Starting phenix.real_space_refine
on Mon Jun  9 07:03:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ayg_7020/06_2025/6ayg_7020.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ayg_7020/06_2025/6ayg_7020.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ayg_7020/06_2025/6ayg_7020.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ayg_7020/06_2025/6ayg_7020.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ayg_7020/06_2025/6ayg_7020.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ayg_7020/06_2025/6ayg_7020.cif"
  }
  resolution = 4.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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      36      5.16       5
     C    6648      2.51       5
     N    1896      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10456
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 2614
          Classifications: {'peptide': 439}
          Incomplete info: {'truncation_to_alanine': 308}
          Link IDs: {'PTRANS': 8, 'TRANS': 430}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 1021
          Unresolved non-hydrogen angles: 1300
          Unresolved non-hydrogen dihedrals: 808
          Unresolved non-hydrogen chiralities: 134
          Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 462
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.28, per 1000 atoms: 0.50
  Number of scatterers: 10456
  At special positions: 0
  Unit cell: (100.35, 100.35, 105.702, 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      36     16.00
     O    1876      8.00
     N    1896      7.00
     C    6648      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: 3.15
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3376

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 8 sheets defined
      66.1% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 47
    Processing helix  chain 'A' and resid 49 through 54
    Processing helix  chain 'A' and resid 60 through 103
      removed outlier: 3.613A  pdb=" N   ALA A  64 " --> pdb=" O   PRO A  60 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A  99 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 140
      removed outlier: 5.014A  pdb=" N   TYR A 137 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ASN A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 233
      removed outlier: 3.508A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   HIS A 232 " --> pdb=" O   GLN A 228 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLN A 233 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 302
    Processing helix  chain 'A' and resid 306 through 318
    Processing helix  chain 'A' and resid 341 through 352
    Processing helix  chain 'A' and resid 352 through 366
    Processing helix  chain 'A' and resid 370 through 397
      removed outlier: 3.905A  pdb=" N   SER A 380 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 433
      Proline residue:  A 410  - end of helix
      removed outlier: 3.815A  pdb=" N   MET A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE A 422 " --> pdb=" O   CYS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 439
      removed outlier: 4.629A  pdb=" N   TYR A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASP A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 456
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 3.536A  pdb=" N   ALA A 465 " --> pdb=" O   PHE A 461 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS A 466 " --> pdb=" O   ALA A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 491
      removed outlier: 3.524A  pdb=" N   ILE A 490 " --> pdb=" O   ILE A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 513
      removed outlier: 3.577A  pdb=" N   PHE A 497 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 526
    Processing helix  chain 'B' and resid 41 through 47
    Processing helix  chain 'B' and resid 49 through 54
    Processing helix  chain 'B' and resid 60 through 103
      removed outlier: 3.613A  pdb=" N   ALA B  64 " --> pdb=" O   PRO B  60 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS B  99 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 140
      removed outlier: 5.014A  pdb=" N   TYR B 137 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ASN B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 233
      removed outlier: 3.508A  pdb=" N   VAL B 230 " --> pdb=" O   ASN B 226 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   HIS B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN B 233 " --> pdb=" O   THR B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 302
    Processing helix  chain 'B' and resid 306 through 318
    Processing helix  chain 'B' and resid 341 through 352
    Processing helix  chain 'B' and resid 352 through 366
    Processing helix  chain 'B' and resid 370 through 397
      removed outlier: 3.905A  pdb=" N   SER B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 433
      Proline residue:  B 410  - end of helix
      removed outlier: 3.814A  pdb=" N   MET B 421 " --> pdb=" O   CYS B 417 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE B 422 " --> pdb=" O   CYS B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 439
      removed outlier: 4.629A  pdb=" N   TYR B 437 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASP B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 456
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 3.537A  pdb=" N   ALA B 465 " --> pdb=" O   PHE B 461 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS B 466 " --> pdb=" O   ALA B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 491
      removed outlier: 3.524A  pdb=" N   ILE B 490 " --> pdb=" O   ILE B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 492 through 513
      removed outlier: 3.577A  pdb=" N   PHE B 497 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 526
    Processing helix  chain 'C' and resid 41 through 47
    Processing helix  chain 'C' and resid 49 through 54
    Processing helix  chain 'C' and resid 60 through 103
      removed outlier: 3.612A  pdb=" N   ALA C  64 " --> pdb=" O   PRO C  60 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS C  99 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 140
      removed outlier: 5.014A  pdb=" N   TYR C 137 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ASN C 138 " --> pdb=" O   LEU C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 226 through 233
      removed outlier: 3.508A  pdb=" N   VAL C 230 " --> pdb=" O   ASN C 226 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   HIS C 232 " --> pdb=" O   GLN C 228 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN C 233 " --> pdb=" O   THR C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 302
    Processing helix  chain 'C' and resid 306 through 318
    Processing helix  chain 'C' and resid 341 through 352
    Processing helix  chain 'C' and resid 352 through 366
    Processing helix  chain 'C' and resid 370 through 397
      removed outlier: 3.905A  pdb=" N   SER C 380 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR C 381 " --> pdb=" O   LEU C 377 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 433
      Proline residue:  C 410  - end of helix
      removed outlier: 3.815A  pdb=" N   MET C 421 " --> pdb=" O   CYS C 417 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE C 422 " --> pdb=" O   CYS C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 439
      removed outlier: 4.629A  pdb=" N   TYR C 437 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASP C 439 " --> pdb=" O   GLY C 435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 456
    Processing helix  chain 'C' and resid 459 through 466
      removed outlier: 3.537A  pdb=" N   ALA C 465 " --> pdb=" O   PHE C 461 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS C 466 " --> pdb=" O   ALA C 462 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 471 through 491
      removed outlier: 3.524A  pdb=" N   ILE C 490 " --> pdb=" O   ILE C 486 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 492 through 513
      removed outlier: 3.578A  pdb=" N   PHE C 497 " --> pdb=" O   ILE C 493 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 526
    Processing helix  chain 'D' and resid 41 through 47
    Processing helix  chain 'D' and resid 49 through 54
    Processing helix  chain 'D' and resid 60 through 103
      removed outlier: 3.612A  pdb=" N   ALA D  64 " --> pdb=" O   PRO D  60 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS D  99 " --> pdb=" O   THR D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 140
      removed outlier: 5.014A  pdb=" N   TYR D 137 " --> pdb=" O   TYR D 133 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ASN D 138 " --> pdb=" O   LEU D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 226 through 233
      removed outlier: 3.508A  pdb=" N   VAL D 230 " --> pdb=" O   ASN D 226 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   HIS D 232 " --> pdb=" O   GLN D 228 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN D 233 " --> pdb=" O   THR D 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 283 through 302
    Processing helix  chain 'D' and resid 306 through 318
    Processing helix  chain 'D' and resid 341 through 352
    Processing helix  chain 'D' and resid 352 through 366
    Processing helix  chain 'D' and resid 370 through 397
      removed outlier: 3.904A  pdb=" N   SER D 380 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR D 381 " --> pdb=" O   LEU D 377 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 433
      Proline residue:  D 410  - end of helix
      removed outlier: 3.815A  pdb=" N   MET D 421 " --> pdb=" O   CYS D 417 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE D 422 " --> pdb=" O   CYS D 418 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 433 through 439
      removed outlier: 4.630A  pdb=" N   TYR D 437 " --> pdb=" O   VAL D 433 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ASP D 439 " --> pdb=" O   GLY D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 443 through 456
    Processing helix  chain 'D' and resid 459 through 466
      removed outlier: 3.537A  pdb=" N   ALA D 465 " --> pdb=" O   PHE D 461 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS D 466 " --> pdb=" O   ALA D 462 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 471 through 491
      removed outlier: 3.524A  pdb=" N   ILE D 490 " --> pdb=" O   ILE D 486 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 492 through 513
      removed outlier: 3.577A  pdb=" N   PHE D 497 " --> pdb=" O   ILE D 493 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 520 through 526
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 188
      removed outlier: 4.244A  pdb=" N   THR A 215 " --> pdb=" O   HIS A 161 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168
    Processing sheet with id=AA3, first strand: chain 'B' and resid 181 through 188
      removed outlier: 4.244A  pdb=" N   THR B 215 " --> pdb=" O   HIS B 161 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 168
    Processing sheet with id=AA5, first strand: chain 'C' and resid 181 through 188
      removed outlier: 4.244A  pdb=" N   THR C 215 " --> pdb=" O   HIS C 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 167 through 168
    Processing sheet with id=AA7, first strand: chain 'D' and resid 181 through 188
      removed outlier: 4.244A  pdb=" N   THR D 215 " --> pdb=" O   HIS D 161 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 167 through 168

    949 hydrogen bonds defined for protein.
    2799 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.47

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 3636
        1.36 -     1.49: 3104
        1.49 -     1.63: 3888
        1.63 -     1.76: 0
        1.76 -     1.89: 48
  Bond restraints: 10676
  Sorted by residual:
  bond pdb=" CB  PHE D 102 "
       pdb=" CG  PHE D 102 "
    ideal  model  delta    sigma   weight residual
    1.502  1.428  0.074 2.30e-02 1.89e+03 1.02e+01
  bond pdb=" CB  PHE B 102 "
       pdb=" CG  PHE B 102 "
    ideal  model  delta    sigma   weight residual
    1.502  1.429  0.073 2.30e-02 1.89e+03 1.02e+01
  bond pdb=" CB  PHE C 102 "
       pdb=" CG  PHE C 102 "
    ideal  model  delta    sigma   weight residual
    1.502  1.429  0.073 2.30e-02 1.89e+03 1.02e+01
  bond pdb=" CB  PHE A 102 "
       pdb=" CG  PHE A 102 "
    ideal  model  delta    sigma   weight residual
    1.502  1.429  0.073 2.30e-02 1.89e+03 1.01e+01
  bond pdb=" CB  PHE B 288 "
       pdb=" CG  PHE B 288 "
    ideal  model  delta    sigma   weight residual
    1.502  1.575 -0.073 2.30e-02 1.89e+03 1.01e+01
  ... (remaining 10671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.14: 14026
        3.14 -     6.28: 595
        6.28 -     9.41: 94
        9.41 -    12.55: 29
       12.55 -    15.69: 8
  Bond angle restraints: 14752
  Sorted by residual:
  angle pdb=" N   ILE B 493 "
        pdb=" CA  ILE B 493 "
        pdb=" C   ILE B 493 "
      ideal   model   delta    sigma   weight residual
     110.42  122.48  -12.06 9.60e-01 1.09e+00 1.58e+02
  angle pdb=" N   ILE A 493 "
        pdb=" CA  ILE A 493 "
        pdb=" C   ILE A 493 "
      ideal   model   delta    sigma   weight residual
     110.42  122.47  -12.05 9.60e-01 1.09e+00 1.58e+02
  angle pdb=" N   ILE C 493 "
        pdb=" CA  ILE C 493 "
        pdb=" C   ILE C 493 "
      ideal   model   delta    sigma   weight residual
     110.42  122.47  -12.05 9.60e-01 1.09e+00 1.58e+02
  angle pdb=" N   ILE D 493 "
        pdb=" CA  ILE D 493 "
        pdb=" C   ILE D 493 "
      ideal   model   delta    sigma   weight residual
     110.42  122.44  -12.02 9.60e-01 1.09e+00 1.57e+02
  angle pdb=" N   PHE A 210 "
        pdb=" CA  PHE A 210 "
        pdb=" C   PHE A 210 "
      ideal   model   delta    sigma   weight residual
     111.07  121.28  -10.21 1.07e+00 8.73e-01 9.11e+01
  ... (remaining 14747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.26: 5477
       13.26 -    26.52: 364
       26.52 -    39.78: 107
       39.78 -    53.04: 16
       53.04 -    66.30: 8
  Dihedral angle restraints: 5972
    sinusoidal: 804
      harmonic: 5168
  Sorted by residual:
  dihedral pdb=" CA  LYS C 466 "
           pdb=" C   LYS C 466 "
           pdb=" N   MET C 467 "
           pdb=" CA  MET C 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.71  -23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  LYS A 466 "
           pdb=" C   LYS A 466 "
           pdb=" N   MET A 467 "
           pdb=" CA  MET A 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.72  -23.28     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  LYS D 466 "
           pdb=" C   LYS D 466 "
           pdb=" N   MET D 467 "
           pdb=" CA  MET D 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.72  -23.28     0      5.00e+00 4.00e-02 2.17e+01
  ... (remaining 5969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1352
       0.076 -    0.152: 318
       0.152 -    0.228: 50
       0.228 -    0.304: 8
       0.304 -    0.380: 16
  Chirality restraints: 1744
  Sorted by residual:
  chirality pdb=" CG  LEU C 482 "
            pdb=" CB  LEU C 482 "
            pdb=" CD1 LEU C 482 "
            pdb=" CD2 LEU C 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.97    0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" CG  LEU B 482 "
            pdb=" CB  LEU B 482 "
            pdb=" CD1 LEU B 482 "
            pdb=" CD2 LEU B 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.97    0.38 2.00e-01 2.50e+01 3.56e+00
  chirality pdb=" CG  LEU D 482 "
            pdb=" CB  LEU D 482 "
            pdb=" CD1 LEU D 482 "
            pdb=" CD2 LEU D 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.97    0.38 2.00e-01 2.50e+01 3.56e+00
  ... (remaining 1741 not shown)

  Planarity restraints: 2004
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  48 "   -0.104 5.00e-02 4.00e+02   1.73e-01 4.81e+01
        pdb=" N   PRO B  49 "    0.300 5.00e-02 4.00e+02
        pdb=" CA  PRO B  49 "   -0.103 5.00e-02 4.00e+02
        pdb=" CD  PRO B  49 "   -0.093 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  48 "    0.104 5.00e-02 4.00e+02   1.73e-01 4.80e+01
        pdb=" N   PRO A  49 "   -0.300 5.00e-02 4.00e+02
        pdb=" CA  PRO A  49 "    0.103 5.00e-02 4.00e+02
        pdb=" CD  PRO A  49 "    0.093 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  48 "    0.104 5.00e-02 4.00e+02   1.73e-01 4.80e+01
        pdb=" N   PRO D  49 "   -0.300 5.00e-02 4.00e+02
        pdb=" CA  PRO D  49 "    0.103 5.00e-02 4.00e+02
        pdb=" CD  PRO D  49 "    0.093 5.00e-02 4.00e+02
  ... (remaining 2001 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 907
        2.72 -     3.27: 11353
        3.27 -     3.81: 15814
        3.81 -     4.36: 18109
        4.36 -     4.90: 28141
  Nonbonded interactions: 74324
  Sorted by model distance:
  nonbonded pdb=" O   PHE D 489 "
            pdb=" N   ILE D 493 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" O   PHE C 489 "
            pdb=" N   ILE C 493 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   PHE B 489 "
            pdb=" N   ILE B 493 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   PHE A 489 "
            pdb=" N   ILE A 493 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   LEU A 488 "
            pdb=" CB  MET A 492 "
     model   vdw
     2.252 3.440
  ... (remaining 74319 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}
Set refine NCS operators
  NCS operators will be refined.
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 group one per residue
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:             0.250
  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:          0.400
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     26.670
  Find NCS groups from input model:        0.240
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
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      :  0.013   0.093  10676  Z= 0.695
  Angle     :  1.563  15.688  14752  Z= 1.006
  Chirality :  0.073   0.380   1744
  Planarity :  0.013   0.173   2004
  Dihedral  : 11.749  66.300   2596
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 19.94
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  7.67 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.22 %
    Favored  : 83.70 %
  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: -4.34 (0.16), residues: 1708
  helix: -3.18 (0.12), residues: 996
  sheet: -1.38 (0.27), residues: 264
  loop : -2.32 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.006   TRP C  61 
 HIS   0.016   0.006   HIS C 252 
 PHE   0.045   0.005   PHE C 291 
 TYR   0.043   0.008   TYR D 481 
 ARG   0.016   0.004   ARG D  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14207 (  949)
  hydrogen bonds       : angle      11.91395 ( 2799)
  covalent geometry    : bond        0.01288 (10676)
  covalent geometry    : angle       1.56337 (14752)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1212
  time to fit residues: 7.3955
Evaluate side-chains
  39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    0.0020
   chunk 130 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 44 optimal weight:    4.9990
   chunk 87 optimal weight:    0.4980
   chunk 69 optimal weight:    9.9990
   chunk 134 optimal weight:    0.9980
   chunk 52 optimal weight:   30.0000
   chunk 81 optimal weight:   30.0000
   chunk 100 optimal weight:    0.0060
   chunk 156 optimal weight:    6.9990
   overall best weight:    0.7006
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.070701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.057081 restraints weight = 19159.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.057888 restraints weight = 14683.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.058331 restraints weight = 12138.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10676  Z= 0.154
  Angle     :  0.586   6.548  14752  Z= 0.343
  Chirality :  0.041   0.142   1744
  Planarity :  0.005   0.053   2004
  Dihedral  :  5.555  20.031   1808
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.18), residues: 1708
  helix: -0.98 (0.14), residues: 1052
  sheet: -1.10 (0.27), residues: 264
  loop : -1.67 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP C 475 
 HIS   0.006   0.001   HIS D 252 
 PHE   0.020   0.002   PHE D 489 
 TYR   0.019   0.003   TYR D 481 
 ARG   0.005   0.001   ARG B  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05031 (  949)
  hydrogen bonds       : angle       6.37103 ( 2799)
  covalent geometry    : bond        0.00261 (10676)
  covalent geometry    : angle       0.58553 (14752)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.9391 (tp-100) cc_final: 0.9087 (tp-100)
REVERT: A  385 TRP cc_start: 0.9513 (m100) cc_final: 0.8948 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0899
  time to fit residues: 5.6091
Evaluate side-chains
  39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 152 optimal weight:    9.9990
   chunk 17 optimal weight:   50.0000
   chunk 106 optimal weight:    0.9990
   chunk 127 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 143 optimal weight:   20.0000
   chunk 117 optimal weight:   20.0000
   chunk 76 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0030
   chunk 44 optimal weight:    6.9990
   chunk 142 optimal weight:    0.0170
   overall best weight:    2.0034
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 513 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.070148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.056831 restraints weight = 19469.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.057632 restraints weight = 14969.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.058241 restraints weight = 12281.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10676  Z= 0.129
  Angle     :  0.489   5.601  14752  Z= 0.279
  Chirality :  0.039   0.117   1744
  Planarity :  0.004   0.050   2004
  Dihedral  :  4.835  19.522   1808
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  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 (0.19), residues: 1708
  helix:  0.78 (0.15), residues: 1064
  sheet: -0.64 (0.27), residues: 268
  loop : -1.74 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 385 
 HIS   0.004   0.001   HIS C 252 
 PHE   0.026   0.002   PHE B 489 
 TYR   0.011   0.001   TYR C 123 
 ARG   0.001   0.000   ARG D  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03787 (  949)
  hydrogen bonds       : angle       5.10815 ( 2799)
  covalent geometry    : bond        0.00221 (10676)
  covalent geometry    : angle       0.48918 (14752)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  255 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7290 (tpp-160)
REVERT: A  385 TRP cc_start: 0.9284 (m100) cc_final: 0.8567 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0954
  time to fit residues: 5.6778
Evaluate side-chains
  38 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 121 optimal weight:    9.9990
   chunk 122 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 52 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 161 optimal weight:    6.9990
   chunk 117 optimal weight:    0.5980
   chunk 158 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 134 optimal weight:    5.9990
   overall best weight:    2.6986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 513 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.069274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.055915 restraints weight = 19752.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.056789 restraints weight = 15164.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.057380 restraints weight = 12386.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10676  Z= 0.142
  Angle     :  0.486   7.272  14752  Z= 0.275
  Chirality :  0.039   0.125   1744
  Planarity :  0.003   0.047   2004
  Dihedral  :  4.499  19.391   1808
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.20), residues: 1708
  helix:  1.53 (0.15), residues: 1076
  sheet: -0.48 (0.28), residues: 268
  loop : -1.78 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 431 
 HIS   0.003   0.001   HIS C 252 
 PHE   0.018   0.001   PHE C 489 
 TYR   0.010   0.001   TYR D 481 
 ARG   0.001   0.000   ARG D  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  949)
  hydrogen bonds       : angle       4.74750 ( 2799)
  covalent geometry    : bond        0.00238 (10676)
  covalent geometry    : angle       0.48562 (14752)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.9364 (ttm) cc_final: 0.8966 (ttt)
REVERT: A   76 GLN cc_start: 0.9283 (tp-100) cc_final: 0.9051 (tp-100)
REVERT: A  255 ARG cc_start: 0.7949 (ptt180) cc_final: 0.7029 (tpp-160)
REVERT: A  385 TRP cc_start: 0.9460 (m100) cc_final: 0.8883 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0980
  time to fit residues: 5.8102
Evaluate side-chains
  38 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 113 optimal weight:    9.9990
   chunk 84 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9990
   chunk 17 optimal weight:   50.0000
   chunk 93 optimal weight:   30.0000
   chunk 16 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 62 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    4.1788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 513 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.066306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.053223 restraints weight = 20091.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.054043 restraints weight = 15473.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.054606 restraints weight = 12695.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.5109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10676  Z= 0.166
  Angle     :  0.513   5.874  14752  Z= 0.293
  Chirality :  0.040   0.136   1744
  Planarity :  0.003   0.045   2004
  Dihedral  :  4.424  16.905   1808
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  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:  1.03 (0.20), residues: 1708
  helix:  1.78 (0.16), residues: 1080
  sheet: -0.50 (0.28), residues: 272
  loop : -1.71 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 385 
 HIS   0.004   0.001   HIS A 100 
 PHE   0.018   0.002   PHE C 485 
 TYR   0.010   0.001   TYR B 398 
 ARG   0.001   0.000   ARG C 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03479 (  949)
  hydrogen bonds       : angle       4.70878 ( 2799)
  covalent geometry    : bond        0.00279 (10676)
  covalent geometry    : angle       0.51281 (14752)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  385 TRP cc_start: 0.9242 (m100) cc_final: 0.8638 (m-10)
REVERT: A  431 TRP cc_start: 0.9211 (t60) cc_final: 0.8987 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0801
  time to fit residues: 4.3629
Evaluate side-chains
  32 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 135 optimal weight:    8.9990
   chunk 99 optimal weight:    8.9990
   chunk 31 optimal weight:   20.0000
   chunk 106 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 153 optimal weight:   40.0000
   chunk 43 optimal weight:   30.0000
   chunk 29 optimal weight:   20.0000
   chunk 171 optimal weight:    8.9990
   chunk 133 optimal weight:   10.0000
   overall best weight:    8.3992
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 513 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.062732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.049997 restraints weight = 21177.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.050768 restraints weight = 15732.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.051346 restraints weight = 12789.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10676  Z= 0.291
  Angle     :  0.625   6.981  14752  Z= 0.380
  Chirality :  0.042   0.204   1744
  Planarity :  0.004   0.045   2004
  Dihedral  :  4.985  19.047   1808
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.20), residues: 1708
  helix:  0.97 (0.15), residues: 1076
  sheet: -0.94 (0.28), residues: 260
  loop : -1.89 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 385 
 HIS   0.004   0.001   HIS C 100 
 PHE   0.025   0.003   PHE B 291 
 TYR   0.021   0.002   TYR D 106 
 ARG   0.003   0.001   ARG C 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04660 (  949)
  hydrogen bonds       : angle       5.63938 ( 2799)
  covalent geometry    : bond        0.00483 (10676)
  covalent geometry    : angle       0.62545 (14752)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   72 MET cc_start: 0.9197 (ttm) cc_final: 0.8959 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0779
  time to fit residues: 4.1961
Evaluate side-chains
  31 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 137 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 167 optimal weight:   40.0000
   chunk 150 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 162 optimal weight:    0.3980
   overall best weight:    1.8384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.065947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.052751 restraints weight = 20607.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.053551 restraints weight = 15655.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.054170 restraints weight = 12775.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.5776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10676  Z= 0.112
  Angle     :  0.471   6.173  14752  Z= 0.267
  Chirality :  0.039   0.130   1744
  Planarity :  0.003   0.045   2004
  Dihedral  :  4.392  17.780   1808
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.20), residues: 1708
  helix:  1.89 (0.16), residues: 1080
  sheet: -0.41 (0.32), residues: 232
  loop : -1.77 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 385 
 HIS   0.002   0.001   HIS C 252 
 PHE   0.023   0.002   PHE D 452 
 TYR   0.020   0.001   TYR C 481 
 ARG   0.001   0.000   ARG A  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  949)
  hydrogen bonds       : angle       4.80678 ( 2799)
  covalent geometry    : bond        0.00195 (10676)
  covalent geometry    : angle       0.47112 (14752)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.308 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0745
  time to fit residues: 4.1023
Evaluate side-chains
  32 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 17 optimal weight:   50.0000
   chunk 0 optimal weight:   20.0000
   chunk 80 optimal weight:    4.9990
   chunk 134 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 21 optimal weight:   20.0000
   chunk 160 optimal weight:    0.0980
   chunk 127 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0770
   chunk 155 optimal weight:    6.9990
   overall best weight:    2.4344
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 513 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.065537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.051682 restraints weight = 18483.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.052659 restraints weight = 13417.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.053398 restraints weight = 10558.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.6002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10676  Z= 0.120
  Angle     :  0.461   5.638  14752  Z= 0.260
  Chirality :  0.039   0.121   1744
  Planarity :  0.003   0.044   2004
  Dihedral  :  4.102  17.264   1808
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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:  1.19 (0.20), residues: 1708
  helix:  1.94 (0.15), residues: 1084
  sheet: -0.26 (0.33), residues: 232
  loop : -1.87 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 385 
 HIS   0.002   0.001   HIS A 252 
 PHE   0.034   0.002   PHE D 291 
 TYR   0.009   0.001   TYR D 106 
 ARG   0.001   0.000   ARG C  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03090 (  949)
  hydrogen bonds       : angle       4.57541 ( 2799)
  covalent geometry    : bond        0.00205 (10676)
  covalent geometry    : angle       0.46112 (14752)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.366 
Fit side-chains
REVERT: D   72 MET cc_start: 0.9530 (ttt) cc_final: 0.9053 (ppp)
REVERT: D   76 GLN cc_start: 0.9330 (tp-100) cc_final: 0.9125 (tp-100)
REVERT: D  431 TRP cc_start: 0.9191 (t60) cc_final: 0.8921 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0918
  time to fit residues: 4.9807
Evaluate side-chains
  33 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 171 optimal weight:    9.9990
   chunk 68 optimal weight:   30.0000
   chunk 86 optimal weight:   30.0000
   chunk 8 optimal weight:    9.9990
   chunk 157 optimal weight:    0.0870
   chunk 113 optimal weight:   10.0000
   chunk 101 optimal weight:   20.0000
   chunk 151 optimal weight:   10.0000
   chunk 11 optimal weight:   30.0000
   chunk 36 optimal weight:    0.1980
   chunk 169 optimal weight:    0.8980
   overall best weight:    4.2362
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.064328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.050849 restraints weight = 18400.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.051798 restraints weight = 13245.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.052461 restraints weight = 10421.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.6098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10676  Z= 0.159
  Angle     :  0.479   5.525  14752  Z= 0.275
  Chirality :  0.040   0.121   1744
  Planarity :  0.003   0.043   2004
  Dihedral  :  4.098  17.466   1808
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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:  1.21 (0.21), residues: 1708
  helix:  2.02 (0.16), residues: 1076
  sheet: -0.62 (0.31), residues: 268
  loop : -1.80 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 385 
 HIS   0.002   0.001   HIS A 100 
 PHE   0.026   0.002   PHE C 291 
 TYR   0.013   0.001   TYR B 106 
 ARG   0.001   0.000   ARG A 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  949)
  hydrogen bonds       : angle       4.57215 ( 2799)
  covalent geometry    : bond        0.00274 (10676)
  covalent geometry    : angle       0.47891 (14752)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.326 
Fit side-chains
REVERT: D   72 MET cc_start: 0.9514 (ttt) cc_final: 0.8992 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0848
  time to fit residues: 4.6595
Evaluate side-chains
  32 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 71 optimal weight:    0.0370
   chunk 113 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 95 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    2.3464
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 513 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.065846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.052041 restraints weight = 18286.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.052993 restraints weight = 13208.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.053686 restraints weight = 10516.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.6323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10676  Z= 0.114
  Angle     :  0.449   5.479  14752  Z= 0.251
  Chirality :  0.039   0.120   1744
  Planarity :  0.003   0.044   2004
  Dihedral  :  3.888  17.278   1808
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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:  1.45 (0.21), residues: 1708
  helix:  2.18 (0.16), residues: 1084
  sheet: -0.46 (0.32), residues: 268
  loop : -1.74 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 431 
 HIS   0.002   0.001   HIS D 252 
 PHE   0.021   0.001   PHE B 291 
 TYR   0.008   0.001   TYR B 106 
 ARG   0.001   0.000   ARG B  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02962 (  949)
  hydrogen bonds       : angle       4.34248 ( 2799)
  covalent geometry    : bond        0.00205 (10676)
  covalent geometry    : angle       0.44898 (14752)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.326 
Fit side-chains
REVERT: D   72 MET cc_start: 0.9527 (ttt) cc_final: 0.9021 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0840
  time to fit residues: 4.5862
Evaluate side-chains
  33 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 81 optimal weight:   30.0000
   chunk 155 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   chunk 95 optimal weight:   20.0000
   chunk 117 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 63 optimal weight:    0.4980
   chunk 50 optimal weight:   20.0000
   chunk 18 optimal weight:    0.8980
   chunk 97 optimal weight:   30.0000
   overall best weight:    2.0584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.066017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.052059 restraints weight = 18084.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.053054 restraints weight = 12726.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.053808 restraints weight = 9875.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.6518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10676  Z= 0.110
  Angle     :  0.458   5.259  14752  Z= 0.253
  Chirality :  0.039   0.119   1744
  Planarity :  0.003   0.044   2004
  Dihedral  :  3.808  17.289   1808
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.67 (0.21), residues: 1708
  helix:  2.36 (0.16), residues: 1084
  sheet: -0.37 (0.32), residues: 268
  loop : -1.70 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP A 431 
 HIS   0.002   0.001   HIS A 252 
 PHE   0.024   0.002   PHE B  80 
 TYR   0.008   0.001   TYR B 106 
 ARG   0.001   0.000   ARG D  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02903 (  949)
  hydrogen bonds       : angle       4.20811 ( 2799)
  covalent geometry    : bond        0.00201 (10676)
  covalent geometry    : angle       0.45802 (14752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2024.39 seconds
wall clock time: 36 minutes 42.63 seconds (2202.63 seconds total)