Starting phenix.real_space_refine
on Fri Feb 14 06:49:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g12_29659/02_2025/8g12_29659_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g12_29659/02_2025/8g12_29659.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g12_29659/02_2025/8g12_29659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g12_29659/02_2025/8g12_29659.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g12_29659/02_2025/8g12_29659_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g12_29659/02_2025/8g12_29659_neut.cif"
  }
  resolution = 2.17
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6296      2.51       5
     N    1736      2.21       5
     O    1900      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9980
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2495
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'CSO:plan-1': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 4.61, per 1000 atoms: 0.46
  Number of scatterers: 9980
  At special positions: 0
  Unit cell: (92.685, 98.53, 91.015, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1900      8.00
     N    1736      7.00
     C    6296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.56
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      36.5% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 26
    Processing helix  chain 'A' and resid 39 through 49
    Processing helix  chain 'A' and resid 81 through 85
      removed outlier: 3.628A  pdb=" N   ILE A  85 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.635A  pdb=" N   ALA A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 110 through 112
      No H-bonds generated for 'chain 'A' and resid 110 through 112'
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 3.641A  pdb=" N   TYR A 140 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 3.818A  pdb=" N   GLY A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.509A  pdb=" N   ASN A 287 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 335
    Processing helix  chain 'B' and resid 12 through 26
    Processing helix  chain 'B' and resid 39 through 49
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.628A  pdb=" N   ILE B  85 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.635A  pdb=" N   ALA B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 110 through 112
      No H-bonds generated for 'chain 'B' and resid 110 through 112'
    Processing helix  chain 'B' and resid 136 through 140
      removed outlier: 3.641A  pdb=" N   TYR B 140 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 169
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 212 through 221
      removed outlier: 3.818A  pdb=" N   GLY B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 254 through 268
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.508A  pdb=" N   ASN B 287 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 335
    Processing helix  chain 'C' and resid 12 through 26
    Processing helix  chain 'C' and resid 39 through 49
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.628A  pdb=" N   ILE C  85 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 91
      removed outlier: 3.635A  pdb=" N   ALA C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 110 through 112
      No H-bonds generated for 'chain 'C' and resid 110 through 112'
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 3.641A  pdb=" N   TYR C 140 " --> pdb=" O   HIS C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 169
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 212 through 221
      removed outlier: 3.817A  pdb=" N   GLY C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS C 219 " --> pdb=" O   LYS C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 254 through 268
    Processing helix  chain 'C' and resid 282 through 287
      removed outlier: 3.508A  pdb=" N   ASN C 287 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 335
    Processing helix  chain 'D' and resid 12 through 26
    Processing helix  chain 'D' and resid 39 through 49
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.628A  pdb=" N   ILE D  85 " --> pdb=" O   PRO D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 91
      removed outlier: 3.634A  pdb=" N   ALA D  90 " --> pdb=" O   LYS D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 110 through 112
      No H-bonds generated for 'chain 'D' and resid 110 through 112'
    Processing helix  chain 'D' and resid 136 through 140
      removed outlier: 3.641A  pdb=" N   TYR D 140 " --> pdb=" O   HIS D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 169
      Proline residue:  D 159  - end of helix
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 3.818A  pdb=" N   GLY D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS D 219 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 254 through 268
    Processing helix  chain 'D' and resid 282 through 287
      removed outlier: 3.509A  pdb=" N   ASN D 287 " --> pdb=" O   SER D 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 319 through 335
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 10.275A  pdb=" N   ASP A  29 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 10.117A  pdb=" N   THR A  75 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   PHE A  77 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ILE A  33 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.738A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR A 177 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 12.497A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 11.402A  pdb=" N   GLY A 300 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
      removed outlier: 10.753A  pdb=" N   LYS A 309 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   GLY A 298 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 10.274A  pdb=" N   ASP B  29 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 10.117A  pdb=" N   THR B  75 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL B  31 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   PHE B  77 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE B  33 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ILE B  33 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.736A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR B 177 " --> pdb=" O   MET B 231 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU B 172 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 12.496A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 11.402A  pdb=" N   GLY B 300 " --> pdb=" O   PHE B 307 " (cutoff:3.500A)
      removed outlier: 10.753A  pdb=" N   LYS B 309 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   GLY B 298 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63
      removed outlier: 10.274A  pdb=" N   ASP C  29 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 10.117A  pdb=" N   THR C  75 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL C  31 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   PHE C  77 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE C  33 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   VAL C   8 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.737A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR C 177 " --> pdb=" O   MET C 231 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU C 172 " --> pdb=" O   ARG C 248 " (cutoff:3.500A)
      removed outlier: 12.496A  pdb=" N   PHE C 307 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 11.401A  pdb=" N   GLY C 300 " --> pdb=" O   PHE C 307 " (cutoff:3.500A)
      removed outlier: 10.753A  pdb=" N   LYS C 309 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   GLY C 298 " --> pdb=" O   LYS C 309 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   ILE C 311 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63
      removed outlier: 10.274A  pdb=" N   ASP D  29 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 10.117A  pdb=" N   THR D  75 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL D  31 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   PHE D  77 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE D  33 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.737A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR D 177 " --> pdb=" O   MET D 231 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU D 172 " --> pdb=" O   ARG D 248 " (cutoff:3.500A)
      removed outlier: 12.497A  pdb=" N   PHE D 307 " --> pdb=" O   GLY D 300 " (cutoff:3.500A)
      removed outlier: 11.402A  pdb=" N   GLY D 300 " --> pdb=" O   PHE D 307 " (cutoff:3.500A)
      removed outlier: 10.753A  pdb=" N   LYS D 309 " --> pdb=" O   GLY D 298 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   GLY D 298 " --> pdb=" O   LYS D 309 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   ILE D 311 " --> pdb=" O   ASP D 296 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1224 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: 2.95

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2821
        1.33 -     1.45: 1630
        1.45 -     1.57: 5641
        1.57 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 10180
  Sorted by residual:
  bond pdb=" SG  CSO B 152 "
       pdb=" OD  CSO B 152 "
    ideal  model  delta    sigma   weight residual
    1.668  1.735 -0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" SG  CSO C 152 "
       pdb=" OD  CSO C 152 "
    ideal  model  delta    sigma   weight residual
    1.668  1.734 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" SG  CSO A 152 "
       pdb=" OD  CSO A 152 "
    ideal  model  delta    sigma   weight residual
    1.668  1.734 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" SG  CSO D 152 "
       pdb=" OD  CSO D 152 "
    ideal  model  delta    sigma   weight residual
    1.668  1.734 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" N   ILE A 206 "
       pdb=" CA  ILE A 206 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.038 1.28e-02 6.10e+03 8.95e+00
  ... (remaining 10175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 12710
        1.49 -     2.97: 883
        2.97 -     4.46: 159
        4.46 -     5.95: 44
        5.95 -     7.44: 12
  Bond angle restraints: 13808
  Sorted by residual:
  angle pdb=" N   ILE A 206 "
        pdb=" CA  ILE A 206 "
        pdb=" C   ILE A 206 "
      ideal   model   delta    sigma   weight residual
     111.56  107.15    4.41 8.60e-01 1.35e+00 2.63e+01
  angle pdb=" N   ILE B 206 "
        pdb=" CA  ILE B 206 "
        pdb=" C   ILE B 206 "
      ideal   model   delta    sigma   weight residual
     111.56  107.16    4.40 8.60e-01 1.35e+00 2.62e+01
  angle pdb=" N   ILE C 206 "
        pdb=" CA  ILE C 206 "
        pdb=" C   ILE C 206 "
      ideal   model   delta    sigma   weight residual
     111.56  107.17    4.39 8.60e-01 1.35e+00 2.61e+01
  angle pdb=" N   ILE D 206 "
        pdb=" CA  ILE D 206 "
        pdb=" C   ILE D 206 "
      ideal   model   delta    sigma   weight residual
     111.56  107.17    4.39 8.60e-01 1.35e+00 2.60e+01
  angle pdb=" C   ALA D 150 "
        pdb=" CA  ALA D 150 "
        pdb=" CB  ALA D 150 "
      ideal   model   delta    sigma   weight residual
     116.34  110.47    5.87 1.40e+00 5.10e-01 1.76e+01
  ... (remaining 13803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 5440
       17.75 -    35.49: 411
       35.49 -    53.24: 101
       53.24 -    70.99: 36
       70.99 -    88.73: 16
  Dihedral angle restraints: 6004
    sinusoidal: 2228
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CA  VAL A 178 "
           pdb=" C   VAL A 178 "
           pdb=" N   HIS A 179 "
           pdb=" CA  HIS A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.53  -15.47     0      5.00e+00 4.00e-02 9.58e+00
  dihedral pdb=" CA  VAL B 178 "
           pdb=" C   VAL B 178 "
           pdb=" N   HIS B 179 "
           pdb=" CA  HIS B 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.56  -15.44     0      5.00e+00 4.00e-02 9.54e+00
  dihedral pdb=" CA  VAL D 178 "
           pdb=" C   VAL D 178 "
           pdb=" N   HIS D 179 "
           pdb=" CA  HIS D 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.56  -15.44     0      5.00e+00 4.00e-02 9.54e+00
  ... (remaining 6001 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 982
       0.040 -    0.080: 343
       0.080 -    0.119: 189
       0.119 -    0.159: 50
       0.159 -    0.199: 8
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CA  ILE B 206 "
            pdb=" N   ILE B 206 "
            pdb=" C   ILE B 206 "
            pdb=" CB  ILE B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.90e-01
  chirality pdb=" CA  ILE A 206 "
            pdb=" N   ILE A 206 "
            pdb=" C   ILE A 206 "
            pdb=" CB  ILE A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.88e-01
  chirality pdb=" CA  ILE C 206 "
            pdb=" N   ILE C 206 "
            pdb=" C   ILE C 206 "
            pdb=" CB  ILE C 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.74e-01
  ... (remaining 1569 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 244 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" CG  ASP A 244 "    0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 244 "   -0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 244 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 244 "    0.014 2.00e-02 2.50e+03   2.76e-02 7.63e+00
        pdb=" CG  ASP D 244 "   -0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 244 "    0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 244 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 244 "   -0.014 2.00e-02 2.50e+03   2.76e-02 7.62e+00
        pdb=" CG  ASP B 244 "    0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 244 "   -0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 244 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.90: 3808
        2.90 -     3.40: 9252
        3.40 -     3.90: 16520
        3.90 -     4.40: 19184
        4.40 -     4.90: 32520
  Nonbonded interactions: 81284
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 201 "
            pdb=" ND2 ASN C 205 "
     model   vdw
     2.394 3.120
  nonbonded pdb=" O   GLY A 201 "
            pdb=" ND2 ASN A 205 "
     model   vdw
     2.394 3.120
  nonbonded pdb=" O   GLY D 201 "
            pdb=" ND2 ASN D 205 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" O   GLY B 201 "
            pdb=" ND2 ASN B 205 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" OE2 GLU C 172 "
            pdb=" NH2 ARG C 248 "
     model   vdw
     2.435 3.120
  ... (remaining 81279 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.270
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9140
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      :  0.006   0.067  10180  Z= 0.384
  Angle     :  0.872   7.436  13808  Z= 0.569
  Chirality :  0.055   0.199   1572
  Planarity :  0.006   0.068   1796
  Dihedral  : 14.955  88.733   3596
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 13.08 %
    Favored  : 86.54 %
  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: -1.26 (0.23), residues: 1316
  helix: -1.32 (0.22), residues: 352
  sheet:  0.24 (0.38), residues: 220
  loop : -0.88 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  87 
 HIS   0.002   0.001   HIS A 165 
 PHE   0.010   0.001   PHE D 286 
 TYR   0.005   0.001   TYR A 276 
 ARG   0.003   0.001   ARG B 234 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 1.154 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 71
  average time/residue: 1.7099
  time to fit residues: 129.0385
Evaluate side-chains
  50 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 100 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0020
   chunk 34 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   chunk 53 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   overall best weight:    1.9394

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.047845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.038920 restraints weight = 30695.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 2.87
r_work: 0.2552 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9208
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10180  Z= 0.193
  Angle     :  0.510   6.656  13808  Z= 0.280
  Chirality :  0.044   0.134   1572
  Planarity :  0.005   0.048   1796
  Dihedral  :  3.987  15.669   1412
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 12.02 %
    Favored  : 87.40 %
  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:  0.07 (0.24), residues: 1316
  helix:  0.95 (0.27), residues: 352
  sheet:  0.35 (0.37), residues: 220
  loop : -0.44 (0.24), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 313 
 HIS   0.004   0.001   HIS D  53 
 PHE   0.007   0.001   PHE A  11 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.009   0.001   ARG B  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 1.141 
Fit side-chains
REVERT: A  264 GLN cc_start: 0.9163 (tt0) cc_final: 0.8831 (tm-30)
REVERT: B  264 GLN cc_start: 0.9154 (tt0) cc_final: 0.8822 (tm-30)
REVERT: C  264 GLN cc_start: 0.9194 (tt0) cc_final: 0.8847 (tm-30)
REVERT: D  264 GLN cc_start: 0.9147 (tt0) cc_final: 0.8854 (tm-30)
  outliers start: 6
  outliers final: 0
  residues processed: 59
  average time/residue: 1.6488
  time to fit residues: 104.0171
Evaluate side-chains
  53 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 116 optimal weight:   10.0000
   chunk 128 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.044991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.035964 restraints weight = 31755.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.2592 rms_B_bonded: 2.88
r_work: 0.2458 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2340 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9333
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10180  Z= 0.280
  Angle     :  0.543   7.660  13808  Z= 0.298
  Chirality :  0.045   0.148   1572
  Planarity :  0.005   0.057   1796
  Dihedral  :  4.107  17.532   1412
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.50 %
    Favored  : 86.44 %
  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:  0.46 (0.24), residues: 1316
  helix:  1.45 (0.28), residues: 356
  sheet:  0.45 (0.37), residues: 224
  loop : -0.27 (0.25), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 313 
 HIS   0.003   0.001   HIS C  53 
 PHE   0.011   0.001   PHE C 318 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.011   0.001   ARG D  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 1.252 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 64
  average time/residue: 1.5679
  time to fit residues: 107.3684
Evaluate side-chains
  60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  195 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 92 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 127 optimal weight:    3.9990
   chunk 115 optimal weight:    0.2980
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 108 optimal weight:    9.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.044856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.035874 restraints weight = 31422.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.2589 rms_B_bonded: 2.86
r_work: 0.2455 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2337 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9335
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10180  Z= 0.262
  Angle     :  0.532   7.615  13808  Z= 0.290
  Chirality :  0.045   0.149   1572
  Planarity :  0.005   0.056   1796
  Dihedral  :  4.082  17.427   1412
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.63 %
    Favored  : 86.63 %
  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:  0.57 (0.25), residues: 1316
  helix:  1.68 (0.28), residues: 356
  sheet:  0.46 (0.37), residues: 224
  loop : -0.25 (0.25), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 313 
 HIS   0.003   0.000   HIS A  53 
 PHE   0.009   0.001   PHE D 318 
 TYR   0.011   0.001   TYR B 314 
 ARG   0.012   0.001   ARG C  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 1.125 
Fit side-chains
  outliers start: 18
  outliers final: 7
  residues processed: 68
  average time/residue: 1.4840
  time to fit residues: 108.4433
Evaluate side-chains
  62 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  244 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 124 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 115 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 46 optimal weight:    0.1980
   chunk 15 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 125 optimal weight:    0.9980
   overall best weight:    3.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.044520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.035633 restraints weight = 31541.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.2582 rms_B_bonded: 2.84
r_work: 0.2446 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2327 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9343
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10180  Z= 0.281
  Angle     :  0.538   7.809  13808  Z= 0.294
  Chirality :  0.045   0.152   1572
  Planarity :  0.005   0.059   1796
  Dihedral  :  4.108  18.254   1412
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.60 %
    Favored  : 86.25 %
  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:  0.62 (0.25), residues: 1316
  helix:  1.75 (0.28), residues: 356
  sheet:  0.44 (0.37), residues: 224
  loop : -0.22 (0.25), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.008   0.001   PHE D 286 
 TYR   0.011   0.001   TYR B 314 
 ARG   0.014   0.001   ARG C  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 1.110 
Fit side-chains
  outliers start: 12
  outliers final: 6
  residues processed: 67
  average time/residue: 1.6236
  time to fit residues: 115.9965
Evaluate side-chains
  62 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   60 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 6 optimal weight:    0.4980
   chunk 68 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 109 optimal weight:    2.9990
   chunk 128 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.045064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.036052 restraints weight = 31466.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2593 rms_B_bonded: 2.87
r_work: 0.2459 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2340 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9333
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10180  Z= 0.226
  Angle     :  0.522   7.304  13808  Z= 0.284
  Chirality :  0.045   0.138   1572
  Planarity :  0.005   0.065   1796
  Dihedral  :  4.055  18.473   1412
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.46 %
    Favored  : 85.58 %
  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:  0.68 (0.25), residues: 1316
  helix:  1.89 (0.28), residues: 352
  sheet:  0.42 (0.36), residues: 224
  loop : -0.21 (0.26), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 313 
 HIS   0.003   0.000   HIS A  53 
 PHE   0.007   0.001   PHE D 286 
 TYR   0.010   0.001   TYR B 314 
 ARG   0.015   0.001   ARG B  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 1.225 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 66
  average time/residue: 1.5880
  time to fit residues: 111.8965
Evaluate side-chains
  60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   60 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 128 optimal weight:    0.2980
   chunk 88 optimal weight:   10.0000
   chunk 121 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 179 HIS
** C  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.044155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.035116 restraints weight = 32059.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.2563 rms_B_bonded: 2.87
r_work: 0.2425 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2308 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9356
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  10180  Z= 0.314
  Angle     :  0.559   8.313  13808  Z= 0.304
  Chirality :  0.046   0.143   1572
  Planarity :  0.005   0.068   1796
  Dihedral  :  4.193  19.871   1412
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.94 %
    Favored  : 85.10 %
  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:  0.64 (0.25), residues: 1316
  helix:  1.77 (0.28), residues: 356
  sheet:  0.36 (0.36), residues: 224
  loop : -0.18 (0.26), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 313 
 HIS   0.004   0.001   HIS B 179 
 PHE   0.009   0.001   PHE D 286 
 TYR   0.011   0.001   TYR C 314 
 ARG   0.016   0.001   ARG A  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 1.170 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.9187 (pm20) cc_final: 0.8979 (pm20)
REVERT: B  113 GLN cc_start: 0.9191 (pm20) cc_final: 0.8985 (pm20)
REVERT: D  113 GLN cc_start: 0.9183 (pm20) cc_final: 0.8976 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 69
  average time/residue: 1.5714
  time to fit residues: 115.8821
Evaluate side-chains
  66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  244 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 120 optimal weight:    9.9990
   chunk 131 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 105 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A  53 HIS
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  53 HIS
D 179 HIS
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.045623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.036678 restraints weight = 31574.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2610 rms_B_bonded: 2.87
r_work: 0.2475 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2356 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9323
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10180  Z= 0.167
  Angle     :  0.503   6.610  13808  Z= 0.272
  Chirality :  0.044   0.128   1572
  Planarity :  0.005   0.076   1796
  Dihedral  :  4.056  20.111   1412
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 14.52 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.72 (0.25), residues: 1316
  helix:  1.96 (0.28), residues: 352
  sheet:  0.41 (0.37), residues: 220
  loop : -0.18 (0.26), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.000   HIS B 179 
 PHE   0.006   0.001   PHE D 286 
 TYR   0.009   0.001   TYR A 314 
 ARG   0.018   0.001   ARG C  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 1.126 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 66
  average time/residue: 1.7471
  time to fit residues: 122.5999
Evaluate side-chains
  63 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   60 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 112 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 109 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.044162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.035119 restraints weight = 31925.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.2565 rms_B_bonded: 2.86
r_work: 0.2428 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2309 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9356
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  10180  Z= 0.322
  Angle     :  0.571   8.507  13808  Z= 0.310
  Chirality :  0.046   0.146   1572
  Planarity :  0.005   0.079   1796
  Dihedral  :  4.240  21.825   1412
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 14.62 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1316
  helix:  1.82 (0.28), residues: 356
  sheet:  0.38 (0.36), residues: 224
  loop : -0.27 (0.25), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 313 
 HIS   0.006   0.001   HIS D 179 
 PHE   0.009   0.001   PHE A 286 
 TYR   0.011   0.001   TYR A 314 
 ARG   0.019   0.001   ARG B  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 1.087 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 61
  average time/residue: 1.6218
  time to fit residues: 105.6895
Evaluate side-chains
  60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.045243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.036347 restraints weight = 31744.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2602 rms_B_bonded: 2.86
r_work: 0.2465 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2346 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9332
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10180  Z= 0.194
  Angle     :  0.520   7.198  13808  Z= 0.281
  Chirality :  0.044   0.129   1572
  Planarity :  0.005   0.081   1796
  Dihedral  :  4.138  22.279   1412
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 14.62 %
    Favored  : 84.90 %
  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:  0.67 (0.25), residues: 1316
  helix:  1.95 (0.28), residues: 352
  sheet:  0.63 (0.38), residues: 212
  loop : -0.32 (0.25), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 313 
 HIS   0.005   0.000   HIS D 179 
 PHE   0.007   0.001   PHE B 286 
 TYR   0.008   0.001   TYR C 314 
 ARG   0.019   0.001   ARG B  80 

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 1.153 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 61
  average time/residue: 1.6527
  time to fit residues: 107.5406
Evaluate side-chains
  60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 129 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 111 optimal weight:    0.5980
   chunk 130 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 131 optimal weight:    3.9990
   chunk 127 optimal weight:    8.9990
   chunk 86 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0060
   overall best weight:    1.9200

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

Flipped N/Q/H residues before XYZ refinement:
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.045504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.036533 restraints weight = 31318.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.2607 rms_B_bonded: 2.86
r_work: 0.2474 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2355 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9326
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10180  Z= 0.185
  Angle     :  0.512   7.201  13808  Z= 0.276
  Chirality :  0.044   0.127   1572
  Planarity :  0.005   0.081   1796
  Dihedral  :  4.079  21.542   1412
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 14.81 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.68 (0.25), residues: 1316
  helix:  2.04 (0.28), residues: 352
  sheet:  0.40 (0.37), residues: 220
  loop : -0.28 (0.25), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 313 
 HIS   0.005   0.000   HIS D 179 
 PHE   0.007   0.001   PHE B 286 
 TYR   0.008   0.001   TYR C 314 
 ARG   0.019   0.001   ARG B  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7473.66 seconds
wall clock time: 132 minutes 47.09 seconds (7967.09 seconds total)