Starting phenix.real_space_refine
on Wed Mar  4 08:18:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrs_21371/03_2026/6vrs_21371.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrs_21371/03_2026/6vrs_21371.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrs_21371/03_2026/6vrs_21371.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrs_21371/03_2026/6vrs_21371.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrs_21371/03_2026/6vrs_21371.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrs_21371/03_2026/6vrs_21371.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.087 sd=   0.769
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
     Mn      8      7.51       5
     S      32      5.16       5
     C    7652      2.51       5
     N    2200      2.21       5
     O    2316      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12208
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 3046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3046
          Classifications: {'peptide': 387}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367}
    Chain: "B"
      Number of atoms: 3046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3046
          Classifications: {'peptide': 387}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367}
    Chain: "C"
      Number of atoms: 3046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3046
          Classifications: {'peptide': 387}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367}
    Chain: "D"
      Number of atoms: 3046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3046
          Classifications: {'peptide': 387}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.53, per 1000 atoms: 0.21
  Number of scatterers: 12208
  At special positions: 0
  Unit cell: (91.91, 84.63, 101.01, 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)
     Mn      8     24.99
     S      32     16.00
     O    2316      8.00
     N    2200      7.00
     C    7652      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: 0.93
  Conformation dependent library (CDL) restraints added in 618.2 milliseconds
  

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2800

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 8 sheets defined
      58.3% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 9
    Processing helix  chain 'A' and resid 15 through 19
    Processing helix  chain 'A' and resid 35 through 46
    Processing helix  chain 'A' and resid 55 through 59
    Processing helix  chain 'A' and resid 64 through 83
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 108 through 129
    Processing helix  chain 'A' and resid 150 through 173
    Processing helix  chain 'A' and resid 195 through 204
      removed outlier: 3.565A  pdb=" N   GLU A 204 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 217 through 223
    Processing helix  chain 'A' and resid 227 through 238
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 295 through 323
      removed outlier: 3.613A  pdb=" N   MET A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 333
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 3.519A  pdb=" N   ALA A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 353
    Processing helix  chain 'A' and resid 354 through 357
    Processing helix  chain 'A' and resid 361 through 368
      removed outlier: 3.602A  pdb=" N   ARG A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 384
    Processing helix  chain 'B' and resid 6 through 9
    Processing helix  chain 'B' and resid 15 through 19
    Processing helix  chain 'B' and resid 35 through 46
    Processing helix  chain 'B' and resid 55 through 59
    Processing helix  chain 'B' and resid 64 through 83
    Processing helix  chain 'B' and resid 96 through 100
    Processing helix  chain 'B' and resid 108 through 129
    Processing helix  chain 'B' and resid 150 through 173
    Processing helix  chain 'B' and resid 195 through 204
      removed outlier: 3.569A  pdb=" N   GLU B 204 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 210
      No H-bonds generated for 'chain 'B' and resid 208 through 210'
    Processing helix  chain 'B' and resid 217 through 223
    Processing helix  chain 'B' and resid 227 through 238
    Processing helix  chain 'B' and resid 264 through 279
    Processing helix  chain 'B' and resid 295 through 323
      removed outlier: 3.615A  pdb=" N   MET B 307 " --> pdb=" O   ALA B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 333
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.518A  pdb=" N   ALA B 339 " --> pdb=" O   LEU B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 353
    Processing helix  chain 'B' and resid 354 through 357
    Processing helix  chain 'B' and resid 361 through 368
      removed outlier: 3.602A  pdb=" N   ARG B 368 " --> pdb=" O   ALA B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 385
    Processing helix  chain 'C' and resid 6 through 9
    Processing helix  chain 'C' and resid 15 through 19
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'C' and resid 64 through 83
    Processing helix  chain 'C' and resid 96 through 100
    Processing helix  chain 'C' and resid 108 through 129
    Processing helix  chain 'C' and resid 150 through 173
    Processing helix  chain 'C' and resid 195 through 204
      removed outlier: 3.570A  pdb=" N   GLU C 204 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 210
      No H-bonds generated for 'chain 'C' and resid 208 through 210'
    Processing helix  chain 'C' and resid 217 through 223
    Processing helix  chain 'C' and resid 227 through 238
    Processing helix  chain 'C' and resid 264 through 279
    Processing helix  chain 'C' and resid 295 through 323
      removed outlier: 3.615A  pdb=" N   MET C 307 " --> pdb=" O   ALA C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 333
    Processing helix  chain 'C' and resid 334 through 339
      removed outlier: 3.520A  pdb=" N   ALA C 339 " --> pdb=" O   LEU C 335 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 353
    Processing helix  chain 'C' and resid 354 through 357
    Processing helix  chain 'C' and resid 361 through 368
      removed outlier: 3.601A  pdb=" N   ARG C 368 " --> pdb=" O   ALA C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 385
    Processing helix  chain 'D' and resid 6 through 9
    Processing helix  chain 'D' and resid 15 through 19
    Processing helix  chain 'D' and resid 35 through 46
    Processing helix  chain 'D' and resid 55 through 59
    Processing helix  chain 'D' and resid 64 through 83
    Processing helix  chain 'D' and resid 96 through 100
    Processing helix  chain 'D' and resid 108 through 129
    Processing helix  chain 'D' and resid 150 through 173
    Processing helix  chain 'D' and resid 195 through 204
      removed outlier: 3.565A  pdb=" N   GLU D 204 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 210
      No H-bonds generated for 'chain 'D' and resid 208 through 210'
    Processing helix  chain 'D' and resid 217 through 223
    Processing helix  chain 'D' and resid 227 through 238
    Processing helix  chain 'D' and resid 264 through 279
    Processing helix  chain 'D' and resid 295 through 323
      removed outlier: 3.613A  pdb=" N   MET D 307 " --> pdb=" O   ALA D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 333
    Processing helix  chain 'D' and resid 334 through 339
      removed outlier: 3.519A  pdb=" N   ALA D 339 " --> pdb=" O   LEU D 335 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 346 through 353
    Processing helix  chain 'D' and resid 354 through 357
    Processing helix  chain 'D' and resid 361 through 368
      removed outlier: 3.602A  pdb=" N   ARG D 368 " --> pdb=" O   ALA D 364 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 384
    Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 214
      removed outlier: 6.655A  pdb=" N   ALA A  89 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL A  51 " --> pdb=" O   MET A  88 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   THR A  90 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   PHE A  53 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE A  11 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   THR A  52 " --> pdb=" O   PHE A  11 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE A  13 " --> pdb=" O   THR A  52 " (cutoff:3.500A)
      removed outlier: 8.542A  pdb=" N   HIS A  54 " --> pdb=" O   PHE A  13 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   THR A  12 " --> pdb=" O   PHE A 286 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 143
    Processing sheet with id=AA3, first strand: chain 'B' and resid 212 through 214
      removed outlier: 6.655A  pdb=" N   ALA B  89 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL B  51 " --> pdb=" O   MET B  88 " (cutoff:3.500A)
      removed outlier: 8.880A  pdb=" N   THR B  90 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   PHE B  53 " --> pdb=" O   THR B  90 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   PHE B  11 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   THR B  52 " --> pdb=" O   PHE B  11 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   PHE B  13 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 8.543A  pdb=" N   HIS B  54 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR B  12 " --> pdb=" O   PHE B 286 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 143
    Processing sheet with id=AA5, first strand: chain 'C' and resid 212 through 214
      removed outlier: 6.651A  pdb=" N   ALA C  89 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL C  51 " --> pdb=" O   MET C  88 " (cutoff:3.500A)
      removed outlier: 8.890A  pdb=" N   THR C  90 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   PHE C  53 " --> pdb=" O   THR C  90 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   PHE C  11 " --> pdb=" O   GLY C  50 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   THR C  52 " --> pdb=" O   PHE C  11 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   PHE C  13 " --> pdb=" O   THR C  52 " (cutoff:3.500A)
      removed outlier: 8.543A  pdb=" N   HIS C  54 " --> pdb=" O   PHE C  13 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR C  12 " --> pdb=" O   PHE C 286 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 142 through 143
    Processing sheet with id=AA7, first strand: chain 'D' and resid 212 through 214
      removed outlier: 6.655A  pdb=" N   ALA D  89 " --> pdb=" O   VAL D 135 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL D  51 " --> pdb=" O   MET D  88 " (cutoff:3.500A)
      removed outlier: 8.879A  pdb=" N   THR D  90 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   PHE D  53 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   PHE D  11 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   THR D  52 " --> pdb=" O   PHE D  11 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   PHE D  13 " --> pdb=" O   THR D  52 " (cutoff:3.500A)
      removed outlier: 8.542A  pdb=" N   HIS D  54 " --> pdb=" O   PHE D  13 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   THR D  12 " --> pdb=" O   PHE D 286 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 142 through 143

    614 hydrogen bonds defined for protein.
    1782 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 2162
        1.30 -     1.43: 3361
        1.43 -     1.56: 6886
        1.56 -     1.69: 3
        1.69 -     1.82: 60
  Bond restraints: 12472
  Sorted by residual:
  bond pdb=" NE  ARG D 177 "
       pdb=" CZ  ARG D 177 "
    ideal  model  delta    sigma   weight residual
    1.326  1.369 -0.043 1.10e-02 8.26e+03 1.51e+01
  bond pdb=" CG  ASP B 255 "
       pdb=" OD1 ASP B 255 "
    ideal  model  delta    sigma   weight residual
    1.249  1.176  0.073 1.90e-02 2.77e+03 1.50e+01
  bond pdb=" CG  ASP B 255 "
       pdb=" OD2 ASP B 255 "
    ideal  model  delta    sigma   weight residual
    1.249  1.177  0.072 1.90e-02 2.77e+03 1.45e+01
  bond pdb=" NE  ARG B 177 "
       pdb=" CZ  ARG B 177 "
    ideal  model  delta    sigma   weight residual
    1.326  1.363 -0.037 1.10e-02 8.26e+03 1.15e+01
  bond pdb=" CE1 HIS B  49 "
       pdb=" NE2 HIS B  49 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.56e+00
  ... (remaining 12467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.34: 16287
        3.34 -     6.67: 548
        6.67 -    10.01: 34
       10.01 -    13.35: 12
       13.35 -    16.68: 3
  Bond angle restraints: 16884
  Sorted by residual:
  angle pdb=" CB  ARG B  42 "
        pdb=" CG  ARG B  42 "
        pdb=" CD  ARG B  42 "
      ideal   model   delta    sigma   weight residual
     111.30  127.98  -16.68 2.30e+00 1.89e-01 5.26e+01
  angle pdb=" CB  ARG D  42 "
        pdb=" CG  ARG D  42 "
        pdb=" CD  ARG D  42 "
      ideal   model   delta    sigma   weight residual
     111.30  127.79  -16.49 2.30e+00 1.89e-01 5.14e+01
  angle pdb=" CB  ARG D 387 "
        pdb=" CG  ARG D 387 "
        pdb=" CD  ARG D 387 "
      ideal   model   delta    sigma   weight residual
     111.30  126.46  -15.16 2.30e+00 1.89e-01 4.34e+01
  angle pdb=" CA  ASP C 245 "
        pdb=" CB  ASP C 245 "
        pdb=" CG  ASP C 245 "
      ideal   model   delta    sigma   weight residual
     112.60  118.80   -6.20 1.00e+00 1.00e+00 3.84e+01
  angle pdb=" CA  ASP D 245 "
        pdb=" CB  ASP D 245 "
        pdb=" CG  ASP D 245 "
      ideal   model   delta    sigma   weight residual
     112.60  118.80   -6.20 1.00e+00 1.00e+00 3.84e+01
  ... (remaining 16879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 6746
       17.06 -    34.12: 468
       34.12 -    51.17: 94
       51.17 -    68.23: 54
       68.23 -    85.29: 26
  Dihedral angle restraints: 7388
    sinusoidal: 3008
      harmonic: 4380
  Sorted by residual:
  dihedral pdb=" CA  PHE D  53 "
           pdb=" C   PHE D  53 "
           pdb=" N   HIS D  54 "
           pdb=" CA  HIS D  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.70   28.30     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  PHE A  53 "
           pdb=" C   PHE A  53 "
           pdb=" N   HIS A  54 "
           pdb=" CA  HIS A  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.72   28.28     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  PHE C  53 "
           pdb=" C   PHE C  53 "
           pdb=" N   HIS C  54 "
           pdb=" CA  HIS C  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.82   28.18     0      5.00e+00 4.00e-02 3.18e+01
  ... (remaining 7385 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 904
       0.072 -    0.144: 521
       0.144 -    0.215: 216
       0.215 -    0.287: 56
       0.287 -    0.359: 43
  Chirality restraints: 1740
  Sorted by residual:
  chirality pdb=" CA  PRO C  97 "
            pdb=" N   PRO C  97 "
            pdb=" C   PRO C  97 "
            pdb=" CB  PRO C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" CA  PRO D  97 "
            pdb=" N   PRO D  97 "
            pdb=" C   PRO D  97 "
            pdb=" CB  PRO D  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.35 2.00e-01 2.50e+01 3.14e+00
  chirality pdb=" CA  PRO B  97 "
            pdb=" N   PRO B  97 "
            pdb=" C   PRO B  97 "
            pdb=" CB  PRO B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.34 2.00e-01 2.50e+01 2.98e+00
  ... (remaining 1737 not shown)

  Planarity restraints: 2300
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 185 "    0.018 2.00e-02 2.50e+03   3.58e-02 1.28e+01
        pdb=" CG  ASN C 185 "   -0.062 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 185 "    0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 185 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 288 "   -0.029 2.00e-02 2.50e+03   2.39e-02 9.98e+00
        pdb=" CG  PHE B 288 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 288 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 288 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 288 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 288 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 288 "   -0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 288 "    0.030 2.00e-02 2.50e+03   2.38e-02 9.94e+00
        pdb=" CG  PHE C 288 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 288 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 288 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 288 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 288 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 288 "    0.043 2.00e-02 2.50e+03
  ... (remaining 2297 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 61
        2.59 -     3.17: 10145
        3.17 -     3.74: 20178
        3.74 -     4.32: 29889
        4.32 -     4.90: 47192
  Nonbonded interactions: 107465
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 287 "
            pdb="MN    MN C 401 "
     model   vdw
     2.012 2.320
  nonbonded pdb=" OD2 ASP B 287 "
            pdb="MN    MN B 402 "
     model   vdw
     2.014 2.320
  nonbonded pdb=" OD2 ASP A 287 "
            pdb="MN    MN A 402 "
     model   vdw
     2.047 2.320
  nonbonded pdb=" OD2 ASP D 287 "
            pdb="MN    MN D 402 "
     model   vdw
     2.048 2.320
  nonbonded pdb=" OE2 GLU A 181 "
            pdb="MN    MN A 402 "
     model   vdw
     2.056 2.320
  ... (remaining 107460 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.320
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.410
  Find NCS groups from input model:        0.100
  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:8.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9029
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      :  0.008   0.082  12472  Z= 0.548
  Angle     :  1.490  16.684  16884  Z= 0.968
  Chirality :  0.110   0.359   1740
  Planarity :  0.008   0.041   2300
  Dihedral  : 14.484  85.288   4588
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.12 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  2.56 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.36 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.20), residues: 1540
  helix:  0.40 (0.16), residues: 804
  sheet: -2.25 (0.54), residues: 88
  loop : -0.52 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.002   ARG B 177 
 TYR   0.039   0.011   TYR A 134 
 PHE   0.043   0.009   PHE B 288 
 TRP   0.035   0.008   TRP B 300 
 HIS   0.020   0.006   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00833 (12472)
  covalent geometry    : angle       1.48974 (16884)
  hydrogen bonds       : bond        0.17734 (  614)
  hydrogen bonds       : angle       5.69095 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 0
  residues processed: 105
  average time/residue: 0.7596
  time to fit residues: 85.5944
Evaluate side-chains
  42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
A 285 HIS
B 230 HIS
B 285 HIS
C 230 HIS
C 285 HIS
D 230 HIS
D 285 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.073065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.062388 restraints weight = 33818.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 2.60
r_work: 0.2704 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12472  Z= 0.167
  Angle     :  0.543   6.284  16884  Z= 0.285
  Chirality :  0.042   0.179   1740
  Planarity :  0.004   0.040   2300
  Dihedral  :  4.576  31.794   1724
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  1.36 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.53 %
    Favored  : 93.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.95 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.22), residues: 1540
  helix:  2.15 (0.18), residues: 836
  sheet: -2.76 (0.54), residues: 68
  loop : -0.37 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 387 
 TYR   0.011   0.001   TYR B 310 
 PHE   0.009   0.002   PHE C 296 
 TRP   0.008   0.001   TRP D 300 
 HIS   0.008   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (12472)
  covalent geometry    : angle       0.54279 (16884)
  hydrogen bonds       : bond        0.04608 (  614)
  hydrogen bonds       : angle       4.04875 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.9180 (tt0) cc_final: 0.8907 (tt0)
  outliers start: 7
  outliers final: 0
  residues processed: 48
  average time/residue: 0.6732
  time to fit residues: 35.4021
Evaluate side-chains
  43 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 145 optimal weight:    0.6980
   chunk 8 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 110 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 127 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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 = 0.3117 r_free = 0.3117 target = 0.073718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 20)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.062840 restraints weight = 34251.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 2.65
r_work: 0.2647 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8848
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12472  Z= 0.208
  Angle     :  0.520   6.544  16884  Z= 0.268
  Chirality :  0.041   0.205   1740
  Planarity :  0.005   0.045   2300
  Dihedral  :  4.182  29.178   1724
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.68 %
    Favored  : 92.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.22), residues: 1540
  helix:  2.44 (0.17), residues: 836
  sheet: -2.52 (0.53), residues: 68
  loop : -0.20 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  42 
 TYR   0.011   0.001   TYR D 168 
 PHE   0.012   0.001   PHE B  75 
 TRP   0.008   0.001   TRP D 300 
 HIS   0.006   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (12472)
  covalent geometry    : angle       0.51980 (16884)
  hydrogen bonds       : bond        0.04273 (  614)
  hydrogen bonds       : angle       3.84934 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.492 
Fit side-chains
REVERT: D  186 GLU cc_start: 0.8987 (tt0) cc_final: 0.8754 (tt0)
  outliers start: 8
  outliers final: 0
  residues processed: 49
  average time/residue: 0.6987
  time to fit residues: 37.3959
Evaluate side-chains
  39 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 137 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 141 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 148 optimal weight:    9.9990
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3130 r_free = 0.3130 target = 0.070254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.059723 restraints weight = 34518.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.65
r_work: 0.2709 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12472  Z= 0.098
  Angle     :  0.433   5.850  16884  Z= 0.224
  Chirality :  0.037   0.171   1740
  Planarity :  0.004   0.044   2300
  Dihedral  :  3.905  30.357   1724
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  7.43 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.22), residues: 1540
  helix:  2.75 (0.18), residues: 836
  sheet: -2.34 (0.55), residues: 68
  loop : -0.17 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 259 
 TYR   0.008   0.001   TYR D 168 
 PHE   0.008   0.001   PHE B  75 
 TRP   0.004   0.001   TRP B 300 
 HIS   0.004   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (12472)
  covalent geometry    : angle       0.43303 (16884)
  hydrogen bonds       : bond        0.03096 (  614)
  hydrogen bonds       : angle       3.55141 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  207 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7963 (tt0)
REVERT: D  207 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7952 (tt0)
REVERT: D  264 ASP cc_start: 0.8685 (t70) cc_final: 0.8396 (t70)
  outliers start: 5
  outliers final: 0
  residues processed: 47
  average time/residue: 0.7338
  time to fit residues: 37.4805
Evaluate side-chains
  42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain D residue  207 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 128 optimal weight:   10.0000
   chunk 117 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 98 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3076 r_free = 0.3076 target = 0.068145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.057446 restraints weight = 35170.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.65
r_work: 0.2640 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  12472  Z= 0.259
  Angle     :  0.519   6.354  16884  Z= 0.266
  Chirality :  0.042   0.209   1740
  Planarity :  0.005   0.046   2300
  Dihedral  :  4.010  29.414   1724
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  7.67 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.22), residues: 1540
  helix:  2.53 (0.18), residues: 836
  sheet: -2.45 (0.59), residues: 48
  loop : -0.19 (0.26), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  23 
 TYR   0.011   0.002   TYR C 134 
 PHE   0.010   0.001   PHE D 162 
 TRP   0.006   0.001   TRP C 270 
 HIS   0.004   0.002   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 (12472)
  covalent geometry    : angle       0.51898 (16884)
  hydrogen bonds       : bond        0.04316 (  614)
  hydrogen bonds       : angle       3.77188 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.521 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 45
  average time/residue: 0.7383
  time to fit residues: 36.1369
Evaluate side-chains
  41 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  221 GLU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  221 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 150 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 146 optimal weight:    0.8980
   chunk 112 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9980
   chunk 142 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3104 r_free = 0.3104 target = 0.069177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.058597 restraints weight = 34649.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 2.63
r_work: 0.2675 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12472  Z= 0.129
  Angle     :  0.440   5.647  16884  Z= 0.228
  Chirality :  0.038   0.174   1740
  Planarity :  0.004   0.045   2300
  Dihedral  :  3.873  29.607   1724
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  8.33 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.22), residues: 1540
  helix:  2.70 (0.18), residues: 836
  sheet: -2.14 (0.55), residues: 68
  loop : -0.20 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 266 
 TYR   0.008   0.001   TYR D 168 
 PHE   0.007   0.001   PHE B  75 
 TRP   0.005   0.001   TRP B 300 
 HIS   0.004   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12472)
  covalent geometry    : angle       0.43999 (16884)
  hydrogen bonds       : bond        0.03432 (  614)
  hydrogen bonds       : angle       3.59853 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.519 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 44
  average time/residue: 0.6626
  time to fit residues: 32.1877
Evaluate side-chains
  39 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 133 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0970
   chunk 82 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   overall best weight:    1.8182

-------------------------------------------------------------------------------
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 = 0.3101 r_free = 0.3101 target = 0.069122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.058516 restraints weight = 34709.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.64
r_work: 0.2673 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12472  Z= 0.142
  Angle     :  0.444   5.714  16884  Z= 0.229
  Chirality :  0.038   0.179   1740
  Planarity :  0.004   0.044   2300
  Dihedral  :  3.831  28.568   1724
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  8.00 %
    Favored  : 91.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.22), residues: 1540
  helix:  2.72 (0.18), residues: 836
  sheet: -2.04 (0.57), residues: 68
  loop : -0.20 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 266 
 TYR   0.009   0.001   TYR D 168 
 PHE   0.007   0.001   PHE B  75 
 TRP   0.004   0.001   TRP B 300 
 HIS   0.004   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12472)
  covalent geometry    : angle       0.44411 (16884)
  hydrogen bonds       : bond        0.03452 (  614)
  hydrogen bonds       : angle       3.57027 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  207 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7986 (tt0)
REVERT: D  207 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7993 (tt0)
  outliers start: 5
  outliers final: 1
  residues processed: 43
  average time/residue: 0.7073
  time to fit residues: 33.3779
Evaluate side-chains
  42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  207 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.3072 r_free = 0.3072 target = 0.068782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.057844 restraints weight = 34364.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 2.64
r_work: 0.2636 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8786
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  12472  Z= 0.249
  Angle     :  0.506   5.559  16884  Z= 0.260
  Chirality :  0.041   0.193   1740
  Planarity :  0.005   0.045   2300
  Dihedral  :  3.992  29.384   1724
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.14 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  8.25 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.22), residues: 1540
  helix:  2.54 (0.18), residues: 836
  sheet: -2.07 (0.55), residues: 68
  loop : -0.24 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  23 
 TYR   0.010   0.002   TYR C 134 
 PHE   0.009   0.001   PHE D 178 
 TRP   0.005   0.001   TRP B 300 
 HIS   0.004   0.001   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 (12472)
  covalent geometry    : angle       0.50606 (16884)
  hydrogen bonds       : bond        0.04171 (  614)
  hydrogen bonds       : angle       3.73906 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.512 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 38
  average time/residue: 0.7216
  time to fit residues: 30.1061
Evaluate side-chains
  35 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 112 optimal weight:   10.0000
   chunk 127 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0970
   chunk 47 optimal weight:    0.8980
   chunk 71 optimal weight:    0.2980
   chunk 78 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3134 r_free = 0.3134 target = 0.070238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.059784 restraints weight = 34577.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.62
r_work: 0.2713 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12472  Z= 0.086
  Angle     :  0.412   5.801  16884  Z= 0.213
  Chirality :  0.036   0.166   1740
  Planarity :  0.004   0.043   2300
  Dihedral  :  3.704  28.225   1724
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  8.42 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.23), residues: 1540
  helix:  2.88 (0.18), residues: 836
  sheet: -2.05 (0.57), residues: 68
  loop : -0.17 (0.27), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 188 
 TYR   0.007   0.001   TYR D 168 
 PHE   0.007   0.001   PHE D 269 
 TRP   0.004   0.001   TRP B 300 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 (12472)
  covalent geometry    : angle       0.41208 (16884)
  hydrogen bonds       : bond        0.02802 (  614)
  hydrogen bonds       : angle       3.45865 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.515 
Fit side-chains
REVERT: A  207 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7935 (tt0)
REVERT: D  207 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7948 (tt0)
  outliers start: 3
  outliers final: 0
  residues processed: 43
  average time/residue: 0.6974
  time to fit residues: 32.9442
Evaluate side-chains
  41 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain D residue  207 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 145 optimal weight:    3.9990
   chunk 149 optimal weight:    7.9990
   chunk 102 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 133 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 120 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3086 r_free = 0.3086 target = 0.069240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.058431 restraints weight = 34288.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 2.62
r_work: 0.2659 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12472  Z= 0.197
  Angle     :  0.469   5.621  16884  Z= 0.240
  Chirality :  0.040   0.186   1740
  Planarity :  0.004   0.044   2300
  Dihedral  :  3.836  28.684   1724
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.23), residues: 1540
  helix:  2.72 (0.18), residues: 836
  sheet: -2.06 (0.56), residues: 68
  loop : -0.22 (0.27), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 266 
 TYR   0.009   0.001   TYR B 168 
 PHE   0.008   0.001   PHE A  75 
 TRP   0.005   0.001   TRP A 300 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (12472)
  covalent geometry    : angle       0.46858 (16884)
  hydrogen bonds       : bond        0.03730 (  614)
  hydrogen bonds       : angle       3.60378 ( 1782)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.489 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.6553
  time to fit residues: 27.4763
Evaluate side-chains
  38 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 151 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 99 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 147 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 143 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3123 r_free = 0.3123 target = 0.071148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.060389 restraints weight = 34005.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.63
r_work: 0.2707 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12472  Z= 0.097
  Angle     :  0.414   5.679  16884  Z= 0.214
  Chirality :  0.037   0.166   1740
  Planarity :  0.004   0.043   2300
  Dihedral  :  3.691  28.392   1724
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  8.58 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.23), residues: 1540
  helix:  2.90 (0.18), residues: 836
  sheet: -2.02 (0.58), residues: 68
  loop : -0.19 (0.27), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 259 
 TYR   0.007   0.001   TYR D 168 
 PHE   0.007   0.001   PHE B  75 
 TRP   0.004   0.001   TRP D 300 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (12472)
  covalent geometry    : angle       0.41378 (16884)
  hydrogen bonds       : bond        0.02964 (  614)
  hydrogen bonds       : angle       3.45929 ( 1782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2448.97 seconds
wall clock time: 42 minutes 56.87 seconds (2576.87 seconds total)