Starting phenix.real_space_refine
on Sat May 10 02:23:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5g_33619/05_2025/7y5g_33619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5g_33619/05_2025/7y5g_33619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5g_33619/05_2025/7y5g_33619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5g_33619/05_2025/7y5g_33619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5g_33619/05_2025/7y5g_33619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5g_33619/05_2025/7y5g_33619.cif"
  }
  resolution = 3.85
  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=   0.125 sd=   0.202
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
     Zn      6      6.06       5
     S      30      5.16       5
     C    3082      2.51       5
     N     780      2.21       5
     O     838      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4736
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2365
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 8, 'TRANS': 293}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2365
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 8, 'TRANS': 293}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2381  SG  CYS A  46      26.060  40.179  23.002  1.00 39.27           S
  ATOM   4684  SG  CYS A 366      51.919  30.262  24.232  1.00 46.10           S
  ATOM   4709  SG  CYS A 369      48.349  29.216  25.198  1.00 39.78           S
  ATOM   2319  SG  CYS B 366      20.695  44.559  24.254  1.00 46.97           S
  ATOM   2344  SG  CYS B 369      24.266  45.584  25.240  1.00 39.28           S
  ATOM     16  SG  CYS B  46      46.540  34.628  23.002  1.00 38.21           S

  Time building chain proxies: 3.22, per 1000 atoms: 0.68
  Number of scatterers: 4736
  At special positions: 0
  Unit cell: (73.7, 75.9, 104.5, 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)
     Zn      6     29.99
     S      30     16.00
     O     838      8.00
     N     780      7.00
     C    3082      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: 1.05
  Conformation dependent library (CDL) restraints added in 534.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  45 "
        pdb="ZN    ZN A 401 " - pdb=" ND1 HIS A  47 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 366 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 369 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS A 323 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS B  46 "
        pdb="ZN    ZN A 402 " - pdb=" NE2 HIS A 306 "
      pdb="  ZN A 403 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS A 225 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS A 100 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B 323 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A  46 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B 306 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 225 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 100 "
      pdb="  ZN B 403 "
        pdb="ZN    ZN B 403 " - pdb=" NE2 HIS B  45 "
        pdb="ZN    ZN B 403 " - pdb=" ND1 HIS B  47 "
        pdb="ZN    ZN B 403 " - pdb=" SG  CYS A 366 "
        pdb="ZN    ZN B 403 " - pdb=" SG  CYS A 369 "
      Number of angles added : 2


  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1156

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      66.6% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 50 through 86
      removed outlier: 3.741A  pdb=" N   ARG B  57 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU B  82 " --> pdb=" O   PHE B  78 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE B  83 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLY B  86 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 92
      removed outlier: 3.666A  pdb=" N   LEU B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 118
      removed outlier: 3.956A  pdb=" N   ASP B 104 " --> pdb=" O   HIS B 100 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER B 111 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU B 112 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU B 115 " --> pdb=" O   SER B 111 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TRP B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU B 117 " --> pdb=" O   CYS B 113 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 138
    Processing helix  chain 'B' and resid 138 through 162
      removed outlier: 3.966A  pdb=" N   VAL B 142 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TRP B 146 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 191
      removed outlier: 3.679A  pdb=" N   MET B 172 " --> pdb=" O   ASP B 168 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 246
      removed outlier: 3.534A  pdb=" N   PHE B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN B 232 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE B 243 " --> pdb=" O   SER B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 260
      removed outlier: 4.509A  pdb=" N   ILE B 255 " --> pdb=" O   MET B 251 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   CYS B 256 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   THR B 257 " --> pdb=" O   ASP B 253 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   PHE B 258 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 268
      removed outlier: 3.730A  pdb=" N   THR B 268 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 275
      removed outlier: 3.999A  pdb=" N   ASP B 274 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 298
    Processing helix  chain 'B' and resid 331 through 345
      removed outlier: 3.957A  pdb=" N   ILE B 335 " --> pdb=" O   GLU B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 362
      No H-bonds generated for 'chain 'B' and resid 360 through 362'
    Processing helix  chain 'B' and resid 366 through 370
      removed outlier: 3.726A  pdb=" N   CYS B 369 " --> pdb=" O   CYS B 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 49
      No H-bonds generated for 'chain 'A' and resid 47 through 49'
    Processing helix  chain 'A' and resid 50 through 86
      removed outlier: 3.745A  pdb=" N   ARG A  57 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU A  82 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE A  83 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLY A  86 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.673A  pdb=" N   LEU A  92 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 118
      removed outlier: 3.976A  pdb=" N   ASP A 104 " --> pdb=" O   HIS A 100 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LEU A 112 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LEU A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TRP A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU A 117 " --> pdb=" O   CYS A 113 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 138
    Processing helix  chain 'A' and resid 138 through 162
      removed outlier: 3.990A  pdb=" N   VAL A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TRP A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 191
      removed outlier: 3.699A  pdb=" N   MET A 172 " --> pdb=" O   ASP A 168 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 246
      removed outlier: 3.542A  pdb=" N   PHE A 231 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLN A 232 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 4.558A  pdb=" N   ILE A 255 " --> pdb=" O   MET A 251 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   CYS A 256 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   THR A 257 " --> pdb=" O   ASP A 253 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 268
      removed outlier: 3.731A  pdb=" N   THR A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
      removed outlier: 4.018A  pdb=" N   ASP A 274 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 298
    Processing helix  chain 'A' and resid 331 through 345
      removed outlier: 3.999A  pdb=" N   ILE A 335 " --> pdb=" O   GLU A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 362
      No H-bonds generated for 'chain 'A' and resid 360 through 362'
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 3.707A  pdb=" N   CYS A 369 " --> pdb=" O   CYS A 366 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 314
      removed outlier: 3.657A  pdb=" N   TRP B 311 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   GLN B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   SER B 351 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 325 through 326
    Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304
      removed outlier: 6.987A  pdb=" N   ALA A 325 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 314
      removed outlier: 3.656A  pdb=" N   TRP A 311 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLN A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   SER A 351 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    732 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: 1.05

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1468
        1.34 -     1.46: 1037
        1.46 -     1.58: 2281
        1.58 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 4828
  Sorted by residual:
  bond pdb=" N   GLU A 281 "
       pdb=" CA  GLU A 281 "
    ideal  model  delta    sigma   weight residual
    1.461  1.470 -0.009 1.52e-02 4.33e+03 3.59e-01
  bond pdb=" N   GLU B 281 "
       pdb=" CA  GLU B 281 "
    ideal  model  delta    sigma   weight residual
    1.461  1.470 -0.009 1.52e-02 4.33e+03 3.58e-01
  bond pdb=" N   LYS B 246 "
       pdb=" CA  LYS B 246 "
    ideal  model  delta    sigma   weight residual
    1.462  1.456  0.005 9.30e-03 1.16e+04 3.30e-01
  bond pdb=" CA  LEU B 272 "
       pdb=" C   LEU B 272 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.80e-02 3.09e+03 3.20e-01
  bond pdb=" CA  LEU A 272 "
       pdb=" C   LEU A 272 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.80e-02 3.09e+03 3.19e-01
  ... (remaining 4823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 6448
        1.34 -     2.69: 87
        2.69 -     4.03: 17
        4.03 -     5.37: 4
        5.37 -     6.72: 2
  Bond angle restraints: 6558
  Sorted by residual:
  angle pdb=" CA  LEU A 275 "
        pdb=" CB  LEU A 275 "
        pdb=" CG  LEU A 275 "
      ideal   model   delta    sigma   weight residual
     116.30  123.02   -6.72 3.50e+00 8.16e-02 3.68e+00
  angle pdb=" CA  LEU B 275 "
        pdb=" CB  LEU B 275 "
        pdb=" CG  LEU B 275 "
      ideal   model   delta    sigma   weight residual
     116.30  123.01   -6.71 3.50e+00 8.16e-02 3.68e+00
  angle pdb=" CA  LEU B 272 "
        pdb=" C   LEU B 272 "
        pdb=" O   LEU B 272 "
      ideal   model   delta    sigma   weight residual
     119.23  122.14   -2.91 1.54e+00 4.22e-01 3.57e+00
  angle pdb=" C   MET B 280 "
        pdb=" N   GLU B 281 "
        pdb=" CA  GLU B 281 "
      ideal   model   delta    sigma   weight residual
     122.07  124.76   -2.69 1.43e+00 4.89e-01 3.54e+00
  angle pdb=" CA  LEU A 272 "
        pdb=" C   LEU A 272 "
        pdb=" O   LEU A 272 "
      ideal   model   delta    sigma   weight residual
     119.23  122.12   -2.89 1.54e+00 4.22e-01 3.53e+00
  ... (remaining 6553 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.89: 2554
       15.89 -    31.77: 248
       31.77 -    47.66: 52
       47.66 -    63.55: 0
       63.55 -    79.43: 4
  Dihedral angle restraints: 2858
    sinusoidal: 1086
      harmonic: 1772
  Sorted by residual:
  dihedral pdb=" CA  THR A 124 "
           pdb=" C   THR A 124 "
           pdb=" N   ARG A 125 "
           pdb=" CA  ARG A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.26   15.74     0      5.00e+00 4.00e-02 9.91e+00
  dihedral pdb=" CA  THR B 124 "
           pdb=" C   THR B 124 "
           pdb=" N   ARG B 125 "
           pdb=" CA  ARG B 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.28   15.72     0      5.00e+00 4.00e-02 9.88e+00
  dihedral pdb=" CA  ARG B 273 "
           pdb=" CB  ARG B 273 "
           pdb=" CG  ARG B 273 "
           pdb=" CD  ARG B 273 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.12   47.12     3      1.50e+01 4.44e-03 8.44e+00
  ... (remaining 2855 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 408
       0.024 -    0.048: 255
       0.048 -    0.072: 104
       0.072 -    0.096: 29
       0.096 -    0.120: 8
  Chirality restraints: 804
  Sorted by residual:
  chirality pdb=" CA  ILE B 319 "
            pdb=" N   ILE B 319 "
            pdb=" C   ILE B 319 "
            pdb=" CB  ILE B 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.60e-01
  chirality pdb=" CA  ILE A 319 "
            pdb=" N   ILE A 319 "
            pdb=" C   ILE A 319 "
            pdb=" CB  ILE A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.34e-01
  chirality pdb=" CA  ILE B 354 "
            pdb=" N   ILE B 354 "
            pdb=" C   ILE B 354 "
            pdb=" CB  ILE B 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.92e-01
  ... (remaining 801 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 363 "   -0.011 5.00e-02 4.00e+02   1.73e-02 4.77e-01
        pdb=" N   PRO A 364 "    0.030 5.00e-02 4.00e+02
        pdb=" CA  PRO A 364 "   -0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO A 364 "   -0.010 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 281 "   -0.003 2.00e-02 2.50e+03   5.81e-03 3.37e-01
        pdb=" C   GLU A 281 "    0.010 2.00e-02 2.50e+03
        pdb=" O   GLU A 281 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   GLY A 282 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 281 "    0.003 2.00e-02 2.50e+03   5.72e-03 3.27e-01
        pdb=" C   GLU B 281 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   GLU B 281 "    0.004 2.00e-02 2.50e+03
        pdb=" N   GLY B 282 "    0.003 2.00e-02 2.50e+03
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 38
        2.65 -     3.21: 4355
        3.21 -     3.77: 6467
        3.77 -     4.34: 8300
        4.34 -     4.90: 13548
  Nonbonded interactions: 32708
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 357 "
            pdb="ZN    ZN B 401 "
     model   vdw
     2.084 2.230
  nonbonded pdb=" OE2 GLU A 357 "
            pdb="ZN    ZN A 402 "
     model   vdw
     2.087 2.230
  nonbonded pdb=" OG  SER B 239 "
            pdb=" OD1 ASP B 253 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OD1 ASP A 229 "
            pdb="ZN    ZN A 403 "
     model   vdw
     2.356 2.230
  nonbonded pdb=" OE1 GLU A 357 "
            pdb="ZN    ZN A 402 "
     model   vdw
     2.371 2.230
  ... (remaining 32703 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.770
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
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      :  0.002   0.017   4846  Z= 0.089
  Angle     :  0.436   6.719   6560  Z= 0.216
  Chirality :  0.036   0.120    804
  Planarity :  0.002   0.017    794
  Dihedral  : 12.736  79.432   1702
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.34), residues: 592
  helix:  0.34 (0.26), residues: 382
  sheet: -1.47 (0.50), residues: 50
  loop : -0.07 (0.53), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 311 
 HIS   0.002   0.001   HIS A 309 
 PHE   0.004   0.000   PHE B  63 
 TYR   0.004   0.000   TYR B 289 
 ARG   0.003   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30073 (  248)
  hydrogen bonds       : angle       5.71764 (  732)
  metal coordination   : bond        0.00357 (   18)
  metal coordination   : angle       3.06832 (    2)
  covalent geometry    : bond        0.00201 ( 4828)
  covalent geometry    : angle       0.43308 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: B  280 MET cc_start: 0.8325 (ptp) cc_final: 0.8124 (ptp)
REVERT: A  280 MET cc_start: 0.8306 (ptp) cc_final: 0.8102 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1792
  time to fit residues: 18.8226
Evaluate side-chains
  48 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0000
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.225858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.197276 restraints weight = 59137.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.199810 restraints weight = 32722.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.198791 restraints weight = 27464.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4846  Z= 0.136
  Angle     :  0.501   5.141   6560  Z= 0.272
  Chirality :  0.036   0.129    804
  Planarity :  0.003   0.026    794
  Dihedral  :  3.562  16.136    638
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.19 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.35), residues: 592
  helix:  1.04 (0.28), residues: 382
  sheet: -1.45 (0.47), residues: 50
  loop : -0.40 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 311 
 HIS   0.002   0.000   HIS A  45 
 PHE   0.018   0.002   PHE A  76 
 TYR   0.018   0.001   TYR A 154 
 ARG   0.004   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07164 (  248)
  hydrogen bonds       : angle       3.65527 (  732)
  metal coordination   : bond        0.00301 (   18)
  metal coordination   : angle       3.23485 (    2)
  covalent geometry    : bond        0.00264 ( 4828)
  covalent geometry    : angle       0.49807 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1563
  time to fit residues: 11.6863
Evaluate side-chains
  50 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain A residue   69 CYS
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  124 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:    0.0980
   chunk 16 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0370
   chunk 15 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.0262

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

Flipped N/Q/H residues before XYZ refinement:
** B  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 GLN
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.212319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.185878 restraints weight = 59833.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.191542 restraints weight = 28084.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.188204 restraints weight = 27270.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4846  Z= 0.110
  Angle     :  0.436   5.040   6560  Z= 0.234
  Chirality :  0.036   0.118    804
  Planarity :  0.003   0.031    794
  Dihedral  :  3.477  15.894    638
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 13.77 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.36), residues: 592
  helix:  1.36 (0.28), residues: 382
  sheet: -1.35 (0.51), residues: 50
  loop : -0.33 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 311 
 HIS   0.002   0.000   HIS B 309 
 PHE   0.018   0.001   PHE B  76 
 TYR   0.017   0.001   TYR B 154 
 ARG   0.007   0.001   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05210 (  248)
  hydrogen bonds       : angle       3.29316 (  732)
  metal coordination   : bond        0.00336 (   18)
  metal coordination   : angle       2.07263 (    2)
  covalent geometry    : bond        0.00227 ( 4828)
  covalent geometry    : angle       0.43418 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
REVERT: B  280 MET cc_start: 0.8326 (ptp) cc_final: 0.8114 (ptp)
REVERT: A  280 MET cc_start: 0.8303 (ptp) cc_final: 0.8086 (ptp)
  outliers start: 5
  outliers final: 4
  residues processed: 51
  average time/residue: 0.1677
  time to fit residues: 11.3713
Evaluate side-chains
  46 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain A residue   69 CYS
Chi-restraints excluded: chain A residue  124 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:   40.0000
   chunk 28 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** B  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 GLN
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 GLN
A 362 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.207898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.176249 restraints weight = 60577.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.178037 restraints weight = 33184.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.177840 restraints weight = 30410.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4846  Z= 0.161
  Angle     :  0.509   5.861   6560  Z= 0.269
  Chirality :  0.039   0.118    804
  Planarity :  0.003   0.024    794
  Dihedral  :  3.994  17.249    638
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.66 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.36), residues: 592
  helix:  1.32 (0.28), residues: 382
  sheet: -1.74 (0.51), residues: 50
  loop : -0.19 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 130 
 HIS   0.004   0.001   HIS B 309 
 PHE   0.018   0.001   PHE B  76 
 TYR   0.017   0.001   TYR B 154 
 ARG   0.006   0.001   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05394 (  248)
  hydrogen bonds       : angle       3.39854 (  732)
  metal coordination   : bond        0.00663 (   18)
  metal coordination   : angle       1.46034 (    2)
  covalent geometry    : bond        0.00387 ( 4828)
  covalent geometry    : angle       0.50842 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
REVERT: B  280 MET cc_start: 0.8560 (ptp) cc_final: 0.8223 (ptp)
REVERT: A  280 MET cc_start: 0.8649 (ptp) cc_final: 0.8320 (ptp)
  outliers start: 15
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1402
  time to fit residues: 11.2665
Evaluate side-chains
  52 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain A residue   69 CYS
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  351 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0980
   chunk 52 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:   40.0000
   chunk 34 optimal weight:   50.0000
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
B 355 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.214628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.204483 restraints weight = 6336.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.202311 restraints weight = 10188.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.199367 restraints weight = 12951.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4846  Z= 0.179
  Angle     :  0.528   6.269   6560  Z= 0.277
  Chirality :  0.039   0.110    804
  Planarity :  0.003   0.023    794
  Dihedral  :  4.258  17.604    638
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.60 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.36), residues: 592
  helix:  1.26 (0.28), residues: 382
  sheet: -1.77 (0.55), residues: 50
  loop : -0.16 (0.53), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 130 
 HIS   0.005   0.001   HIS B 309 
 PHE   0.019   0.002   PHE B  76 
 TYR   0.018   0.001   TYR A 154 
 ARG   0.004   0.001   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05395 (  248)
  hydrogen bonds       : angle       3.46193 (  732)
  metal coordination   : bond        0.00648 (   18)
  metal coordination   : angle       1.55023 (    2)
  covalent geometry    : bond        0.00437 ( 4828)
  covalent geometry    : angle       0.52726 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.545 
Fit side-chains
REVERT: B  280 MET cc_start: 0.8545 (ptp) cc_final: 0.8194 (ptp)
REVERT: A  280 MET cc_start: 0.8537 (ptp) cc_final: 0.8202 (ptp)
  outliers start: 19
  outliers final: 13
  residues processed: 61
  average time/residue: 0.1365
  time to fit residues: 11.5220
Evaluate side-chains
  56 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain A residue   69 CYS
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  351 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 47 optimal weight:   30.0000
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0570
   chunk 43 optimal weight:    7.9990
   overall best weight:    1.0100

-------------------------------------------------------------------------------
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 = 0.4555 r_free = 0.4555 target = 0.218801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.207609 restraints weight = 6429.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.206593 restraints weight = 12477.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.203721 restraints weight = 11878.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.4419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4846  Z= 0.104
  Angle     :  0.438   6.183   6560  Z= 0.231
  Chirality :  0.036   0.123    804
  Planarity :  0.002   0.017    794
  Dihedral  :  3.746  16.411    638
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.74 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.37), residues: 592
  helix:  1.56 (0.28), residues: 382
  sheet: -1.56 (0.60), residues: 50
  loop : -0.19 (0.53), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 311 
 HIS   0.002   0.000   HIS B 309 
 PHE   0.011   0.001   PHE B  63 
 TYR   0.018   0.001   TYR A 154 
 ARG   0.002   0.000   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  248)
  hydrogen bonds       : angle       3.16252 (  732)
  metal coordination   : bond        0.00181 (   18)
  metal coordination   : angle       2.12099 (    2)
  covalent geometry    : bond        0.00219 ( 4828)
  covalent geometry    : angle       0.43690 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.489 
Fit side-chains
REVERT: B  280 MET cc_start: 0.8433 (ptp) cc_final: 0.8173 (ptp)
REVERT: A  280 MET cc_start: 0.8411 (ptp) cc_final: 0.8183 (ptp)
  outliers start: 15
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1500
  time to fit residues: 11.4016
Evaluate side-chains
  48 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain A residue   69 CYS
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  136 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0770
   chunk 30 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.1942

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

Flipped N/Q/H residues before XYZ refinement:
B 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.228610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.208407 restraints weight = 60332.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.210308 restraints weight = 37449.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.209626 restraints weight = 31644.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4846  Z= 0.105
  Angle     :  0.463  10.912   6560  Z= 0.238
  Chirality :  0.037   0.117    804
  Planarity :  0.002   0.016    794
  Dihedral  :  3.773  17.852    638
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.79 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.36), residues: 592
  helix:  1.62 (0.28), residues: 382
  sheet: -1.50 (0.61), residues: 50
  loop : -0.23 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 311 
 HIS   0.003   0.001   HIS B 309 
 PHE   0.023   0.001   PHE B  76 
 TYR   0.024   0.001   TYR B 249 
 ARG   0.007   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  248)
  hydrogen bonds       : angle       3.14178 (  732)
  metal coordination   : bond        0.00262 (   18)
  metal coordination   : angle       1.83949 (    2)
  covalent geometry    : bond        0.00228 ( 4828)
  covalent geometry    : angle       0.46165 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 39
  time to evaluate  : 0.519 
Fit side-chains
REVERT: B  280 MET cc_start: 0.8529 (ptp) cc_final: 0.8281 (ptp)
REVERT: A  280 MET cc_start: 0.8522 (ptp) cc_final: 0.8266 (ptp)
  outliers start: 19
  outliers final: 14
  residues processed: 57
  average time/residue: 0.1346
  time to fit residues: 10.6127
Evaluate side-chains
  52 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain A residue   69 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.4690 r_free = 0.4690 target = 0.225922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.205559 restraints weight = 60169.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.206759 restraints weight = 36200.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.206729 restraints weight = 31930.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.4271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4846  Z= 0.147
  Angle     :  0.513   9.693   6560  Z= 0.265
  Chirality :  0.038   0.110    804
  Planarity :  0.003   0.019    794
  Dihedral  :  4.141  17.825    638
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.11 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.36), residues: 592
  helix:  1.53 (0.28), residues: 382
  sheet: -1.71 (0.57), residues: 50
  loop : -0.18 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 311 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.020   0.001   PHE A  76 
 TYR   0.021   0.002   TYR B 249 
 ARG   0.005   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04594 (  248)
  hydrogen bonds       : angle       3.28959 (  732)
  metal coordination   : bond        0.00497 (   18)
  metal coordination   : angle       1.58193 (    2)
  covalent geometry    : bond        0.00350 ( 4828)
  covalent geometry    : angle       0.51228 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.528 
Fit side-chains
REVERT: B  280 MET cc_start: 0.8601 (ptp) cc_final: 0.8278 (ptp)
REVERT: A  280 MET cc_start: 0.8583 (ptp) cc_final: 0.8277 (ptp)
  outliers start: 18
  outliers final: 17
  residues processed: 56
  average time/residue: 0.1400
  time to fit residues: 10.8073
Evaluate side-chains
  56 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain A residue   69 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  367 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0060
   chunk 56 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0370
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:   30.0000
   chunk 38 optimal weight:    0.6980
   chunk 41 optimal weight:   10.0000
   overall best weight:    0.5076

-------------------------------------------------------------------------------
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 = 0.4565 r_free = 0.4565 target = 0.212906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.182203 restraints weight = 60572.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.184733 restraints weight = 33191.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.184303 restraints weight = 28766.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4846  Z= 0.087
  Angle     :  0.435   9.203   6560  Z= 0.225
  Chirality :  0.036   0.127    804
  Planarity :  0.002   0.015    794
  Dihedral  :  3.596  17.766    638
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.25 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.37), residues: 592
  helix:  1.75 (0.28), residues: 382
  sheet: -1.57 (0.59), residues: 50
  loop : -0.14 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 311 
 HIS   0.001   0.000   HIS A 306 
 PHE   0.020   0.001   PHE B  76 
 TYR   0.021   0.001   TYR B 249 
 ARG   0.004   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  248)
  hydrogen bonds       : angle       3.02292 (  732)
  metal coordination   : bond        0.00193 (   18)
  metal coordination   : angle       2.45032 (    2)
  covalent geometry    : bond        0.00169 ( 4828)
  covalent geometry    : angle       0.43290 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.576 
Fit side-chains
  outliers start: 10
  outliers final: 9
  residues processed: 48
  average time/residue: 0.1913
  time to fit residues: 11.9749
Evaluate side-chains
  45 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 5 optimal weight:    0.1980
   chunk 19 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 55 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.230095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.210597 restraints weight = 60767.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.213011 restraints weight = 36526.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.212139 restraints weight = 31125.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4846  Z= 0.097
  Angle     :  0.470   8.696   6560  Z= 0.238
  Chirality :  0.036   0.121    804
  Planarity :  0.002   0.015    794
  Dihedral  :  3.647  17.678    638
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 19.25 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.36), residues: 592
  helix:  1.76 (0.28), residues: 382
  sheet: -1.57 (0.58), residues: 50
  loop : -0.11 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 311 
 HIS   0.002   0.001   HIS A 309 
 PHE   0.023   0.001   PHE A  76 
 TYR   0.022   0.001   TYR B 249 
 ARG   0.007   0.001   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  248)
  hydrogen bonds       : angle       3.04068 (  732)
  metal coordination   : bond        0.00206 (   18)
  metal coordination   : angle       2.08845 (    2)
  covalent geometry    : bond        0.00207 ( 4828)
  covalent geometry    : angle       0.46831 ( 6558)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.482 
Fit side-chains
  outliers start: 11
  outliers final: 10
  residues processed: 48
  average time/residue: 0.1826
  time to fit residues: 11.2547
Evaluate side-chains
  49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 44 optimal weight:    0.4980
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.4718 r_free = 0.4718 target = 0.225398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.197906 restraints weight = 60156.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.199758 restraints weight = 34476.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.199470 restraints weight = 29603.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4846  Z= 0.123
  Angle     :  0.529  14.374   6560  Z= 0.261
  Chirality :  0.038   0.115    804
  Planarity :  0.002   0.016    794
  Dihedral  :  3.912  17.768    638
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.68 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.36), residues: 592
  helix:  1.71 (0.28), residues: 382
  sheet: -1.80 (0.56), residues: 50
  loop :  0.04 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 130 
 HIS   0.003   0.001   HIS A 309 
 PHE   0.022   0.001   PHE B  76 
 TYR   0.022   0.002   TYR B 249 
 ARG   0.009   0.001   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  248)
  hydrogen bonds       : angle       3.11068 (  732)
  metal coordination   : bond        0.00348 (   18)
  metal coordination   : angle       1.97822 (    2)
  covalent geometry    : bond        0.00286 ( 4828)
  covalent geometry    : angle       0.52787 ( 6558)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1467.08 seconds
wall clock time: 26 minutes 24.31 seconds (1584.31 seconds total)