Starting phenix.real_space_refine
on Tue Jul 29 01:20:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x19_21993/07_2025/6x19_21993.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x19_21993/07_2025/6x19_21993.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x19_21993/07_2025/6x19_21993.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x19_21993/07_2025/6x19_21993.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x19_21993/07_2025/6x19_21993.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x19_21993/07_2025/6x19_21993.cif"
  }
  resolution = 2.1
  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=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 843 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    6462      2.51       5
     N    1748      2.21       5
     O    2003      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10277
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2876
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 13, 'TRANS': 336}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 3203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3203
          Classifications: {'peptide': 387}
          Link IDs: {'PTRANS': 14, 'TRANS': 372}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 65
          Unusual residues: {'UK1': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 42
          Classifications: {'water': 42}
          Link IDs: {None: 41}
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 56
          Classifications: {'water': 56}
          Link IDs: {None: 55}
    Chain: "N"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "R"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 30
          Classifications: {'water': 30}
          Link IDs: {None: 29}
  Time building chain proxies: 7.78, per 1000 atoms: 0.76
  Number of scatterers: 10277
  At special positions: 0
  Unit cell: (115.37, 96.28, 170.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      62     16.00
     F       2      9.00
     O    2003      8.00
     N    1748      7.00
     C    6462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.01
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.01

  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: 2.62
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2386

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      46.4% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 91 through 112
    Processing helix  chain 'A' and resid 121 through 134
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 156 through 165
    Processing helix  chain 'A' and resid 175 through 181
    Processing helix  chain 'A' and resid 181 through 187
    Processing helix  chain 'A' and resid 193 through 200
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.053A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.848A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.728A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.548A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 31 through 53
      removed outlier: 4.029A  pdb=" N   GLN R  37 " --> pdb=" O   TRP R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 117
      removed outlier: 3.820A  pdb=" N   SER R 117 " --> pdb=" O   ASP R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 127
      removed outlier: 3.724A  pdb=" N   GLU R 127 " --> pdb=" O   SER R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 141
    Processing helix  chain 'R' and resid 141 through 167
    Processing helix  chain 'R' and resid 169 through 173
    Processing helix  chain 'R' and resid 174 through 208
    Processing helix  chain 'R' and resid 210 through 212
      No H-bonds generated for 'chain 'R' and resid 210 through 212'
    Processing helix  chain 'R' and resid 213 through 223
      removed outlier: 3.626A  pdb=" N   LEU R 217 " --> pdb=" O   GLN R 213 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 256
      removed outlier: 3.956A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 275
      removed outlier: 3.698A  pdb=" N   PHE R 266 " --> pdb=" O   GLU R 262 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG R 267 " --> pdb=" O   GLN R 263 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU R 268 " --> pdb=" O   TRP R 264 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 292
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 306 through 338
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 341 through 361
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 362 through 369
    Processing helix  chain 'R' and resid 379 through 393
      removed outlier: 3.691A  pdb=" N   LYS R 383 " --> pdb=" O   LEU R 379 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLU R 387 " --> pdb=" O   LYS R 383 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 403
    Processing helix  chain 'R' and resid 406 through 423
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.292A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.193A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.159A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.562A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.764A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.542A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.738A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.687A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.649A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 5.939A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66
      removed outlier: 3.550A  pdb=" N   THR R  65 " --> pdb=" O   TRP R  72 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 80 through 83

    525 hydrogen bonds defined for protein.
    1485 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.75

  Time building geometry restraints manager: 3.19 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1661
        1.32 -     1.44: 2925
        1.44 -     1.57: 5697
        1.57 -     1.69: 11
        1.69 -     1.82: 85
  Bond restraints: 10379
  Sorted by residual:
  bond pdb=" C03 UK1 R 501 "
       pdb=" N07 UK1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.423  1.722 -0.299 2.00e-02 2.50e+03 2.23e+02
  bond pdb=" C46 UK1 R 501 "
       pdb=" N43 UK1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.419  1.628 -0.209 2.00e-02 2.50e+03 1.09e+02
  bond pdb=" C31 UK1 R 501 "
       pdb=" N33 UK1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.605 -0.192 2.00e-02 2.50e+03 9.20e+01
  bond pdb=" C57 UK1 R 501 "
       pdb=" C58 UK1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.620  1.435  0.185 2.00e-02 2.50e+03 8.56e+01
  bond pdb=" C28 UK1 R 501 "
       pdb=" C60 UK1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.521  1.674 -0.153 2.00e-02 2.50e+03 5.83e+01
  ... (remaining 10374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.01: 14072
        8.01 -    16.01: 12
       16.01 -    24.02: 1
       24.02 -    32.03: 0
       32.03 -    40.03: 1
  Bond angle restraints: 14086
  Sorted by residual:
  angle pdb=" C28 UK1 R 501 "
        pdb=" C57 UK1 R 501 "
        pdb=" C58 UK1 R 501 "
      ideal   model   delta    sigma   weight residual
     110.03   70.00   40.03 3.00e+00 1.11e-01 1.78e+02
  angle pdb=" N   PRO A 115 "
        pdb=" CA  PRO A 115 "
        pdb=" C   PRO A 115 "
      ideal   model   delta    sigma   weight residual
     110.70   99.23   11.47 1.22e+00 6.72e-01 8.83e+01
  angle pdb=" C   PHE A 142 "
        pdb=" N   PRO A 143 "
        pdb=" CA  PRO A 143 "
      ideal   model   delta    sigma   weight residual
     119.66  125.30   -5.64 7.30e-01 1.88e+00 5.96e+01
  angle pdb=" N   ASN A  14 "
        pdb=" CA  ASN A  14 "
        pdb=" C   ASN A  14 "
      ideal   model   delta    sigma   weight residual
     113.41  105.34    8.07 1.22e+00 6.72e-01 4.37e+01
  angle pdb=" N   GLN A  19 "
        pdb=" CA  GLN A  19 "
        pdb=" C   GLN A  19 "
      ideal   model   delta    sigma   weight residual
     113.23  105.99    7.24 1.24e+00 6.50e-01 3.41e+01
  ... (remaining 14081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 5619
       17.78 -    35.56: 467
       35.56 -    53.34: 69
       53.34 -    71.12: 25
       71.12 -    88.89: 10
  Dihedral angle restraints: 6190
    sinusoidal: 2505
      harmonic: 3685
  Sorted by residual:
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.06  -26.94     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" C   ASN A 371 "
           pdb=" N   ASN A 371 "
           pdb=" CA  ASN A 371 "
           pdb=" CB  ASN A 371 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.35   12.75     0      2.50e+00 1.60e-01 2.60e+01
  dihedral pdb=" C   ARG A 317 "
           pdb=" N   ARG A 317 "
           pdb=" CA  ARG A 317 "
           pdb=" CB  ARG A 317 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.51  -12.09     0      2.50e+00 1.60e-01 2.34e+01
  ... (remaining 6187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1274
       0.090 -    0.179: 202
       0.179 -    0.269: 45
       0.269 -    0.358: 17
       0.358 -    0.448: 4
  Chirality restraints: 1542
  Sorted by residual:
  chirality pdb=" CA  ASP R 293 "
            pdb=" N   ASP R 293 "
            pdb=" C   ASP R 293 "
            pdb=" CB  ASP R 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.01e+00
  chirality pdb=" CA  ASN A 371 "
            pdb=" N   ASN A 371 "
            pdb=" C   ASN A 371 "
            pdb=" CB  ASN A 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.16e+00
  chirality pdb=" CA  GLU R 125 "
            pdb=" N   GLU R 125 "
            pdb=" C   GLU R 125 "
            pdb=" CB  GLU R 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.37e+00
  ... (remaining 1539 not shown)

  Planarity restraints: 1793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 290 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.71e+00
        pdb=" C   LEU R 290 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LEU R 290 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR R 291 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 101 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.66e+00
        pdb=" C   TYR R 101 "    0.045 2.00e-02 2.50e+03
        pdb=" O   TYR R 101 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG R 102 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 155 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.64e+00
        pdb=" C   GLU A 155 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLU A 155 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A 156 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1790 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 299
        2.69 -     3.24: 10501
        3.24 -     3.79: 16930
        3.79 -     4.35: 24127
        4.35 -     4.90: 37142
  Nonbonded interactions: 88999
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 105 "
            pdb=" O   HOH B 401 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OD1 ASP A 141 "
            pdb=" CD  PRO A 143 "
     model   vdw
     2.158 3.440
  nonbonded pdb=" OE1 GLU A 392 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OE2 GLU A 209 "
            pdb=" O   HOH A 402 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" N   GLU A 145 "
            pdb=" OE1 GLU A 145 "
     model   vdw
     2.269 3.120
  ... (remaining 88994 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             35.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     29.400
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  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:21.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   86.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.299  10385  Z= 0.604
  Angle     :  1.150  40.033  14098  Z= 0.768
  Chirality :  0.078   0.448   1542
  Planarity :  0.005   0.047   1793
  Dihedral  : 13.948  88.894   3786
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.66 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  4.04 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.50 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.22), residues: 1240
  helix: -1.26 (0.20), residues: 519
  sheet: -0.58 (0.31), residues: 241
  loop : -0.83 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R  87 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.018   0.002   PHE A 363 
 TYR   0.030   0.002   TYR B  59 
 ARG   0.005   0.001   ARG R 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23772 (  525)
  hydrogen bonds       : angle       8.54453 ( 1485)
  SS BOND              : bond        0.01505 (    6)
  SS BOND              : angle       3.12622 (   12)
  covalent geometry    : bond        0.00984 (10379)
  covalent geometry    : angle       1.14672 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 2.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 GLU cc_start: 0.8032 (pt0) cc_final: 0.7744 (pt0)
REVERT: A  344 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7435 (mm-30)
REVERT: R  117 SER cc_start: 0.2598 (OUTLIER) cc_final: 0.1520 (t)
REVERT: R  267 ARG cc_start: 0.6435 (mmt180) cc_final: 0.6220 (tpt170)
  outliers start: 11
  outliers final: 1
  residues processed: 187
  average time/residue: 2.1802
  time to fit residues: 430.2768
Evaluate side-chains
  125 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 387 HIS
B  17 GLN
B  44 GLN
B  88 ASN
B 268 ASN
B 340 ASN
G  59 ASN
N  31 ASN
R  45 GLN
R  99 HIS
R 140 GLN
R 338 ASN
R 407 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.167531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102424 restraints weight = 11800.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.98
r_work: 0.3131 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10385  Z= 0.193
  Angle     :  0.662   8.742  14098  Z= 0.356
  Chirality :  0.045   0.144   1542
  Planarity :  0.005   0.044   1793
  Dihedral  :  5.520  44.849   1435
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 10.00 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.01 (0.23), residues: 1240
  helix:  0.58 (0.21), residues: 535
  sheet: -0.28 (0.31), residues: 248
  loop : -0.32 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.036   0.002   TYR R 148 
 ARG   0.006   0.001   ARG R  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06020 (  525)
  hydrogen bonds       : angle       5.27052 ( 1485)
  SS BOND              : bond        0.00918 (    6)
  SS BOND              : angle       2.00252 (   12)
  covalent geometry    : bond        0.00423 (10379)
  covalent geometry    : angle       0.65942 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6616 (tt0)
REVERT: A  344 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8439 (mm-30)
REVERT: B   23 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8040 (tptt)
REVERT: B   59 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8797 (m-80)
REVERT: N   19 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8271 (ttt180)
REVERT: R   68 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5587 (pp20)
REVERT: R  215 ASP cc_start: 0.7251 (p0) cc_final: 0.6781 (m-30)
REVERT: R  380 ARG cc_start: 0.5474 (mmp80) cc_final: 0.5211 (mmm160)
REVERT: R  411 LEU cc_start: 0.8351 (tt) cc_final: 0.8087 (tm)
  outliers start: 21
  outliers final: 4
  residues processed: 127
  average time/residue: 1.7824
  time to fit residues: 238.9935
Evaluate side-chains
  112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  232 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 118 optimal weight:    0.0000
   chunk 100 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 109 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  88 ASN
B 156 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.168756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.104622 restraints weight = 12044.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.99
r_work: 0.3168 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10385  Z= 0.132
  Angle     :  0.554   9.372  14098  Z= 0.299
  Chirality :  0.042   0.138   1542
  Planarity :  0.004   0.048   1793
  Dihedral  :  4.901  29.380   1433
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.20 %
    Favored  : 85.87 %
  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:  0.82 (0.24), residues: 1240
  helix:  1.54 (0.22), residues: 536
  sheet: -0.10 (0.32), residues: 246
  loop : -0.17 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.028   0.002   TYR R 148 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04998 (  525)
  hydrogen bonds       : angle       4.78518 ( 1485)
  SS BOND              : bond        0.00568 (    6)
  SS BOND              : angle       1.47575 (   12)
  covalent geometry    : bond        0.00277 (10379)
  covalent geometry    : angle       0.55213 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.8243 (ttm170)
REVERT: B   59 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8723 (m-80)
REVERT: B  214 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7662 (mmt180)
REVERT: N   19 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8175 (ttt180)
REVERT: R   41 GLU cc_start: 0.7732 (tp30) cc_final: 0.7330 (tp30)
REVERT: R   68 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5688 (pp20)
REVERT: R  215 ASP cc_start: 0.7276 (p0) cc_final: 0.6682 (m-30)
REVERT: R  336 LYS cc_start: 0.7688 (mmtp) cc_final: 0.7438 (mmtm)
REVERT: R  380 ARG cc_start: 0.5346 (mmp80) cc_final: 0.5041 (mmm160)
REVERT: R  408 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7381 (mp0)
  outliers start: 21
  outliers final: 8
  residues processed: 131
  average time/residue: 1.7180
  time to fit residues: 237.6286
Evaluate side-chains
  120 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  408 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 88 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0040
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.169188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105146 restraints weight = 11962.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.99
r_work: 0.3178 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10385  Z= 0.116
  Angle     :  0.522   8.138  14098  Z= 0.280
  Chirality :  0.041   0.139   1542
  Planarity :  0.004   0.051   1793
  Dihedral  :  4.702  30.188   1433
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.22 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.24), residues: 1240
  helix:  2.01 (0.22), residues: 535
  sheet:  0.04 (0.31), residues: 256
  loop : -0.06 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.026   0.001   TYR R 148 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04467 (  525)
  hydrogen bonds       : angle       4.52796 ( 1485)
  SS BOND              : bond        0.00315 (    6)
  SS BOND              : angle       1.20349 (   12)
  covalent geometry    : bond        0.00243 (10379)
  covalent geometry    : angle       0.52109 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.7915 (tt0) cc_final: 0.7670 (tm-30)
REVERT: B   59 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8671 (m-80)
REVERT: B  217 MET cc_start: 0.8891 (pmt) cc_final: 0.8678 (pmm)
REVERT: B  260 GLU cc_start: 0.8569 (tt0) cc_final: 0.8341 (tt0)
REVERT: N   19 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8160 (ttt180)
REVERT: R   45 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7186 (mp10)
REVERT: R   68 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5609 (pp20)
REVERT: R  215 ASP cc_start: 0.7419 (p0) cc_final: 0.6740 (m-30)
REVERT: R  336 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7379 (mmtm)
REVERT: R  344 ASP cc_start: 0.6322 (t0) cc_final: 0.6091 (t0)
REVERT: R  380 ARG cc_start: 0.5323 (mmp80) cc_final: 0.4945 (mmm160)
REVERT: R  411 LEU cc_start: 0.8371 (tt) cc_final: 0.8104 (tm)
  outliers start: 14
  outliers final: 5
  residues processed: 129
  average time/residue: 1.6550
  time to fit residues: 226.0502
Evaluate side-chains
  121 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   45 GLN
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 112 optimal weight:    2.9990
   chunk 117 optimal weight:    0.0270
   chunk 94 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   overall best weight:    0.9840

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.168515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.103981 restraints weight = 11922.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.99
r_work: 0.3163 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10385  Z= 0.128
  Angle     :  0.529   8.491  14098  Z= 0.284
  Chirality :  0.041   0.141   1542
  Planarity :  0.004   0.051   1793
  Dihedral  :  4.717  27.768   1433
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.31 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.24), residues: 1240
  helix:  2.15 (0.22), residues: 536
  sheet:  0.07 (0.32), residues: 250
  loop :  0.04 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.009   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  525)
  hydrogen bonds       : angle       4.53578 ( 1485)
  SS BOND              : bond        0.00329 (    6)
  SS BOND              : angle       1.24315 (   12)
  covalent geometry    : bond        0.00274 (10379)
  covalent geometry    : angle       0.52770 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.4698 (mmm)
REVERT: B   59 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8678 (m-80)
REVERT: B  217 MET cc_start: 0.8941 (pmt) cc_final: 0.8739 (pmm)
REVERT: N    3 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8195 (mt0)
REVERT: N   19 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8135 (ttt180)
REVERT: R   68 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5533 (pp20)
REVERT: R  110 TRP cc_start: 0.3928 (m100) cc_final: 0.3456 (m100)
REVERT: R  215 ASP cc_start: 0.7484 (p0) cc_final: 0.6835 (m-30)
REVERT: R  336 LYS cc_start: 0.7650 (mmtp) cc_final: 0.7353 (mmtm)
REVERT: R  344 ASP cc_start: 0.6263 (t0) cc_final: 0.5971 (t0)
REVERT: R  369 PHE cc_start: 0.5782 (m-10) cc_final: 0.5501 (m-10)
REVERT: R  380 ARG cc_start: 0.5118 (mmp80) cc_final: 0.4912 (mmm160)
  outliers start: 19
  outliers final: 8
  residues processed: 126
  average time/residue: 1.6737
  time to fit residues: 222.8723
Evaluate side-chains
  123 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 101 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 109 optimal weight:    5.9990
   chunk 105 optimal weight:    0.7980
   chunk 85 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.168863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105067 restraints weight = 12021.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.97
r_work: 0.3176 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10385  Z= 0.117
  Angle     :  0.519   8.078  14098  Z= 0.277
  Chirality :  0.041   0.140   1542
  Planarity :  0.004   0.050   1793
  Dihedral  :  4.620  26.021   1433
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.50 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.24), residues: 1240
  helix:  2.28 (0.23), residues: 536
  sheet:  0.12 (0.32), residues: 240
  loop :  0.05 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.007   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  525)
  hydrogen bonds       : angle       4.45212 ( 1485)
  SS BOND              : bond        0.00304 (    6)
  SS BOND              : angle       1.10198 (   12)
  covalent geometry    : bond        0.00248 (10379)
  covalent geometry    : angle       0.51810 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.4624 (mmm)
REVERT: B   59 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8661 (m-80)
REVERT: B  172 GLU cc_start: 0.8504 (tp30) cc_final: 0.8292 (tp30)
REVERT: B  217 MET cc_start: 0.8889 (pmt) cc_final: 0.8681 (pmm)
REVERT: G   20 LYS cc_start: 0.8084 (mttp) cc_final: 0.7882 (mttp)
REVERT: G   46 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8208 (mmmm)
REVERT: N    3 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8185 (mt0)
REVERT: N   19 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8089 (ttt180)
REVERT: R   68 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5468 (pp20)
REVERT: R  110 TRP cc_start: 0.3963 (m100) cc_final: 0.3435 (m100)
REVERT: R  336 LYS cc_start: 0.7658 (mmtp) cc_final: 0.7347 (mmtm)
REVERT: R  344 ASP cc_start: 0.6300 (t0) cc_final: 0.6038 (t0)
REVERT: R  380 ARG cc_start: 0.5168 (mmp80) cc_final: 0.4909 (mmm160)
REVERT: R  408 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7376 (mp0)
REVERT: R  411 LEU cc_start: 0.8437 (tt) cc_final: 0.8173 (tm)
  outliers start: 18
  outliers final: 7
  residues processed: 124
  average time/residue: 1.6462
  time to fit residues: 216.2038
Evaluate side-chains
  123 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  408 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 2 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 53 optimal weight:    0.3980
   chunk 109 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B  44 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.168673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.104203 restraints weight = 12081.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.01
r_work: 0.3163 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10385  Z= 0.123
  Angle     :  0.524   8.098  14098  Z= 0.280
  Chirality :  0.041   0.141   1542
  Planarity :  0.004   0.050   1793
  Dihedral  :  4.642  25.099   1433
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.31 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.24), residues: 1240
  helix:  2.28 (0.22), residues: 536
  sheet:  0.18 (0.32), residues: 241
  loop :  0.09 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.023   0.002   TYR R 148 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 (  525)
  hydrogen bonds       : angle       4.44724 ( 1485)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       1.03450 (   12)
  covalent geometry    : bond        0.00261 (10379)
  covalent geometry    : angle       0.52296 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.4453 (mmm)
REVERT: B   15 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7794 (mttm)
REVERT: B   59 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8673 (m-80)
REVERT: B  217 MET cc_start: 0.8913 (pmt) cc_final: 0.8689 (pmm)
REVERT: G   20 LYS cc_start: 0.8068 (mttp) cc_final: 0.7843 (mttp)
REVERT: G   46 LYS cc_start: 0.8510 (mmpt) cc_final: 0.8238 (mmmm)
REVERT: N    3 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8190 (mt0)
REVERT: N   19 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8102 (ttt180)
REVERT: R   68 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5516 (pp20)
REVERT: R  336 LYS cc_start: 0.7678 (mmtp) cc_final: 0.7356 (mmtm)
REVERT: R  344 ASP cc_start: 0.6340 (t0) cc_final: 0.6079 (t0)
REVERT: R  380 ARG cc_start: 0.5195 (mmp80) cc_final: 0.4919 (mmm160)
REVERT: R  408 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7344 (mp0)
REVERT: R  411 LEU cc_start: 0.8470 (tt) cc_final: 0.8189 (tm)
  outliers start: 21
  outliers final: 7
  residues processed: 125
  average time/residue: 1.7277
  time to fit residues: 228.5677
Evaluate side-chains
  122 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  408 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 87 optimal weight:   20.0000
   chunk 55 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 70 optimal weight:    0.2980
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 101 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
B  16 ASN
B  44 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.169560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.105542 restraints weight = 12015.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.99
r_work: 0.3187 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10385  Z= 0.110
  Angle     :  0.515  10.564  14098  Z= 0.273
  Chirality :  0.041   0.139   1542
  Planarity :  0.004   0.050   1793
  Dihedral  :  4.538  23.611   1433
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.77 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.24), residues: 1240
  helix:  2.33 (0.23), residues: 536
  sheet:  0.20 (0.32), residues: 240
  loop :  0.10 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.023   0.001   TYR R 148 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04251 (  525)
  hydrogen bonds       : angle       4.37579 ( 1485)
  SS BOND              : bond        0.00289 (    6)
  SS BOND              : angle       0.99475 (   12)
  covalent geometry    : bond        0.00232 (10379)
  covalent geometry    : angle       0.51417 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.7563 (tp40) cc_final: 0.7307 (tp40)
REVERT: B   15 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7819 (mttm)
REVERT: B   59 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8648 (m-80)
REVERT: G   20 LYS cc_start: 0.8092 (mttp) cc_final: 0.7860 (mttp)
REVERT: G   46 LYS cc_start: 0.8497 (mmpt) cc_final: 0.8226 (mmmm)
REVERT: N    3 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8183 (mt0)
REVERT: N   19 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8071 (ttt180)
REVERT: N   43 LYS cc_start: 0.8616 (mttp) cc_final: 0.8352 (mtpt)
REVERT: R   68 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5415 (pp20)
REVERT: R  110 TRP cc_start: 0.3908 (m100) cc_final: 0.3318 (m100)
REVERT: R  114 ASP cc_start: 0.5823 (t0) cc_final: 0.5611 (t0)
REVERT: R  336 LYS cc_start: 0.7644 (mmtp) cc_final: 0.7379 (mptt)
REVERT: R  344 ASP cc_start: 0.6386 (t0) cc_final: 0.6125 (t0)
REVERT: R  408 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7361 (mp0)
REVERT: R  411 LEU cc_start: 0.8489 (tt) cc_final: 0.8208 (tm)
  outliers start: 18
  outliers final: 6
  residues processed: 127
  average time/residue: 1.6703
  time to fit residues: 224.8121
Evaluate side-chains
  123 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 1.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  408 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0000
   chunk 69 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  44 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.169363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.105194 restraints weight = 12094.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.99
r_work: 0.3185 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10385  Z= 0.113
  Angle     :  0.520   9.539  14098  Z= 0.276
  Chirality :  0.041   0.137   1542
  Planarity :  0.004   0.053   1793
  Dihedral  :  4.553  23.313   1433
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.60 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.24), residues: 1240
  helix:  2.31 (0.23), residues: 536
  sheet:  0.20 (0.32), residues: 240
  loop :  0.12 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.023   0.001   TYR R 148 
 ARG   0.015   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04250 (  525)
  hydrogen bonds       : angle       4.36677 ( 1485)
  SS BOND              : bond        0.00306 (    6)
  SS BOND              : angle       1.00018 (   12)
  covalent geometry    : bond        0.00240 (10379)
  covalent geometry    : angle       0.51967 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 1.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.7515 (tp40) cc_final: 0.7261 (tp40)
REVERT: B   15 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7837 (mttm)
REVERT: B   59 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8641 (m-80)
REVERT: G   20 LYS cc_start: 0.8094 (mttp) cc_final: 0.7858 (mttp)
REVERT: G   46 LYS cc_start: 0.8486 (mmpt) cc_final: 0.8214 (mmmm)
REVERT: N    3 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8187 (mt0)
REVERT: N   19 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8051 (ttt180)
REVERT: N   43 LYS cc_start: 0.8615 (mttp) cc_final: 0.8349 (mtpt)
REVERT: R   68 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.5173 (pp20)
REVERT: R  110 TRP cc_start: 0.3974 (m100) cc_final: 0.3392 (m100)
REVERT: R  114 ASP cc_start: 0.5846 (t0) cc_final: 0.5627 (t70)
REVERT: R  336 LYS cc_start: 0.7633 (mmtp) cc_final: 0.7362 (mptt)
REVERT: R  411 LEU cc_start: 0.8507 (tt) cc_final: 0.8222 (tm)
  outliers start: 16
  outliers final: 7
  residues processed: 122
  average time/residue: 2.3058
  time to fit residues: 299.9988
Evaluate side-chains
  126 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 2.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 113 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 93 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  44 GLN
B  88 ASN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.167388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.101551 restraints weight = 11953.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.09
r_work: 0.3120 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10385  Z= 0.180
  Angle     :  0.596   9.514  14098  Z= 0.315
  Chirality :  0.044   0.145   1542
  Planarity :  0.005   0.056   1793
  Dihedral  :  4.970  25.723   1433
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.50 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.24), residues: 1240
  helix:  2.18 (0.22), residues: 531
  sheet:  0.25 (0.32), residues: 242
  loop :  0.15 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 234 
 HIS   0.006   0.001   HIS B 311 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.022   0.002   TYR R 148 
 ARG   0.014   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05095 (  525)
  hydrogen bonds       : angle       4.64927 ( 1485)
  SS BOND              : bond        0.00466 (    6)
  SS BOND              : angle       1.03378 (   12)
  covalent geometry    : bond        0.00402 (10379)
  covalent geometry    : angle       0.59503 (14086)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.7552 (tp40) cc_final: 0.7269 (tp40)
REVERT: B   15 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7807 (mttm)
REVERT: B   59 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8737 (m-80)
REVERT: G   20 LYS cc_start: 0.8143 (mttp) cc_final: 0.7925 (mttp)
REVERT: G   42 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7162 (mp0)
REVERT: G   46 LYS cc_start: 0.8522 (mmpt) cc_final: 0.8293 (mmmm)
REVERT: N   19 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8117 (ttt180)
REVERT: R   68 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5351 (pp20)
REVERT: R  110 TRP cc_start: 0.4044 (m100) cc_final: 0.3467 (m100)
REVERT: R  344 ASP cc_start: 0.6405 (t0) cc_final: 0.6169 (t0)
REVERT: R  408 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7352 (mp0)
  outliers start: 16
  outliers final: 7
  residues processed: 127
  average time/residue: 1.6400
  time to fit residues: 220.7898
Evaluate side-chains
  123 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain R residue   68 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  408 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0020
   chunk 68 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   overall best weight:    1.7792

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B  44 GLN
B 268 ASN
G  59 ASN
N   1 GLN
R 407 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.167534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102204 restraints weight = 11857.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.05
r_work: 0.3132 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10385  Z= 0.172
  Angle     :  0.593   9.150  14098  Z= 0.313
  Chirality :  0.043   0.146   1542
  Planarity :  0.005   0.054   1793
  Dihedral  :  4.932  25.912   1433
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 15.78 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1240
  helix:  2.14 (0.22), residues: 531
  sheet:  0.25 (0.33), residues: 241
  loop :  0.11 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.019   0.002   PHE B 151 
 TYR   0.023   0.002   TYR R 148 
 ARG   0.014   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04998 (  525)
  hydrogen bonds       : angle       4.63454 ( 1485)
  SS BOND              : bond        0.00449 (    6)
  SS BOND              : angle       1.02377 (   12)
  covalent geometry    : bond        0.00383 (10379)
  covalent geometry    : angle       0.59201 (14086)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 18173.07 seconds
wall clock time: 315 minutes 45.09 seconds (18945.09 seconds total)