Starting phenix.real_space_refine
on Mon Jun 23 06:32:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jmh_36421/06_2025/8jmh_36421_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jmh_36421/06_2025/8jmh_36421.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jmh_36421/06_2025/8jmh_36421.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jmh_36421/06_2025/8jmh_36421.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jmh_36421/06_2025/8jmh_36421_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jmh_36421/06_2025/8jmh_36421_neut_trim.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      96      5.16       5
     C    8872      2.51       5
     N    2212      2.21       5
     O    2264      1.98       5
     H   13812      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 27256
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "B"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "C"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "D"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "E"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'FRU': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'FRU': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'FRU': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'FRU': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 12.03, per 1000 atoms: 0.44
  Number of scatterers: 27256
  At special positions: 0
  Unit cell: (116.25, 116.25, 101.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      96     16.00
     O    2264      8.00
     N    2212      7.00
     C    8872      6.00
     H   13812      1.00
    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
  Links applied
    ALPHA1-2
      " GLC E   1 " - " FRU E   2 "
       ~> Even though FRU is a beta isomer, an alpha linkage is required...
      " GLC F   1 " - " FRU F   2 "
      " GLC G   1 " - " FRU G   2 "
      " GLC H   1 " - " FRU H   2 "
  Time building additional restraints: 6.70
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3136

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 0 sheets defined
      79.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 73
      Proline residue:  A  65  - end of helix
      removed outlier: 3.858A  pdb=" N   VAL A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 95 through 123
    Processing helix  chain 'A' and resid 128 through 164
      removed outlier: 3.927A  pdb=" N   LEU A 132 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 177 through 214
    Processing helix  chain 'A' and resid 223 through 232
    Processing helix  chain 'A' and resid 232 through 237
    Processing helix  chain 'A' and resid 242 through 287
      removed outlier: 4.551A  pdb=" N   ASP A 264 " --> pdb=" O   TRP A 260 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 319
      removed outlier: 3.592A  pdb=" N   PHE A 298 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 339
    Processing helix  chain 'A' and resid 347 through 382
      removed outlier: 4.137A  pdb=" N   ILE A 375 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ASN A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 395 through 408
    Processing helix  chain 'A' and resid 421 through 443
      removed outlier: 4.085A  pdb=" N   GLN A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE A 442 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 450
      removed outlier: 3.843A  pdb=" N   GLY A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 73
      Proline residue:  B  65  - end of helix
      removed outlier: 3.856A  pdb=" N   VAL B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 89
    Processing helix  chain 'B' and resid 95 through 123
    Processing helix  chain 'B' and resid 128 through 164
      removed outlier: 3.927A  pdb=" N   LEU B 132 " --> pdb=" O   ASN B 128 " (cutoff:3.500A)
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 177 through 214
    Processing helix  chain 'B' and resid 223 through 232
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 242 through 287
      removed outlier: 4.557A  pdb=" N   ASP B 264 " --> pdb=" O   TRP B 260 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ARG B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 319
      removed outlier: 3.591A  pdb=" N   PHE B 298 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 339
    Processing helix  chain 'B' and resid 347 through 382
      removed outlier: 4.135A  pdb=" N   ILE B 375 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ASN B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLY B 382 " --> pdb=" O   GLU B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 387
    Processing helix  chain 'B' and resid 395 through 408
    Processing helix  chain 'B' and resid 421 through 443
      removed outlier: 4.081A  pdb=" N   GLN B 441 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   PHE B 442 " --> pdb=" O   VAL B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 3.842A  pdb=" N   GLY B 450 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 73
      Proline residue:  C  65  - end of helix
      removed outlier: 3.852A  pdb=" N   VAL C  73 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 89
    Processing helix  chain 'C' and resid 95 through 123
    Processing helix  chain 'C' and resid 128 through 164
      removed outlier: 4.022A  pdb=" N   LEU C 132 " --> pdb=" O   ASN C 128 " (cutoff:3.500A)
      Proline residue:  C 153  - end of helix
    Processing helix  chain 'C' and resid 165 through 168
    Processing helix  chain 'C' and resid 177 through 214
    Processing helix  chain 'C' and resid 223 through 232
    Processing helix  chain 'C' and resid 232 through 237
    Processing helix  chain 'C' and resid 242 through 287
      removed outlier: 4.554A  pdb=" N   ASP C 264 " --> pdb=" O   TRP C 260 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG C 277 " --> pdb=" O   GLY C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 319
      removed outlier: 3.590A  pdb=" N   PHE C 298 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 339
    Processing helix  chain 'C' and resid 347 through 382
      removed outlier: 4.132A  pdb=" N   ILE C 375 " --> pdb=" O   THR C 371 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ASN C 376 " --> pdb=" O   ALA C 372 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY C 382 " --> pdb=" O   GLU C 378 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 387
    Processing helix  chain 'C' and resid 395 through 408
    Processing helix  chain 'C' and resid 421 through 443
      removed outlier: 4.064A  pdb=" N   GLN C 441 " --> pdb=" O   LEU C 437 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   PHE C 442 " --> pdb=" O   VAL C 438 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 450
      removed outlier: 3.843A  pdb=" N   GLY C 450 " --> pdb=" O   ASN C 446 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 73
      Proline residue:  D  65  - end of helix
      removed outlier: 3.729A  pdb=" N   VAL D  73 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 89
    Processing helix  chain 'D' and resid 95 through 123
    Processing helix  chain 'D' and resid 128 through 164
      removed outlier: 4.137A  pdb=" N   LEU D 132 " --> pdb=" O   ASN D 128 " (cutoff:3.500A)
      Proline residue:  D 153  - end of helix
    Processing helix  chain 'D' and resid 165 through 168
    Processing helix  chain 'D' and resid 177 through 214
    Processing helix  chain 'D' and resid 223 through 232
    Processing helix  chain 'D' and resid 232 through 237
    Processing helix  chain 'D' and resid 242 through 287
      removed outlier: 4.342A  pdb=" N   ASP D 264 " --> pdb=" O   TRP D 260 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG D 277 " --> pdb=" O   GLY D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 339
      removed outlier: 3.536A  pdb=" N   PHE D 298 " --> pdb=" O   CYS D 294 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   SER D 321 " --> pdb=" O   SER D 317 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   LEU D 322 " --> pdb=" O   ALA D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 387
      removed outlier: 4.015A  pdb=" N   ILE D 375 " --> pdb=" O   THR D 371 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ASN D 376 " --> pdb=" O   ALA D 372 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLY D 382 " --> pdb=" O   GLU D 378 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   LEU D 383 " --> pdb=" O   SER D 379 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLY D 384 " --> pdb=" O   LYS D 380 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   VAL D 385 " --> pdb=" O   ARG D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 395 through 408
    Processing helix  chain 'D' and resid 421 through 440
    Processing helix  chain 'D' and resid 443 through 450
      removed outlier: 3.734A  pdb=" N   GLY D 450 " --> pdb=" O   ASN D 446 " (cutoff:3.500A)

    984 hydrogen bonds defined for protein.
    2916 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: 10.27

  Time building geometry restraints manager: 8.13 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 13772
        1.03 -     1.23: 40
        1.23 -     1.42: 5796
        1.42 -     1.61: 7828
        1.61 -     1.81: 156
  Bond restraints: 27592
  Sorted by residual:
  bond pdb=" C4  FRU G   2 "
       pdb=" C5  FRU G   2 "
    ideal  model  delta    sigma   weight residual
    1.528  1.301  0.227 2.00e-02 2.50e+03 1.29e+02
  bond pdb=" C4  FRU E   2 "
       pdb=" C5  FRU E   2 "
    ideal  model  delta    sigma   weight residual
    1.528  1.301  0.227 2.00e-02 2.50e+03 1.29e+02
  bond pdb=" C4  FRU F   2 "
       pdb=" C5  FRU F   2 "
    ideal  model  delta    sigma   weight residual
    1.528  1.301  0.227 2.00e-02 2.50e+03 1.29e+02
  bond pdb=" C4  FRU H   2 "
       pdb=" C5  FRU H   2 "
    ideal  model  delta    sigma   weight residual
    1.528  1.301  0.227 2.00e-02 2.50e+03 1.29e+02
  bond pdb=" C5  FRU F   2 "
       pdb=" O5  FRU F   2 "
    ideal  model  delta    sigma   weight residual
    1.420  1.619 -0.199 2.00e-02 2.50e+03 9.94e+01
  ... (remaining 27587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.41: 49804
        5.41 -    10.81: 20
       10.81 -    16.22: 1
       16.22 -    21.62: 0
       21.62 -    27.03: 3
  Bond angle restraints: 49828
  Sorted by residual:
  angle pdb=" CG2 THR A  54 "
        pdb=" CB  THR A  54 "
        pdb=" HB  THR A  54 "
      ideal   model   delta    sigma   weight residual
     108.00   80.97   27.03 3.00e+00 1.11e-01 8.12e+01
  angle pdb=" OG1 THR A  54 "
        pdb=" CB  THR A  54 "
        pdb=" HB  THR A  54 "
      ideal   model   delta    sigma   weight residual
     109.00   82.70   26.30 3.00e+00 1.11e-01 7.69e+01
  angle pdb=" CA  THR A  54 "
        pdb=" CB  THR A  54 "
        pdb=" HB  THR A  54 "
      ideal   model   delta    sigma   weight residual
     109.00   83.66   25.34 3.00e+00 1.11e-01 7.13e+01
  angle pdb=" OG1 THR A  54 "
        pdb=" CB  THR A  54 "
        pdb=" CG2 THR A  54 "
      ideal   model   delta    sigma   weight residual
     109.30  120.58  -11.28 2.00e+00 2.50e-01 3.18e+01
  angle pdb=" CA  THR A  54 "
        pdb=" CB  THR A  54 "
        pdb=" CG2 THR A  54 "
      ideal   model   delta    sigma   weight residual
     110.50  118.56   -8.06 1.70e+00 3.46e-01 2.25e+01
  ... (remaining 49823 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.72: 11348
       14.72 -    29.44: 1208
       29.44 -    44.16: 354
       44.16 -    58.89: 153
       58.89 -    73.61: 25
  Dihedral angle restraints: 13088
    sinusoidal: 7084
      harmonic: 6004
  Sorted by residual:
  dihedral pdb=" CG  LYS D 449 "
           pdb=" CD  LYS D 449 "
           pdb=" CE  LYS D 449 "
           pdb=" NZ  LYS D 449 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.72  -57.28     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CG  LYS B 449 "
           pdb=" CD  LYS B 449 "
           pdb=" CE  LYS B 449 "
           pdb=" NZ  LYS B 449 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.57  -56.43     3      1.50e+01 4.44e-03 9.40e+00
  dihedral pdb=" CG  LYS A 449 "
           pdb=" CD  LYS A 449 "
           pdb=" CE  LYS A 449 "
           pdb=" NZ  LYS A 449 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.57  -56.43     3      1.50e+01 4.44e-03 9.40e+00
  ... (remaining 13085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.280: 2175
       0.280 -    0.559: 0
       0.559 -    0.839: 0
       0.839 -    1.118: 0
       1.118 -    1.398: 1
  Chirality restraints: 2176
  Sorted by residual:
  chirality pdb=" CB  THR A  54 "
            pdb=" CA  THR A  54 "
            pdb=" OG1 THR A  54 "
            pdb=" CG2 THR A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.15    1.40 2.00e-01 2.50e+01 4.89e+01
  chirality pdb=" C1  GLC E   1 "
            pdb=" C2  GLC E   1 "
            pdb=" O5  GLC E   1 "
            pdb=" O2  FRU E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.34    0.06 2.00e-02 2.50e+03 9.66e+00
  chirality pdb=" C1  GLC F   1 "
            pdb=" C2  GLC F   1 "
            pdb=" O5  GLC F   1 "
            pdb=" O2  FRU F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.34    0.06 2.00e-02 2.50e+03 8.51e+00
  ... (remaining 2173 not shown)

  Planarity restraints: 3836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 211 "   -0.181 9.50e-02 1.11e+02   6.05e-02 4.26e+00
        pdb=" NE  ARG D 211 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 211 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 211 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 211 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG D 211 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG D 211 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG D 211 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG D 211 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 164 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO D 165 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO D 165 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 165 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 164 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO B 165 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 165 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 165 "    0.016 5.00e-02 4.00e+02
  ... (remaining 3833 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1846
        2.21 -     2.81: 58108
        2.81 -     3.41: 79260
        3.41 -     4.00: 102843
        4.00 -     4.60: 159628
  Nonbonded interactions: 401685
  Sorted by model distance:
  nonbonded pdb=" O   ILE D 249 "
            pdb="HD22 ASN D 253 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" OD2 ASP A 264 "
            pdb="HD21 ASN A 330 "
     model   vdw
     1.648 2.450
  nonbonded pdb=" O   PHE B 367 "
            pdb=" HG1 THR B 371 "
     model   vdw
     1.654 2.450
  nonbonded pdb=" O   PHE C 367 "
            pdb=" HG1 THR C 371 "
     model   vdw
     1.655 2.450
  nonbonded pdb=" OD2 ASP C 264 "
            pdb="HD21 ASN C 330 "
     model   vdw
     1.656 2.450
  ... (remaining 401680 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 'B'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:             0.700
  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:             0.410
  Extract box with map and model:          0.920
  Check model and map are aligned:         0.180
  Set scattering table:                    0.220
  Process input model:                     54.560
  Find NCS groups from input model:        0.760
  Set up NCS constraints:                  0.110
  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:13.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   71.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
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      :  0.007   0.227  13784  Z= 0.342
  Angle     :  0.573  11.277  18716  Z= 0.288
  Chirality :  0.047   1.398   2176
  Planarity :  0.003   0.080   2276
  Dihedral  : 15.006  73.607   5168
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  : 11.41 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  3.05 (0.21), residues: 1620
  helix:  2.80 (0.15), residues: 1172
  sheet:  None (None), residues: 0
  loop : -0.13 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 355 
 HIS   0.001   0.000   HIS D 197 
 PHE   0.012   0.001   PHE C  64 
 TYR   0.011   0.001   TYR D 241 
 ARG   0.009   0.000   ARG D 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.06394 (    4)
  link_ALPHA1-2        : angle       2.42325 (   12)
  hydrogen bonds       : bond        0.16203 (  984)
  hydrogen bonds       : angle       5.39975 ( 2916)
  covalent geometry    : bond        0.00681 (13780)
  covalent geometry    : angle       0.56975 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 2.169 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 2.7811
  time to fit residues: 539.1247
Evaluate side-chains
  175 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 121 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 145 optimal weight:    3.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3371 r_free = 0.3371 target = 0.110978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.081485 restraints weight = 46674.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.88
r_work: 0.2769 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2635 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.0674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13784  Z= 0.148
  Angle     :  0.536  11.302  18716  Z= 0.287
  Chirality :  0.047   1.412   2176
  Planarity :  0.004   0.041   2276
  Dihedral  :  5.431  29.211   1996
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 11.21 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.64 (0.20), residues: 1620
  helix:  2.48 (0.14), residues: 1228
  sheet:  None (None), residues: 0
  loop : -0.69 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 355 
 HIS   0.002   0.001   HIS D  60 
 PHE   0.013   0.001   PHE B  64 
 TYR   0.012   0.001   TYR D 241 
 ARG   0.005   0.000   ARG D 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00109 (    4)
  link_ALPHA1-2        : angle       1.62756 (   12)
  hydrogen bonds       : bond        0.05565 (  984)
  hydrogen bonds       : angle       4.29516 ( 2916)
  covalent geometry    : bond        0.00298 (13780)
  covalent geometry    : angle       0.53477 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 184
  time to evaluate  : 1.982 
Fit side-chains
REVERT: A   94 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7109 (tptp)
REVERT: B   94 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7110 (tptp)
REVERT: C   94 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7116 (tptp)
REVERT: D  180 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7699 (tpp-160)
  outliers start: 5
  outliers final: 0
  residues processed: 185
  average time/residue: 3.0168
  time to fit residues: 606.5179
Evaluate side-chains
  179 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 176
  time to evaluate  : 2.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain C residue   94 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.110764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.081185 restraints weight = 47021.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 1.89
r_work: 0.2780 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13784  Z= 0.163
  Angle     :  0.507  11.262  18716  Z= 0.272
  Chirality :  0.047   1.402   2176
  Planarity :  0.003   0.048   2276
  Dihedral  :  4.178  17.817   1996
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 11.68 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.81 (0.20), residues: 1620
  helix:  2.65 (0.14), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.58 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 355 
 HIS   0.002   0.001   HIS C  60 
 PHE   0.013   0.001   PHE A  64 
 TYR   0.011   0.001   TYR B 241 
 ARG   0.005   0.000   ARG D 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00053 (    4)
  link_ALPHA1-2        : angle       1.29032 (   12)
  hydrogen bonds       : bond        0.05106 (  984)
  hydrogen bonds       : angle       4.07785 ( 2916)
  covalent geometry    : bond        0.00352 (13780)
  covalent geometry    : angle       0.50579 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 179
  time to evaluate  : 1.981 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7122 (tptt)
REVERT: B   94 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7132 (tptt)
REVERT: C   94 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7129 (tptt)
REVERT: D  180 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7709 (tpp-160)
  outliers start: 7
  outliers final: 0
  residues processed: 183
  average time/residue: 2.9063
  time to fit residues: 579.8539
Evaluate side-chains
  179 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 176
  time to evaluate  : 1.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain C residue   94 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 153 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 138 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.110182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.080464 restraints weight = 47346.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.89
r_work: 0.2768 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13784  Z= 0.190
  Angle     :  0.518  11.290  18716  Z= 0.278
  Chirality :  0.047   1.405   2176
  Planarity :  0.003   0.050   2276
  Dihedral  :  3.955  14.336   1996
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 12.64 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.75 (0.20), residues: 1620
  helix:  2.63 (0.14), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.66 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 355 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.014   0.001   PHE D  66 
 TYR   0.012   0.002   TYR B 241 
 ARG   0.005   0.000   ARG D 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00021 (    4)
  link_ALPHA1-2        : angle       1.17786 (   12)
  hydrogen bonds       : bond        0.04973 (  984)
  hydrogen bonds       : angle       4.01558 ( 2916)
  covalent geometry    : bond        0.00418 (13780)
  covalent geometry    : angle       0.51737 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 182
  time to evaluate  : 2.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  180 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7704 (tpp80)
  outliers start: 4
  outliers final: 0
  residues processed: 186
  average time/residue: 2.9863
  time to fit residues: 604.7741
Evaluate side-chains
  179 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 129 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.110151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.080498 restraints weight = 47135.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 1.88
r_work: 0.2768 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2635 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13784  Z= 0.187
  Angle     :  0.509  11.280  18716  Z= 0.275
  Chirality :  0.047   1.402   2176
  Planarity :  0.004   0.059   2276
  Dihedral  :  3.838  14.091   1996
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 12.64 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.75 (0.20), residues: 1620
  helix:  2.62 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.69 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 355 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.014   0.001   PHE D  66 
 TYR   0.012   0.002   TYR A 241 
 ARG   0.007   0.000   ARG D 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00054 (    4)
  link_ALPHA1-2        : angle       1.08936 (   12)
  hydrogen bonds       : bond        0.04903 (  984)
  hydrogen bonds       : angle       3.97130 ( 2916)
  covalent geometry    : bond        0.00412 (13780)
  covalent geometry    : angle       0.50866 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 174
  time to evaluate  : 2.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   94 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7103 (tptt)
REVERT: D  180 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7723 (tpp80)
  outliers start: 9
  outliers final: 4
  residues processed: 181
  average time/residue: 3.2543
  time to fit residues: 647.7411
Evaluate side-chains
  181 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 176
  time to evaluate  : 1.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain D residue  215 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 134 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.109930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.080141 restraints weight = 47424.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 1.90
r_work: 0.2759 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13784  Z= 0.202
  Angle     :  0.518  11.293  18716  Z= 0.278
  Chirality :  0.048   1.403   2176
  Planarity :  0.004   0.057   2276
  Dihedral  :  3.858  14.149   1996
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.77 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.73 (0.20), residues: 1620
  helix:  2.61 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.70 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 355 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.014   0.001   PHE D  66 
 TYR   0.012   0.002   TYR D 241 
 ARG   0.007   0.000   ARG D 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00025 (    4)
  link_ALPHA1-2        : angle       1.11823 (   12)
  hydrogen bonds       : bond        0.04924 (  984)
  hydrogen bonds       : angle       3.96556 ( 2916)
  covalent geometry    : bond        0.00448 (13780)
  covalent geometry    : angle       0.51789 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 176
  time to evaluate  : 1.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7106 (tptt)
REVERT: B   94 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7114 (tptt)
REVERT: D  180 ARG cc_start: 0.8019 (tpp-160) cc_final: 0.7726 (tpp80)
  outliers start: 10
  outliers final: 4
  residues processed: 183
  average time/residue: 3.2040
  time to fit residues: 637.7870
Evaluate side-chains
  182 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 176
  time to evaluate  : 2.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   94 LYS
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain D residue  215 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 153 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
D 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.109590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.079742 restraints weight = 47265.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 1.89
r_work: 0.2754 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2623 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13784  Z= 0.219
  Angle     :  0.528  11.289  18716  Z= 0.284
  Chirality :  0.048   1.403   2176
  Planarity :  0.004   0.062   2276
  Dihedral  :  3.889  14.131   1996
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 12.36 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.71 (0.20), residues: 1620
  helix:  2.61 (0.14), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.71 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 355 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.015   0.001   PHE D  66 
 TYR   0.012   0.002   TYR B 241 
 ARG   0.007   0.000   ARG A 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00121 (    4)
  link_ALPHA1-2        : angle       1.14418 (   12)
  hydrogen bonds       : bond        0.04981 (  984)
  hydrogen bonds       : angle       3.97256 ( 2916)
  covalent geometry    : bond        0.00488 (13780)
  covalent geometry    : angle       0.52753 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 2.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7132 (tptt)
REVERT: D  180 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7759 (tpp80)
  outliers start: 14
  outliers final: 6
  residues processed: 182
  average time/residue: 3.3373
  time to fit residues: 659.5394
Evaluate side-chains
  180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 173
  time to evaluate  : 3.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain D residue  215 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 135 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
D 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.110278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.080437 restraints weight = 47106.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.89
r_work: 0.2766 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13784  Z= 0.171
  Angle     :  0.512  11.263  18716  Z= 0.274
  Chirality :  0.047   1.398   2176
  Planarity :  0.004   0.068   2276
  Dihedral  :  3.808  14.166   1996
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 13.04 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.78 (0.20), residues: 1620
  helix:  2.65 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.67 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 355 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.013   0.001   PHE D  66 
 TYR   0.012   0.001   TYR B 241 
 ARG   0.010   0.000   ARG C 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00115 (    4)
  link_ALPHA1-2        : angle       1.05318 (   12)
  hydrogen bonds       : bond        0.04804 (  984)
  hydrogen bonds       : angle       3.94322 ( 2916)
  covalent geometry    : bond        0.00374 (13780)
  covalent geometry    : angle       0.51158 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 2.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   84 SER cc_start: 0.8932 (m) cc_final: 0.8543 (p)
REVERT: D   94 LYS cc_start: 0.7663 (tptp) cc_final: 0.7398 (tptt)
REVERT: D  180 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7756 (tpp80)
  outliers start: 7
  outliers final: 5
  residues processed: 176
  average time/residue: 3.2681
  time to fit residues: 627.8463
Evaluate side-chains
  175 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 170
  time to evaluate  : 2.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  329 ASN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain D residue  215 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 123 optimal weight:    0.2980
   chunk 150 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 131 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.110886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.081142 restraints weight = 47354.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 1.90
r_work: 0.2778 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13784  Z= 0.143
  Angle     :  0.503  11.245  18716  Z= 0.268
  Chirality :  0.046   1.394   2176
  Planarity :  0.004   0.066   2276
  Dihedral  :  3.701  14.183   1996
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 13.11 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.88 (0.20), residues: 1620
  helix:  2.72 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.65 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 355 
 HIS   0.001   0.001   HIS D 197 
 PHE   0.012   0.001   PHE A  64 
 TYR   0.013   0.001   TYR B 241 
 ARG   0.009   0.000   ARG B 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00125 (    4)
  link_ALPHA1-2        : angle       0.99160 (   12)
  hydrogen bonds       : bond        0.04645 (  984)
  hydrogen bonds       : angle       3.90962 ( 2916)
  covalent geometry    : bond        0.00304 (13780)
  covalent geometry    : angle       0.50267 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 173
  time to evaluate  : 3.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7408 (mm-30)
REVERT: D  180 ARG cc_start: 0.8021 (tpp-160) cc_final: 0.7741 (tpp80)
  outliers start: 5
  outliers final: 5
  residues processed: 178
  average time/residue: 4.0947
  time to fit residues: 800.5324
Evaluate side-chains
  177 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 172
  time to evaluate  : 3.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain B residue  329 ASN
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain D residue  215 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 150 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 159 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 147 optimal weight:    0.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3364 r_free = 0.3364 target = 0.110631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.080834 restraints weight = 47308.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.89
r_work: 0.2774 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13784  Z= 0.166
  Angle     :  0.504  11.253  18716  Z= 0.270
  Chirality :  0.047   1.396   2176
  Planarity :  0.004   0.068   2276
  Dihedral  :  3.710  14.176   1996
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 13.04 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  2.87 (0.20), residues: 1620
  helix:  2.71 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.65 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 355 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.013   0.001   PHE D  66 
 TYR   0.012   0.001   TYR C 241 
 ARG   0.009   0.000   ARG A 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00102 (    4)
  link_ALPHA1-2        : angle       1.01156 (   12)
  hydrogen bonds       : bond        0.04710 (  984)
  hydrogen bonds       : angle       3.90594 ( 2916)
  covalent geometry    : bond        0.00362 (13780)
  covalent geometry    : angle       0.50354 (18704)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 1.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  180 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7741 (tpp80)
  outliers start: 8
  outliers final: 8
  residues processed: 180
  average time/residue: 3.1679
  time to fit residues: 617.8773
Evaluate side-chains
  179 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 171
  time to evaluate  : 2.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  329 ASN
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  215 CYS
Chi-restraints excluded: chain D residue  215 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 154 optimal weight:    0.0470
   chunk 21 optimal weight:    2.9990
   chunk 156 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 125 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.111831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.082136 restraints weight = 47336.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.90
r_work: 0.2800 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2668 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13784  Z= 0.119
  Angle     :  0.492  11.223  18716  Z= 0.260
  Chirality :  0.046   1.391   2176
  Planarity :  0.004   0.071   2276
  Dihedral  :  3.606  14.189   1996
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 13.18 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  3.01 (0.20), residues: 1620
  helix:  2.82 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.60 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 355 
 HIS   0.001   0.000   HIS D  60 
 PHE   0.011   0.001   PHE C  64 
 TYR   0.012   0.001   TYR B 241 
 ARG   0.009   0.000   ARG C 211 

Details of bonding type rmsd
  link_ALPHA1-2        : bond        0.00136 (    4)
  link_ALPHA1-2        : angle       0.89246 (   12)
  hydrogen bonds       : bond        0.04461 (  984)
  hydrogen bonds       : angle       3.85727 ( 2916)
  covalent geometry    : bond        0.00243 (13780)
  covalent geometry    : angle       0.49121 (18704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 18904.44 seconds
wall clock time: 327 minutes 30.57 seconds (19650.57 seconds total)