Starting phenix.real_space_refine
on Sat Jan 20 00:32:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/01_2024/7xjg_33226.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/01_2024/7xjg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/01_2024/7xjg_33226.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/01_2024/7xjg_33226.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/01_2024/7xjg_33226.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjg_33226/01_2024/7xjg_33226.pdb"
  }
  resolution = 2.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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
    Residue "A PHE   46": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  119": "OD1" <-> "OD2"
    Residue "B TYR  184": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/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: 7.69, per 1000 atoms: 0.58
  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  - 3.50
        Amino acid           : False - 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: 5.88
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 4.78
  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: 4.61

  Time building geometry restraints manager: 6.31 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:
       98.87 -   105.90: 1271
      105.90 -   112.92: 7572
      112.92 -   119.95: 4927
      119.95 -   126.98: 5302
      126.98 -   134.00: 593
  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: 7454
       35.95 -    71.89: 758
       71.89 -   107.84: 39
      107.84 -   143.78: 8
      143.78 -   179.73: 15
  Dihedral angle restraints: 8274
    sinusoidal: 5147
      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 8271 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 2.440
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE2 GLU B 121 "
     model   vdw
     2.010 2.520
  nonbonded pdb=" N2    G E  20 "
            pdb=" O2    U E  41 "
     model   vdw
     2.209 2.520
  nonbonded pdb=" OP1  DG D  14 "
            pdb=" NH2 ARG J 276 "
     model   vdw
     2.211 2.520
  nonbonded pdb=" O   TYR C 211 "
            pdb=" NH2 ARG B  31 "
     model   vdw
     2.234 2.520
  ... (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
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:             1.620
  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:          7.130
  Check model and map are aligned:         0.210
  Set scattering table:                    0.120
  Process input model:                     40.950
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.260
-------------------------------------------------------------------------------
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= 0.297
  Angle     :  0.712  10.322  19665  Z= 0.419
  Chirality :  0.046   0.278   2319
  Planarity :  0.005   0.060   1697
  Dihedral  : 24.125 179.725   6254
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (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
 TRP   0.007   0.002   TRP B  78 
 HIS   0.007   0.001   HIS B 280 
 PHE   0.015   0.002   PHE B  96 
 TYR   0.024   0.002   TYR B 184 
 ARG   0.008   0.001   ARG B  31 

*********************** 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 fitting.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 1.039 
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: 1.2164
  time to fit residues: 270.2847
Evaluate side-chains
  209 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
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 103 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0770
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 49 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 110 optimal weight:    6.9990
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
A 296 HIS
B 157 ASN
J 198 ASN
J 298 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.0740

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= 0.193
  Angle     :  0.557   6.437  19665  Z= 0.301
  Chirality :  0.038   0.178   2319
  Planarity :  0.004   0.046   1697
  Dihedral  : 24.833 179.739   4132
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 23.98 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1054
  helix:  0.80 (0.22), residues: 566
  sheet:  1.69 (0.53), residues: 90
  loop : -1.20 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  78 
 HIS   0.006   0.001   HIS B 280 
 PHE   0.012   0.001   PHE B  96 
 TYR   0.016   0.001   TYR B 179 
 ARG   0.004   0.000   ARG A  49 

*********************** 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
  236 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 182
  time to evaluate  : 1.194 
Fit side-chains
REVERT: C  292 ARG cc_start: 0.7833 (mtp-110) cc_final: 0.7608 (mtm180)
REVERT: B  142 ASN cc_start: 0.7944 (p0) cc_final: 0.7486 (p0)
REVERT: J   30 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6833 (pt)
REVERT: J  230 LYS cc_start: 0.6874 (mmmt) cc_final: 0.6499 (mmmt)
  outliers start: 54
  outliers final: 23
  residues processed: 215
  average time/residue: 1.2364
  time to fit residues: 289.0487
Evaluate side-chains
  202 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain C residue  233 ASP
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   30 ILE
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0970
   chunk 75 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   chunk 119 optimal weight:    0.4980
   chunk 98 optimal weight:    0.0010
   chunk 37 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    0.4584

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

Flipped N/Q/H residues before XYZ refinement:
B 104 ASN
J 136 ASN
J 198 ASN
J 298 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.1116

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= 0.165
  Angle     :  0.527   6.583  19665  Z= 0.283
  Chirality :  0.037   0.176   2319
  Planarity :  0.004   0.044   1697
  Dihedral  : 24.561 179.704   4095
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 24.09 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.26), residues: 1054
  helix:  1.21 (0.22), residues: 564
  sheet:  1.86 (0.53), residues: 90
  loop : -1.10 (0.29), residues: 400

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

*********************** 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
  225 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 176
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
REVERT: J   30 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6864 (pt)
  outliers start: 49
  outliers final: 26
  residues processed: 207
  average time/residue: 1.2182
  time to fit residues: 274.6518
Evaluate side-chains
  202 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
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  219 ILE
Chi-restraints excluded: chain A residue  242 LYS
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  233 ASP
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  177 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   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
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  239 ILE
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
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 83 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 111 optimal weight:    0.0070
   chunk 117 optimal weight:    0.2980
   chunk 58 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 98 optimal weight:    0.3980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
J 115 ASN
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13862  Z= 0.168
  Angle     :  0.522   6.998  19665  Z= 0.279
  Chirality :  0.036   0.176   2319
  Planarity :  0.004   0.041   1697
  Dihedral  : 24.443 179.702   4080
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 23.77 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.26), residues: 1054
  helix:  1.39 (0.22), residues: 568
  sheet:  1.58 (0.54), residues: 94
  loop : -1.08 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  78 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.011   0.001   PHE J 205 
 TYR   0.015   0.001   TYR B 179 
 ARG   0.006   0.000   ARG A  49 

*********************** 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
  225 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 175
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8033 (p0)
REVERT: C  251 ARG cc_start: 0.7925 (mpt180) cc_final: 0.7675 (mpt180)
REVERT: J   30 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6814 (pt)
REVERT: J  230 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6482 (mmpt)
REVERT: J  298 ASN cc_start: 0.8325 (t0) cc_final: 0.8089 (t0)
  outliers start: 50
  outliers final: 34
  residues processed: 208
  average time/residue: 1.2203
  time to fit residues: 277.0358
Evaluate side-chains
  212 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 175
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   69 SER
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  193 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  242 LYS
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  233 ASP
Chi-restraints excluded: chain C residue  256 MET
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  193 THR
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   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
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  230 LYS
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
Chi-restraints excluded: chain J residue  262 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  277 LYS
Chi-restraints excluded: chain J residue  278 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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
B 240 GLN
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.1186

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= 0.252
  Angle     :  0.573   7.127  19665  Z= 0.304
  Chirality :  0.039   0.178   2319
  Planarity :  0.004   0.046   1697
  Dihedral  : 24.484 179.958   4080
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.26), residues: 1054
  helix:  1.24 (0.22), residues: 570
  sheet:  1.93 (0.53), residues: 89
  loop : -1.23 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  78 
 HIS   0.007   0.001   HIS B 280 
 PHE   0.015   0.002   PHE B  10 
 TYR   0.017   0.002   TYR B 179 
 ARG   0.006   0.000   ARG A  49 

*********************** 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
  221 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 176
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8097 (p0)
REVERT: C  292 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7625 (mtm180)
REVERT: B  139 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7507 (mp)
REVERT: B  142 ASN cc_start: 0.7933 (p0) cc_final: 0.7516 (p0)
REVERT: J   30 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6729 (pp)
REVERT: J  298 ASN cc_start: 0.8333 (t0) cc_final: 0.8104 (t0)
  outliers start: 45
  outliers final: 36
  residues processed: 205
  average time/residue: 1.2385
  time to fit residues: 276.3406
Evaluate side-chains
  211 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 172
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
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  193 THR
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  233 ASP
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  177 LEU
Chi-restraints excluded: chain B residue  193 THR
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   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
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  189 GLU
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  230 LYS
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
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
Chi-restraints excluded: chain J residue  278 THR
Chi-restraints excluded: chain J residue  295 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 69 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0070
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.0202

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13862  Z= 0.273
  Angle     :  0.585   7.471  19665  Z= 0.313
  Chirality :  0.040   0.177   2319
  Planarity :  0.005   0.060   1697
  Dihedral  : 24.512 179.606   4080
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 23.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1054
  helix:  1.11 (0.22), residues: 570
  sheet:  1.89 (0.53), residues: 89
  loop : -1.30 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B  78 
 HIS   0.006   0.001   HIS B 280 
 PHE   0.018   0.002   PHE B  10 
 TYR   0.018   0.002   TYR A 179 
 ARG   0.005   0.000   ARG A  11 

*********************** 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
  228 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 178
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8186 (p0)
REVERT: C  292 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7613 (mtm180)
REVERT: B  139 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7511 (mp)
REVERT: B  142 ASN cc_start: 0.7957 (p0) cc_final: 0.7539 (p0)
REVERT: J   30 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6775 (pt)
REVERT: J  298 ASN cc_start: 0.8325 (t0) cc_final: 0.8082 (t0)
  outliers start: 50
  outliers final: 41
  residues processed: 209
  average time/residue: 1.2399
  time to fit residues: 282.1936
Evaluate side-chains
  219 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 175
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   69 SER
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  193 THR
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  233 ASP
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  139 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  219 ILE
Chi-restraints excluded: chain B residue  276 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
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  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  230 LYS
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
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
Chi-restraints excluded: chain J residue  278 THR
Chi-restraints excluded: chain J residue  295 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 117 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0470
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
J 115 ASN
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13862  Z= 0.200
  Angle     :  0.558   6.840  19665  Z= 0.299
  Chirality :  0.038   0.174   2319
  Planarity :  0.004   0.058   1697
  Dihedral  : 24.487 179.683   4080
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.46 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1054
  helix:  1.22 (0.22), residues: 570
  sheet:  1.94 (0.53), residues: 89
  loop : -1.28 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  78 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.013   0.001   PHE B  96 
 TYR   0.015   0.001   TYR B 179 
 ARG   0.008   0.000   ARG A  49 

*********************** 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
  226 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 177
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8035 (p0)
REVERT: C  292 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7591 (mtm180)
REVERT: B  139 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7497 (mp)
REVERT: B  142 ASN cc_start: 0.7939 (p0) cc_final: 0.7522 (p0)
REVERT: J   30 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6768 (pt)
REVERT: J  298 ASN cc_start: 0.8320 (t0) cc_final: 0.8072 (t0)
  outliers start: 49
  outliers final: 38
  residues processed: 211
  average time/residue: 1.2349
  time to fit residues: 284.0664
Evaluate side-chains
  215 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 174
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
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  193 THR
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  233 ASP
Chi-restraints excluded: chain C residue  256 MET
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  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   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   93 VAL
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  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  230 LYS
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
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
Chi-restraints excluded: chain J residue  278 THR
Chi-restraints excluded: chain J residue  295 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 70 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 74 optimal weight:    0.2980
   chunk 80 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   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 115 ASN
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13862  Z= 0.210
  Angle     :  0.557   6.739  19665  Z= 0.298
  Chirality :  0.038   0.174   2319
  Planarity :  0.004   0.085   1697
  Dihedral  : 24.471 179.688   4080
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 23.88 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1054
  helix:  1.23 (0.22), residues: 571
  sheet:  1.95 (0.54), residues: 89
  loop : -1.26 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  78 
 HIS   0.006   0.001   HIS B 280 
 PHE   0.013   0.001   PHE B  96 
 TYR   0.015   0.001   TYR B 179 
 ARG   0.007   0.000   ARG A  49 

*********************** 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
  224 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 177
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8039 (p0)
REVERT: C  292 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7588 (mtm180)
REVERT: B  139 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7518 (mp)
REVERT: B  142 ASN cc_start: 0.7945 (p0) cc_final: 0.7547 (p0)
REVERT: J   30 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6769 (pt)
REVERT: J  298 ASN cc_start: 0.8320 (t0) cc_final: 0.8073 (t0)
  outliers start: 47
  outliers final: 39
  residues processed: 210
  average time/residue: 1.2727
  time to fit residues: 290.6473
Evaluate side-chains
  217 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 175
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
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  193 THR
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  233 ASP
Chi-restraints excluded: chain C residue  256 MET
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 J residue    6 THR
Chi-restraints excluded: chain J residue   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
Chi-restraints excluded: chain J residue   93 VAL
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  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  230 LYS
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
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
Chi-restraints excluded: chain J residue  278 THR
Chi-restraints excluded: chain J residue  295 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 112 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 99 optimal weight:    9.9990
   chunk 103 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
J 115 ASN
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.1291

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= 0.239
  Angle     :  0.568   6.886  19665  Z= 0.304
  Chirality :  0.039   0.177   2319
  Planarity :  0.004   0.061   1697
  Dihedral  : 24.462 179.920   4080
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.67 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1054
  helix:  1.17 (0.22), residues: 573
  sheet:  1.97 (0.54), residues: 89
  loop : -1.31 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  78 
 HIS   0.006   0.001   HIS B 280 
 PHE   0.014   0.002   PHE B  96 
 TYR   0.017   0.001   TYR A 179 
 ARG   0.007   0.000   ARG A  49 

*********************** 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
  224 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 175
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8084 (p0)
REVERT: C  292 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7585 (mtm180)
REVERT: B  139 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7499 (mp)
REVERT: B  142 ASN cc_start: 0.7940 (p0) cc_final: 0.7542 (p0)
REVERT: J   30 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6749 (pt)
REVERT: J  230 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6068 (mmmt)
REVERT: J  298 ASN cc_start: 0.8326 (t0) cc_final: 0.8072 (t0)
  outliers start: 49
  outliers final: 41
  residues processed: 209
  average time/residue: 1.2302
  time to fit residues: 279.8227
Evaluate side-chains
  218 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 173
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   69 SER
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  193 THR
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  233 ASP
Chi-restraints excluded: chain C residue  256 MET
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  177 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    1 MET
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
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  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  230 LYS
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
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
Chi-restraints excluded: chain J residue  278 THR
Chi-restraints excluded: chain J residue  295 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 111 optimal weight:    0.0970
   chunk 96 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 74 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
J 115 ASN
J 136 ASN
J 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13862  Z= 0.191
  Angle     :  0.554   6.640  19665  Z= 0.296
  Chirality :  0.037   0.173   2319
  Planarity :  0.004   0.049   1697
  Dihedral  : 24.449 179.944   4080
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.67 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1054
  helix:  1.30 (0.22), residues: 566
  sheet:  2.00 (0.54), residues: 89
  loop : -1.27 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  78 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.014   0.001   PHE A  10 
 TYR   0.016   0.001   TYR B 179 
 ARG   0.010   0.000   ARG A  11 

********************** 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
  222 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 173
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7252 (ttt-90)
REVERT: A   22 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8035 (p0)
REVERT: C  292 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7593 (mtm180)
REVERT: B  139 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7497 (mp)
REVERT: B  142 ASN cc_start: 0.7940 (p0) cc_final: 0.7545 (p0)
REVERT: J   30 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6745 (pt)
REVERT: J  230 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6056 (mmmt)
REVERT: J  298 ASN cc_start: 0.8320 (t0) cc_final: 0.8072 (t0)
  outliers start: 49
  outliers final: 40
  residues processed: 207
  average time/residue: 1.2885
  time to fit residues: 290.2521
Evaluate side-chains
  217 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 172
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   69 SER
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  193 THR
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  233 ASP
Chi-restraints excluded: chain C residue  256 MET
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    4 LYS
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue   30 ILE
Chi-restraints excluded: chain J residue   49 LEU
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  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  230 LYS
Chi-restraints excluded: chain J residue  239 ILE
Chi-restraints excluded: chain J residue  256 MET
Chi-restraints excluded: chain J residue  258 ASP
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
Chi-restraints excluded: chain J residue  278 THR
Chi-restraints excluded: chain J residue  295 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 96 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 12 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
J 115 ASN
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 = 0.4193 r_free = 0.4193 target = 0.179139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.143848 restraints weight = 15963.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 1.20
r_work: 0.3554 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1337

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= 0.218
  Angle     :  0.558   6.871  19665  Z= 0.298
  Chirality :  0.038   0.175   2319
  Planarity :  0.004   0.043   1697
  Dihedral  : 24.443 179.997   4080
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 23.98 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1054
  helix:  1.29 (0.22), residues: 566
  sheet:  2.01 (0.54), residues: 89
  loop : -1.26 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  78 
 HIS   0.005   0.001   HIS B 280 
 PHE   0.013   0.002   PHE B  96 
 TYR   0.015   0.001   TYR B 179 
 ARG   0.007   0.000   ARG A  11 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5067.89 seconds
wall clock time: 90 minutes 38.51 seconds (5438.51 seconds total)