Starting phenix.real_space_refine
on Fri Nov 15 23:38:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/11_2024/8g12_29659_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/11_2024/8g12_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/11_2024/8g12_29659.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/11_2024/8g12_29659.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/11_2024/8g12_29659_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/11_2024/8g12_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-5513/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: 4.44, per 1000 atoms: 0.44
  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: 2.68
  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: 1.20
  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: 2.96

  Time building geometry restraints manager: 2.96 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     23.210
  Find NCS groups from input model:        0.310
  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:             0.010
  Load rotamer database and sin/cos tables:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.370
-------------------------------------------------------------------------------
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  : 1.282 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 71
  average time/residue: 1.7329
  time to fit residues: 131.1188
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  : 1.286 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9242
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  : 1.105 
Fit side-chains
REVERT: A  264 GLN cc_start: 0.8989 (tt0) cc_final: 0.8743 (tm-30)
REVERT: B  264 GLN cc_start: 0.9000 (tt0) cc_final: 0.8748 (tm-30)
REVERT: C  264 GLN cc_start: 0.9042 (tt0) cc_final: 0.8770 (tm-30)
REVERT: D  264 GLN cc_start: 0.8964 (tt0) cc_final: 0.8760 (tm-30)
  outliers start: 6
  outliers final: 0
  residues processed: 59
  average time/residue: 1.6307
  time to fit residues: 102.8495
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  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 120 optimal weight:    9.9990
   chunk 129 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 119 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    3.9588

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9319
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027  10180  Z= 0.340
  Angle     :  0.575   8.393  13808  Z= 0.316
  Chirality :  0.046   0.161   1572
  Planarity :  0.005   0.053   1796
  Dihedral  :  4.235  18.627   1412
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.40 %
    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:  0.42 (0.24), residues: 1316
  helix:  1.43 (0.28), residues: 356
  sheet:  0.41 (0.37), residues: 224
  loop : -0.29 (0.25), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 313 
 HIS   0.004   0.001   HIS C  53 
 PHE   0.013   0.001   PHE C 318 
 TYR   0.013   0.001   TYR C 314 
 ARG   0.011   0.001   ARG C  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
  63 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 1.181 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 1.4911
  time to fit residues: 101.3125
Evaluate side-chains
  61 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
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 C residue  195 LEU
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 118 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 13 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 127 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9310
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  10180  Z= 0.274
  Angle     :  0.535   7.677  13808  Z= 0.292
  Chirality :  0.045   0.150   1572
  Planarity :  0.005   0.055   1796
  Dihedral  :  4.130  17.895   1412
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.06 %
    Favored  : 86.92 %
  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:  0.53 (0.25), residues: 1316
  helix:  1.65 (0.28), residues: 356
  sheet:  0.40 (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 C 313 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.009   0.001   PHE D 286 
 TYR   0.011   0.001   TYR B 314 
 ARG   0.012   0.001   ARG D  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
  74 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 1.128 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9090 (tt0)
REVERT: B   48 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9091 (tt0)
  outliers start: 21
  outliers final: 9
  residues processed: 71
  average time/residue: 1.4823
  time to fit residues: 112.6544
Evaluate side-chains
  65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  244 ASP
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 72 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 95 optimal weight:    0.0070
   chunk 52 optimal weight:    4.9990
   chunk 108 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 114 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    3.2006

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9313
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      :  0.004   0.028  10180  Z= 0.279
  Angle     :  0.539   7.959  13808  Z= 0.294
  Chirality :  0.045   0.152   1572
  Planarity :  0.005   0.061   1796
  Dihedral  :  4.138  18.464   1412
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.50 %
    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:  0.61 (0.25), residues: 1316
  helix:  1.73 (0.28), residues: 356
  sheet:  0.43 (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 D 313 
 HIS   0.004   0.001   HIS B 179 
 PHE   0.008   0.001   PHE D 286 
 TYR   0.011   0.001   TYR C 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
  68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 1.286 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9091 (tt0)
  outliers start: 13
  outliers final: 4
  residues processed: 68
  average time/residue: 1.6008
  time to fit residues: 116.4864
Evaluate side-chains
  60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 127 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 123 optimal weight:    5.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 179 HIS
D 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9333
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031  10180  Z= 0.387
  Angle     :  0.595   8.775  13808  Z= 0.324
  Chirality :  0.047   0.154   1572
  Planarity :  0.005   0.065   1796
  Dihedral  :  4.304  19.825   1412
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.27 %
    Favored  : 85.38 %
  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:  0.53 (0.25), residues: 1316
  helix:  1.67 (0.28), residues: 356
  sheet:  0.36 (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   0.005   0.001   HIS B 179 
 PHE   0.010   0.001   PHE D 286 
 TYR   0.011   0.001   TYR A 314 
 ARG   0.015   0.001   ARG D  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
  70 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 1.122 
Fit side-chains
  outliers start: 14
  outliers final: 9
  residues processed: 70
  average time/residue: 1.5859
  time to fit residues: 118.7579
Evaluate side-chains
  65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
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 C residue  195 LEU
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  316 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 58 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0870
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.9760

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9268
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      :  0.002   0.035  10180  Z= 0.130
  Angle     :  0.484   5.900  13808  Z= 0.261
  Chirality :  0.043   0.127   1572
  Planarity :  0.005   0.068   1796
  Dihedral  :  3.953  21.029   1412
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 14.71 %
    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:  0.74 (0.25), residues: 1316
  helix:  1.99 (0.28), residues: 352
  sheet:  0.49 (0.37), residues: 220
  loop : -0.21 (0.26), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 313 
 HIS   0.004   0.000   HIS B 179 
 PHE   0.005   0.001   PHE D 286 
 TYR   0.006   0.001   TYR B 314 
 ARG   0.017   0.001   ARG C  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
  64 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 1.166 
Fit side-chains
  outliers start: 5
  outliers final: 0
  residues processed: 64
  average time/residue: 1.6601
  time to fit residues: 113.4107
Evaluate side-chains
  57 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 100 optimal weight:    8.9990
   chunk 115 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 111 optimal weight:    3.9990
   overall best weight:    5.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9337
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033  10180  Z= 0.431
  Angle     :  0.605   8.905  13808  Z= 0.329
  Chirality :  0.048   0.156   1572
  Planarity :  0.005   0.073   1796
  Dihedral  :  4.335  21.781   1412
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 14.81 %
    Favored  : 85.00 %
  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:  0.59 (0.25), residues: 1316
  helix:  1.79 (0.28), residues: 356
  sheet:  0.39 (0.37), residues: 224
  loop : -0.27 (0.25), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 313 
 HIS   0.006   0.001   HIS B 179 
 PHE   0.010   0.001   PHE A 286 
 TYR   0.013   0.001   TYR B 314 
 ARG   0.018   0.001   ARG B  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
  57 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 1.077 
Fit side-chains
  outliers start: 2
  outliers final: 5
  residues processed: 57
  average time/residue: 1.6786
  time to fit residues: 102.1120
Evaluate side-chains
  60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain D residue  316 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 121 optimal weight:    8.9990
   chunk 71 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0470
   chunk 93 optimal weight:    0.5980
   chunk 36 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 125 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    3.1284

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9319
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10180  Z= 0.272
  Angle     :  0.551   8.067  13808  Z= 0.299
  Chirality :  0.045   0.142   1572
  Planarity :  0.005   0.079   1796
  Dihedral  :  4.271  22.142   1412
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.38 %
    Favored  : 84.62 %
  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:  1.88 (0.28), residues: 352
  sheet:  0.34 (0.37), residues: 224
  loop : -0.32 (0.25), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.005   0.001   HIS B 179 
 PHE   0.008   0.001   PHE B 286 
 TYR   0.010   0.001   TYR B 314 
 ARG   0.019   0.001   ARG D  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
  56 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.214 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 1.8110
  time to fit residues: 108.3161
Evaluate side-chains
  56 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 87 optimal weight:    9.9990
   chunk 131 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    2.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9303
moved from start:          0.2163

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= 0.204
  Angle     :  0.525   7.328  13808  Z= 0.284
  Chirality :  0.044   0.132   1572
  Planarity :  0.005   0.081   1796
  Dihedral  :  4.150  21.680   1412
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.48 %
    Favored  : 84.52 %
  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:  1.96 (0.28), residues: 352
  sheet:  0.65 (0.37), residues: 216
  loop : -0.32 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.005   0.000   HIS B 179 
 PHE   0.007   0.001   PHE B 286 
 TYR   0.008   0.001   TYR B 314 
 ARG   0.019   0.001   ARG C  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
  55 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.229 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 1.7667
  time to fit residues: 103.5103
Evaluate side-chains
  55 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 96 optimal weight:    0.1980
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 92 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    1.6504

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.045697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.036671 restraints weight = 31534.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.2610 rms_B_bonded: 2.87
r_work: 0.2476 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2357 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9319
moved from start:          0.2152

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= 0.168
  Angle     :  0.502   6.730  13808  Z= 0.271
  Chirality :  0.044   0.127   1572
  Planarity :  0.005   0.081   1796
  Dihedral  :  4.041  21.244   1412
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 15.48 %
    Favored  : 84.33 %
  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:  0.69 (0.25), residues: 1316
  helix:  2.02 (0.28), residues: 352
  sheet:  0.42 (0.37), residues: 220
  loop : -0.27 (0.25), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 313 
 HIS   0.005   0.000   HIS B 179 
 PHE   0.006   0.001   PHE B 286 
 TYR   0.007   0.001   TYR B 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: 3010.11 seconds
wall clock time: 55 minutes 21.10 seconds (3321.10 seconds total)