 through 213
      Proline residue:  J 208  - end of helix
    Processing helix  chain 'J' and resid 217 through 229
    Processing helix  chain 'J' and resid 233 through 235
      No H-bonds generated for 'chain 'J' and resid 233 through 235'
    Processing helix  chain 'J' and resid 236 through 250
      removed outlier: 3.757A  pdb=" N   VAL J 240 " --> pdb=" O   SER J 236 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG J 241 " --> pdb=" O   LYS J 237 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 263 through 274
    Processing helix  chain 'J' and resid 275 through 292
      removed outlier: 3.814A  pdb=" N   LEU J 279 " --> pdb=" O   ASP J 275 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG J 292 " --> pdb=" O   ASN J 288 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53
      removed outlier: 3.604A  pdb=" N   ARG A  63 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195
    Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243
    Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256
    Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 52
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195
      removed outlier: 4.570A  pdb=" N   VAL B 226 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 195
    Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243
    Processing sheet with id=AA9, first strand: chain 'J' and resid 59 through 62
      removed outlier: 6.601A  pdb=" N   ILE J  30 " --> pdb=" O   ASP J  60 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   PHE J  62 " --> pdb=" O   ILE J  30 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE J  32 " --> pdb=" O   PHE J  62 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   ILE J  94 " --> pdb=" O   ILE J 121 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   ILE J 123 " --> pdb=" O   ILE J  94 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LEU J  96 " --> pdb=" O   ILE J 123 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   LEU J 152 " --> pdb=" O   LEU J 120 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   CYS J 122 " --> pdb=" O   LEU J 152 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 253 through 256

    449 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      170 hydrogen bonds
      308 hydrogen bond angles
      0 basepair planarities
      68 basepair parallelities
      120 stacking parallelities
  Total time for adding SS restraints: 1.96

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1964
        1.33 -     1.45: 4683
        1.45 -     1.57: 6743
        1.57 -     1.69: 422
        1.69 -     1.81: 50
  Bond restraints: 13862
  Sorted by residual:
  bond pdb=" CA  SER B 218 "
       pdb=" CB  SER B 218 "
    ideal  model  delta    sigma   weight residual
    1.532  1.473  0.059 1.53e-02 4.27e+03 1.50e+01
  bond pdb=" N   ARG B 213 "
       pdb=" CA  ARG B 213 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.23e-02 6.61e+03 8.28e+00
  bond pdb=" N   ILE A  41 "
       pdb=" CA  ILE A  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.23e-02 6.61e+03 8.22e+00
  bond pdb=" N   VAL B 210 "
       pdb=" CA  VAL B 210 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.036 1.30e-02 5.92e+03 7.77e+00
  bond pdb=" N   ARG A  47 "
       pdb=" CA  ARG A  47 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.66e+00
  ... (remaining 13857 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 19163
        2.06 -     4.13: 437
        4.13 -     6.19: 57
        6.19 -     8.26: 4
        8.26 -    10.32: 4
  Bond angle restraints: 19665
  Sorted by residual:
  angle pdb=" C   GLU B  59 "
        pdb=" CA  GLU B  59 "
        pdb=" CB  GLU B  59 "
      ideal   model   delta    sigma   weight residual
     116.54  109.75    6.79 1.15e+00 7.56e-01 3.49e+01
  angle pdb=" C   ILE B 219 "
        pdb=" N   ILE B 220 "
        pdb=" CA  ILE B 220 "
      ideal   model   delta    sigma   weight residual
     122.13  111.81   10.32 1.85e+00 2.92e-01 3.11e+01
  angle pdb=" C4'  DC G   3 "
        pdb=" C3'  DC G   3 "
        pdb=" O3'  DC G   3 "
      ideal   model   delta    sigma   weight residual
     110.00  116.83   -6.83 1.50e+00 4.44e-01 2.07e+01
  angle pdb=" CB  LYS J 184 "
        pdb=" CG  LYS J 184 "
        pdb=" CD  LYS J 184 "
      ideal   model   delta    sigma   weight residual
     111.30  121.22   -9.92 2.30e+00 1.89e-01 1.86e+01
  angle pdb=" C   LYS B 211 "
        pdb=" CA  LYS B 211 "
        pdb=" CB  LYS B 211 "
      ideal   model   delta    sigma   weight residual
     110.38  119.11   -8.73 2.04e+00 2.40e-01 1.83e+01
  ... (remaining 19660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 7552
       35.95 -    71.89: 820
       71.89 -   107.84: 39
      107.84 -   143.78: 8
      143.78 -   179.73: 15
  Dihedral angle restraints: 8434
    sinusoidal: 5307
      harmonic: 3127
  Sorted by residual:
  dihedral pdb=" O4'   U H  68 "
           pdb=" C1'   U H  68 "
           pdb=" N1    U H  68 "
           pdb=" C2    U H  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   20.41  179.59     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U E  68 "
           pdb=" C1'   U E  68 "
           pdb=" N1    U E  68 "
           pdb=" C2    U E  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.56  146.44     1      1.50e+01 4.44e-03 7.82e+01
  dihedral pdb=" O4'   C H  65 "
           pdb=" C1'   C H  65 "
           pdb=" N1    C H  65 "
           pdb=" C2    C H  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   63.30  136.70     1      1.50e+01 4.44e-03 7.37e+01
  ... (remaining 8431 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1927
       0.056 -    0.111: 305
       0.111 -    0.167: 70
       0.167 -    0.222: 16
       0.222 -    0.278: 1
  Chirality restraints: 2319
  Sorted by residual:
  chirality pdb=" P     G F   1 "
            pdb=" OP1   G F   1 "
            pdb=" OP2   G F   1 "
            pdb=" O5'   G F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.69   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  TYR A 195 "
            pdb=" N   TYR A 195 "
            pdb=" C   TYR A 195 "
            pdb=" CB  TYR A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" P     G I   1 "
            pdb=" OP1   G I   1 "
            pdb=" OP2   G I   1 "
            pdb=" O5'   G I   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.63   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 2316 not shown)

  Planarity restraints: 1697
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU J 223 "    0.012 2.00e-02 2.50e+03   2.46e-02 6.05e+00
        pdb=" CD  GLU J 223 "   -0.043 2.00e-02 2.50e+03
        pdb=" OE1 GLU J 223 "    0.015 2.00e-02 2.50e+03
        pdb=" OE2 GLU J 223 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE J 302 "    0.040 5.00e-02 4.00e+02   6.02e-02 5.80e+00
        pdb=" N   PRO J 303 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO J 303 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO J 303 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 124 "    0.039 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO A 125 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 125 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 125 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1694 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 60
        2.55 -     3.14: 9033
        3.14 -     3.72: 21354
        3.72 -     4.31: 31367
        4.31 -     4.90: 47292
  Nonbonded interactions: 109106
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  39 "
            pdb=" OG1 THR A  43 "
     model   vdw
     1.962 3.040
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE2 GLU B 121 "
     model   vdw
     2.010 3.120
  nonbonded pdb=" N2    G E  20 "
            pdb=" O2    U E  41 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OP1  DG D  14 "
            pdb=" NH2 ARG J 276 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   TYR C 211 "
            pdb=" NH2 ARG B  31 "
     model   vdw
     2.234 3.120
  ... (remaining 109101 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'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'D' and (resid 1 through 19 or resid 66 through 85))
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.010
  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:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.450
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  13862  Z= 0.255
  Angle     :  0.712  10.322  19665  Z= 0.419
  Chirality :  0.046   0.278   2319
  Planarity :  0.005   0.060   1697
  Dihedral  : 24.504 179.725   6414
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 26.38 %
    Favored  : 70.18 %
  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: 1054
  helix:  0.43 (0.23), residues: 547
  sheet:  1.77 (0.53), residues: 87
  loop : -1.32 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  31 
 TYR   0.024   0.002   TYR B 184 
 PHE   0.015   0.002   PHE B  96 
 TRP   0.007   0.002   TRP B  78 
 HIS   0.007   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (13862)
  covalent geometry    : angle       0.71244 (19665)
  hydrogen bonds       : bond        0.16129 (  607)
  hydrogen bonds       : angle       5.30362 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.395 
Fit side-chains
REVERT: C  282 LEU cc_start: 0.7679 (mt) cc_final: 0.7461 (mt)
REVERT: C  292 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7652 (mtm180)
  outliers start: 33
  outliers final: 30
  residues processed: 204
  average time/residue: 0.5796
  time to fit residues: 128.4176
Evaluate side-chains
  209 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   53 LEU
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  135 ILE
Chi-restraints excluded: chain J residue  145 LYS
Chi-restraints excluded: chain J residue  149 LYS
Chi-restraints excluded: chain J residue  153 ARG
Chi-restraints excluded: chain J residue  156 SER
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  188 LYS
Chi-restraints excluded: chain J residue  192 VAL
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  195 ASP
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  220 THR
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  234 VAL
Chi-restraints excluded: chain J residue  295 SER
Chi-restraints excluded: chain J residue  306 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    0.0050
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    0.4980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
A 296 HIS
B 104 ASN
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 198 ASN
J 298 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.188642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.152906 restraints weight = 16120.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 1.32
r_work: 0.3572 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.0924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13862  Z= 0.132
  Angle     :  0.558   6.540  19665  Z= 0.300
  Chirality :  0.038   0.162   2319
  Planarity :  0.004   0.044   1697
  Dihedral  : 25.278 178.430   4292
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.36 %
    Favored  : 71.53 %
  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:  0.26 (0.26), residues: 1054
  helix:  0.85 (0.22), residues: 569
  sheet:  1.77 (0.53), residues: 90
  loop : -1.18 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  31 
 TYR   0.013   0.001   TYR B 179 
 PHE   0.011   0.001   PHE J 205 
 TRP   0.004   0.001   TRP B  78 
 HIS   0.004   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13862)
  covalent geometry    : angle       0.55781 (19665)
  hydrogen bonds       : bond        0.04651 (  607)
  hydrogen bonds       : angle       3.75519 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 175
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  130 ASN cc_start: 0.7600 (p0) cc_final: 0.7207 (p0)
REVERT: J   91 VAL cc_start: 0.7168 (OUTLIER) cc_final: 0.6960 (p)
REVERT: J  230 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6785 (mmmt)
  outliers start: 49
  outliers final: 20
  residues processed: 205
  average time/residue: 0.6315
  time to fit residues: 139.9324
Evaluate side-chains
  192 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  270 ILE
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain J residue   53 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  149 LYS
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  295 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9990
   chunk 104 optimal weight:    9.9990
   chunk 102 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
B  76 GLN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.177729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.142154 restraints weight = 16080.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.26
r_work: 0.3525 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.0888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13862  Z= 0.213
  Angle     :  0.619   7.983  19665  Z= 0.330
  Chirality :  0.041   0.182   2319
  Planarity :  0.005   0.046   1697
  Dihedral  : 25.211 179.998   4253
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 23.04 %
    Favored  : 71.64 %
  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 (0.25), residues: 1054
  helix:  0.82 (0.22), residues: 565
  sheet:  1.69 (0.53), residues: 90
  loop : -1.24 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  49 
 TYR   0.019   0.002   TYR A 179 
 PHE   0.016   0.002   PHE B  96 
 TRP   0.007   0.002   TRP B  78 
 HIS   0.007   0.002   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (13862)
  covalent geometry    : angle       0.61948 (19665)
  hydrogen bonds       : bond        0.05686 (  607)
  hydrogen bonds       : angle       3.81950 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 176
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6750 (ttm-80)
REVERT: B   62 MET cc_start: 0.5170 (mpp) cc_final: 0.4952 (mpp)
REVERT: B  158 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8431 (pp)
REVERT: J   91 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6980 (p)
REVERT: J  298 ASN cc_start: 0.8621 (t0) cc_final: 0.8398 (t0)
  outliers start: 51
  outliers final: 30
  residues processed: 206
  average time/residue: 0.5927
  time to fit residues: 132.4597
Evaluate side-chains
  208 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 175
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   19 LYS
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0870
   chunk 79 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.179232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.143822 restraints weight = 16051.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 1.24
r_work: 0.3549 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13862  Z= 0.152
  Angle     :  0.573   8.560  19665  Z= 0.306
  Chirality :  0.038   0.177   2319
  Planarity :  0.004   0.044   1697
  Dihedral  : 25.137 179.900   4243
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 23.25 %
    Favored  : 71.85 %
  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:  0.40 (0.26), residues: 1054
  helix:  1.05 (0.22), residues: 566
  sheet:  1.66 (0.53), residues: 90
  loop : -1.20 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  49 
 TYR   0.014   0.001   TYR B 179 
 PHE   0.012   0.001   PHE B  96 
 TRP   0.005   0.001   TRP B  78 
 HIS   0.006   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (13862)
  covalent geometry    : angle       0.57305 (19665)
  hydrogen bonds       : bond        0.04824 (  607)
  hydrogen bonds       : angle       3.65532 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 173
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.5245 (mpp) cc_final: 0.5014 (mpp)
REVERT: B  139 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7767 (mp)
REVERT: J   91 VAL cc_start: 0.7188 (OUTLIER) cc_final: 0.6976 (p)
REVERT: J  298 ASN cc_start: 0.8595 (t0) cc_final: 0.8357 (t0)
  outliers start: 47
  outliers final: 29
  residues processed: 202
  average time/residue: 0.5739
  time to fit residues: 125.8326
Evaluate side-chains
  203 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  261 GLN
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 117 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 102 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0770
   chunk 59 optimal weight:    0.0770
   chunk 54 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
C 261 GLN
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.180067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.144767 restraints weight = 16222.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 1.22
r_work: 0.3563 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13862  Z= 0.131
  Angle     :  0.552   6.966  19665  Z= 0.295
  Chirality :  0.037   0.173   2319
  Planarity :  0.004   0.052   1697
  Dihedral  : 25.078 179.713   4243
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 22.63 %
    Favored  : 72.16 %
  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:  0.56 (0.26), residues: 1054
  helix:  1.18 (0.22), residues: 568
  sheet:  1.83 (0.53), residues: 90
  loop : -1.18 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  49 
 TYR   0.013   0.001   TYR B 179 
 PHE   0.011   0.001   PHE J 205 
 TRP   0.004   0.001   TRP B  78 
 HIS   0.005   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (13862)
  covalent geometry    : angle       0.55228 (19665)
  hydrogen bonds       : bond        0.04481 (  607)
  hydrogen bonds       : angle       3.54804 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 176
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.5203 (mpp) cc_final: 0.4953 (mpp)
REVERT: B  251 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7079 (mm-30)
REVERT: J   23 TYR cc_start: 0.8293 (t80) cc_final: 0.8066 (t80)
REVERT: J   91 VAL cc_start: 0.7174 (OUTLIER) cc_final: 0.6947 (p)
REVERT: J  298 ASN cc_start: 0.8604 (t0) cc_final: 0.8368 (t0)
  outliers start: 50
  outliers final: 31
  residues processed: 205
  average time/residue: 0.5523
  time to fit residues: 123.2205
Evaluate side-chains
  206 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 174
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  155 SER
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  223 GLU
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  257 THR
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 73 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
B 240 GLN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.179308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.143696 restraints weight = 16000.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 1.24
r_work: 0.3548 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13862  Z= 0.157
  Angle     :  0.567   7.013  19665  Z= 0.302
  Chirality :  0.038   0.175   2319
  Planarity :  0.004   0.057   1697
  Dihedral  : 25.013 179.136   4241
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 23.25 %
    Favored  : 72.37 %
  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:  0.58 (0.26), residues: 1054
  helix:  1.24 (0.22), residues: 567
  sheet:  1.87 (0.52), residues: 90
  loop : -1.24 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  49 
 TYR   0.016   0.001   TYR B 179 
 PHE   0.012   0.001   PHE B  96 
 TRP   0.005   0.001   TRP B  78 
 HIS   0.007   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (13862)
  covalent geometry    : angle       0.56701 (19665)
  hydrogen bonds       : bond        0.04751 (  607)
  hydrogen bonds       : angle       3.54879 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 174
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.5159 (mpp) cc_final: 0.4920 (mpp)
REVERT: B  139 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7779 (mp)
REVERT: B  251 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7104 (mm-30)
REVERT: J   91 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6927 (p)
REVERT: J  298 ASN cc_start: 0.8607 (t0) cc_final: 0.8373 (t0)
  outliers start: 42
  outliers final: 33
  residues processed: 202
  average time/residue: 0.5792
  time to fit residues: 126.8801
Evaluate side-chains
  210 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   39 VAL
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  223 GLU
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  257 THR
Chi-restraints excluded: chain J residue  261 GLN
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0000
   chunk 104 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.179540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144529 restraints weight = 16103.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.20
r_work: 0.3555 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13862  Z= 0.155
  Angle     :  0.565   7.025  19665  Z= 0.300
  Chirality :  0.038   0.172   2319
  Planarity :  0.004   0.049   1697
  Dihedral  : 24.988 178.925   4241
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 23.67 %
    Favored  : 71.85 %
  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:  0.61 (0.26), residues: 1054
  helix:  1.26 (0.22), residues: 569
  sheet:  1.91 (0.52), residues: 90
  loop : -1.25 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  49 
 TYR   0.015   0.001   TYR B 179 
 PHE   0.012   0.001   PHE B  96 
 TRP   0.005   0.001   TRP B  78 
 HIS   0.006   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13862)
  covalent geometry    : angle       0.56471 (19665)
  hydrogen bonds       : bond        0.04674 (  607)
  hydrogen bonds       : angle       3.52173 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.8004 (mtm-85)
REVERT: B   62 MET cc_start: 0.5134 (mpp) cc_final: 0.4895 (mpp)
REVERT: B  139 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7785 (mp)
REVERT: B  251 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7104 (mm-30)
REVERT: J   91 VAL cc_start: 0.7148 (OUTLIER) cc_final: 0.6928 (p)
REVERT: J  298 ASN cc_start: 0.8603 (t0) cc_final: 0.8375 (t0)
  outliers start: 43
  outliers final: 33
  residues processed: 203
  average time/residue: 0.6027
  time to fit residues: 132.6202
Evaluate side-chains
  208 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 172
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   31 ARG
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  188 LYS
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  223 GLU
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  257 THR
Chi-restraints excluded: chain J residue  261 GLN
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 114 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.178102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.142454 restraints weight = 15907.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 1.25
r_work: 0.3531 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13862  Z= 0.196
  Angle     :  0.603   7.275  19665  Z= 0.320
  Chirality :  0.040   0.181   2319
  Planarity :  0.005   0.064   1697
  Dihedral  : 25.016 179.011   4240
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 23.46 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.26), residues: 1054
  helix:  1.09 (0.22), residues: 571
  sheet:  1.90 (0.52), residues: 90
  loop : -1.35 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  49 
 TYR   0.018   0.002   TYR A 179 
 PHE   0.016   0.002   PHE B  10 
 TRP   0.007   0.002   TRP B  78 
 HIS   0.007   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (13862)
  covalent geometry    : angle       0.60313 (19665)
  hydrogen bonds       : bond        0.05277 (  607)
  hydrogen bonds       : angle       3.61032 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 175
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: C  279 LEU cc_start: 0.7124 (mt) cc_final: 0.6908 (mt)
REVERT: B   31 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8009 (mtm-85)
REVERT: B   62 MET cc_start: 0.5118 (mpp) cc_final: 0.4888 (mpp)
REVERT: B  139 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7773 (mp)
REVERT: J   91 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6925 (p)
REVERT: J  298 ASN cc_start: 0.8619 (t0) cc_final: 0.8376 (t0)
  outliers start: 46
  outliers final: 38
  residues processed: 206
  average time/residue: 0.5663
  time to fit residues: 127.0015
Evaluate side-chains
  215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 174
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   31 ARG
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  155 SER
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  188 LYS
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  223 GLU
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  257 THR
Chi-restraints excluded: chain J residue  261 GLN
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 115 optimal weight:    0.2980
   chunk 60 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.178724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.142991 restraints weight = 16047.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 1.25
r_work: 0.3539 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13862  Z= 0.160
  Angle     :  0.585   6.904  19665  Z= 0.311
  Chirality :  0.039   0.175   2319
  Planarity :  0.004   0.063   1697
  Dihedral  : 25.004 179.034   4240
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 23.98 %
    Favored  : 71.53 %
  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:  0.52 (0.26), residues: 1054
  helix:  1.22 (0.22), residues: 565
  sheet:  1.94 (0.53), residues: 90
  loop : -1.34 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  11 
 TYR   0.016   0.001   TYR B 179 
 PHE   0.013   0.002   PHE B  96 
 TRP   0.005   0.001   TRP B  78 
 HIS   0.006   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (13862)
  covalent geometry    : angle       0.58534 (19665)
  hydrogen bonds       : bond        0.04921 (  607)
  hydrogen bonds       : angle       3.57508 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: C  279 LEU cc_start: 0.7089 (mt) cc_final: 0.6857 (mt)
REVERT: B   31 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8022 (mtm-85)
REVERT: B   62 MET cc_start: 0.5128 (mpp) cc_final: 0.4886 (mpp)
REVERT: B  139 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7760 (mp)
REVERT: J   91 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6926 (p)
REVERT: J  298 ASN cc_start: 0.8618 (t0) cc_final: 0.8374 (t0)
  outliers start: 43
  outliers final: 37
  residues processed: 204
  average time/residue: 0.6041
  time to fit residues: 133.8879
Evaluate side-chains
  215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   31 ARG
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  155 SER
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  223 GLU
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  257 THR
Chi-restraints excluded: chain J residue  261 GLN
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0030
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.9192

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.178498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.142753 restraints weight = 16049.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.26
r_work: 0.3533 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13862  Z= 0.186
  Angle     :  0.595   7.160  19665  Z= 0.316
  Chirality :  0.040   0.174   2319
  Planarity :  0.005   0.057   1697
  Dihedral  : 24.996 179.128   4240
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 23.88 %
    Favored  : 71.64 %
  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 (0.26), residues: 1054
  helix:  1.12 (0.22), residues: 570
  sheet:  1.89 (0.52), residues: 90
  loop : -1.37 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  49 
 TYR   0.017   0.002   TYR A 179 
 PHE   0.014   0.002   PHE B  96 
 TRP   0.006   0.002   TRP B  78 
 HIS   0.006   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (13862)
  covalent geometry    : angle       0.59532 (19665)
  hydrogen bonds       : bond        0.05103 (  607)
  hydrogen bonds       : angle       3.57700 ( 1589)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 178
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: C  279 LEU cc_start: 0.7104 (mt) cc_final: 0.6858 (mt)
REVERT: B   31 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8023 (mtm-85)
REVERT: B   62 MET cc_start: 0.5135 (mpp) cc_final: 0.4895 (mpp)
REVERT: B  139 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7790 (mp)
REVERT: B  251 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7168 (mm-30)
REVERT: J   91 VAL cc_start: 0.7206 (OUTLIER) cc_final: 0.6972 (p)
REVERT: J  298 ASN cc_start: 0.8612 (t0) cc_final: 0.8380 (t0)
  outliers start: 43
  outliers final: 35
  residues processed: 209
  average time/residue: 0.6084
  time to fit residues: 138.0651
Evaluate side-chains
  214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 176
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   31 ARG
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   91 VAL
Chi-restraints excluded: chain J residue   93 VAL
Chi-restraints excluded: chain J residue  115 ASN
Chi-restraints excluded: chain J residue  155 SER
Chi-restraints excluded: chain J residue  169 VAL
Chi-restraints excluded: chain J residue  179 LEU
Chi-restraints excluded: chain J residue  184 LYS
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain J residue  194 LYS
Chi-restraints excluded: chain J residue  196 ILE
Chi-restraints excluded: chain J residue  205 PHE
Chi-restraints excluded: chain J residue  207 LEU
Chi-restraints excluded: chain J residue  216 VAL
Chi-restraints excluded: chain J residue  223 GLU
Chi-restraints excluded: chain J residue  229 ILE
Chi-restraints excluded: chain J residue  257 THR
Chi-restraints excluded: chain J residue  261 GLN
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 111 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 72 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0000
   chunk 101 optimal weight:    0.7980
   overall best weight:    1.0388

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
** J  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.177976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.142587 restraints weight = 15908.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 1.24
r_work: 0.3529 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13862  Z= 0.202
  Angle     :  0.608   7.248  19665  Z= 0.322
  Chirality :  0.040   0.176   2319
  Planarity :  0.005   0.061   1697
  Dihedral  : 25.008 179.309   4240
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.88 %
    Favored  : 71.43 %
  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: 1054
  helix:  1.17 (0.22), residues: 559
  sheet:  1.89 (0.52), residues: 90
  loop : -1.38 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  49 
 TYR   0.018   0.002   TYR A 179 
 PHE   0.015   0.002   PHE B  96 
 TRP   0.007   0.002   TRP B  78 
 HIS   0.006   0.001   HIS B 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (13862)
  covalent geometry    : angle       0.60797 (19665)
  hydrogen bonds       : bond        0.05335 (  607)
  hydrogen bonds       : angle       3.61996 ( 1589)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 6103.30 seconds
wall clock time: 104 minutes 8.57 seconds (6248.57 seconds total)