Starting phenix.real_space_refine
on Thu Jun 19 08:56:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ef8_9046/06_2025/6ef8_9046_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ef8_9046/06_2025/6ef8_9046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2025/6ef8_9046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2025/6ef8_9046.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2025/6ef8_9046_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2025/6ef8_9046_neut.cif"
  }
  resolution = 3.7
  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
-------------------------------------------------------------------------------
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=   0.101 sd=   0.576
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
     Fe     42      7.16       5
     S     140      5.16       5
     C   14385      2.51       5
     N    3927      2.21       5
     O    4417      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 22911
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3015
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388}
    Chain: "A"
      Number of atoms: 258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 258
          Unusual residues: {'HEC': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 8.82, per 1000 atoms: 0.38
  Number of scatterers: 22911
  At special positions: 0
  Unit cell: (85.05, 84, 358.05, 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)
     Fe     42     26.01
     S     140     16.00
     O    4417      8.00
     N    3927      7.00
     C   14385      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=119, symmetry=0
  Number of additional bonds: simple=119, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 6.85
  Conformation dependent library (CDL) restraints added in 3.2 seconds
  

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5068

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 28 sheets defined
      17.0% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 13
      removed outlier: 4.202A  pdb=" N   CYS A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   HIS A  13 " --> pdb=" O   CYS A   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 8 through 13'
    Processing helix  chain 'A' and resid 34 through 38
      removed outlier: 3.509A  pdb=" N   LEU A  37 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 91
      removed outlier: 3.527A  pdb=" N   LYS A  91 " --> pdb=" O   TRP A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 143
      removed outlier: 3.898A  pdb=" N   CYS A 143 " --> pdb=" O   CYS A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 241
    Processing helix  chain 'A' and resid 266 through 276
    Processing helix  chain 'A' and resid 302 through 309
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 4.339A  pdb=" N   ALA A 316 " --> pdb=" O   ASP A 313 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LEU A 317 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 317'
    Processing helix  chain 'A' and resid 376 through 384
    Processing helix  chain 'A' and resid 398 through 402
    Processing helix  chain 'B' and resid 8 through 13
      removed outlier: 4.201A  pdb=" N   CYS B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   HIS B  13 " --> pdb=" O   CYS B   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 8 through 13'
    Processing helix  chain 'B' and resid 34 through 38
      removed outlier: 3.509A  pdb=" N   LEU B  37 " --> pdb=" O   GLY B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 91
      removed outlier: 3.526A  pdb=" N   LYS B  91 " --> pdb=" O   TRP B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 143
      removed outlier: 3.898A  pdb=" N   CYS B 143 " --> pdb=" O   CYS B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 241
    Processing helix  chain 'B' and resid 266 through 276
    Processing helix  chain 'B' and resid 302 through 309
    Processing helix  chain 'B' and resid 313 through 317
      removed outlier: 4.340A  pdb=" N   ALA B 316 " --> pdb=" O   ASP B 313 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LEU B 317 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 313 through 317'
    Processing helix  chain 'B' and resid 376 through 384
    Processing helix  chain 'B' and resid 398 through 402
    Processing helix  chain 'C' and resid 8 through 13
      removed outlier: 4.201A  pdb=" N   CYS C  12 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   HIS C  13 " --> pdb=" O   CYS C   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 8 through 13'
    Processing helix  chain 'C' and resid 34 through 38
      removed outlier: 3.508A  pdb=" N   LEU C  37 " --> pdb=" O   GLY C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 91
      removed outlier: 3.526A  pdb=" N   LYS C  91 " --> pdb=" O   TRP C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 143
      removed outlier: 3.897A  pdb=" N   CYS C 143 " --> pdb=" O   CYS C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 241
    Processing helix  chain 'C' and resid 266 through 276
    Processing helix  chain 'C' and resid 302 through 309
    Processing helix  chain 'C' and resid 313 through 317
      removed outlier: 4.339A  pdb=" N   ALA C 316 " --> pdb=" O   ASP C 313 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LEU C 317 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 313 through 317'
    Processing helix  chain 'C' and resid 376 through 384
    Processing helix  chain 'C' and resid 398 through 402
    Processing helix  chain 'D' and resid 8 through 13
      removed outlier: 4.201A  pdb=" N   CYS D  12 " --> pdb=" O   GLU D   8 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   HIS D  13 " --> pdb=" O   CYS D   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 8 through 13'
    Processing helix  chain 'D' and resid 34 through 38
      removed outlier: 3.509A  pdb=" N   LEU D  37 " --> pdb=" O   GLY D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.526A  pdb=" N   LYS D  91 " --> pdb=" O   TRP D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 143
      removed outlier: 3.898A  pdb=" N   CYS D 143 " --> pdb=" O   CYS D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 241
    Processing helix  chain 'D' and resid 266 through 276
    Processing helix  chain 'D' and resid 302 through 309
    Processing helix  chain 'D' and resid 313 through 317
      removed outlier: 4.339A  pdb=" N   ALA D 316 " --> pdb=" O   ASP D 313 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LEU D 317 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 313 through 317'
    Processing helix  chain 'D' and resid 376 through 384
    Processing helix  chain 'D' and resid 398 through 402
    Processing helix  chain 'E' and resid 8 through 13
      removed outlier: 4.201A  pdb=" N   CYS E  12 " --> pdb=" O   GLU E   8 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   HIS E  13 " --> pdb=" O   CYS E   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 8 through 13'
    Processing helix  chain 'E' and resid 34 through 38
      removed outlier: 3.509A  pdb=" N   LEU E  37 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 91
      removed outlier: 3.526A  pdb=" N   LYS E  91 " --> pdb=" O   TRP E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 143
      removed outlier: 3.898A  pdb=" N   CYS E 143 " --> pdb=" O   CYS E 140 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 234 through 241
    Processing helix  chain 'E' and resid 266 through 276
    Processing helix  chain 'E' and resid 302 through 309
    Processing helix  chain 'E' and resid 313 through 317
      removed outlier: 4.339A  pdb=" N   ALA E 316 " --> pdb=" O   ASP E 313 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LEU E 317 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 313 through 317'
    Processing helix  chain 'E' and resid 376 through 384
    Processing helix  chain 'E' and resid 398 through 402
    Processing helix  chain 'F' and resid 8 through 13
      removed outlier: 4.201A  pdb=" N   CYS F  12 " --> pdb=" O   GLU F   8 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   HIS F  13 " --> pdb=" O   CYS F   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 8 through 13'
    Processing helix  chain 'F' and resid 34 through 38
      removed outlier: 3.509A  pdb=" N   LEU F  37 " --> pdb=" O   GLY F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 85 through 91
      removed outlier: 3.527A  pdb=" N   LYS F  91 " --> pdb=" O   TRP F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 143
      removed outlier: 3.898A  pdb=" N   CYS F 143 " --> pdb=" O   CYS F 140 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 234 through 241
    Processing helix  chain 'F' and resid 266 through 276
    Processing helix  chain 'F' and resid 302 through 309
    Processing helix  chain 'F' and resid 313 through 317
      removed outlier: 4.339A  pdb=" N   ALA F 316 " --> pdb=" O   ASP F 313 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU F 317 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 313 through 317'
    Processing helix  chain 'F' and resid 376 through 384
    Processing helix  chain 'F' and resid 398 through 402
    Processing helix  chain 'G' and resid 8 through 13
      removed outlier: 4.201A  pdb=" N   CYS G  12 " --> pdb=" O   GLU G   8 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   HIS G  13 " --> pdb=" O   CYS G   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 8 through 13'
    Processing helix  chain 'G' and resid 34 through 38
      removed outlier: 3.509A  pdb=" N   LEU G  37 " --> pdb=" O   GLY G  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 91
      removed outlier: 3.527A  pdb=" N   LYS G  91 " --> pdb=" O   TRP G  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 139 through 143
      removed outlier: 3.898A  pdb=" N   CYS G 143 " --> pdb=" O   CYS G 140 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 234 through 241
    Processing helix  chain 'G' and resid 266 through 276
    Processing helix  chain 'G' and resid 302 through 309
    Processing helix  chain 'G' and resid 313 through 317
      removed outlier: 4.339A  pdb=" N   ALA G 316 " --> pdb=" O   ASP G 313 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU G 317 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 313 through 317'
    Processing helix  chain 'G' and resid 376 through 384
    Processing helix  chain 'G' and resid 398 through 402
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95
      removed outlier: 3.578A  pdb=" N   TRP A  95 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152
    Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 264
      removed outlier: 4.078A  pdb=" N   VAL A 326 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 356
      removed outlier: 3.930A  pdb=" N   ASN A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95
      removed outlier: 3.577A  pdb=" N   TRP B  95 " --> pdb=" O   ASN B 101 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 152
    Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 264
      removed outlier: 4.078A  pdb=" N   VAL B 326 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.931A  pdb=" N   ASN B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 95
      removed outlier: 3.577A  pdb=" N   TRP C  95 " --> pdb=" O   ASN C 101 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 151 through 152
    Processing sheet with id=AB2, first strand: chain 'C' and resid 260 through 264
      removed outlier: 4.078A  pdb=" N   VAL C 326 " --> pdb=" O   GLY C 260 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 354 through 356
      removed outlier: 3.931A  pdb=" N   ASN C 360 " --> pdb=" O   ASP C 356 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 95
      removed outlier: 3.578A  pdb=" N   TRP D  95 " --> pdb=" O   ASN D 101 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 152
    Processing sheet with id=AB6, first strand: chain 'D' and resid 260 through 264
      removed outlier: 4.078A  pdb=" N   VAL D 326 " --> pdb=" O   GLY D 260 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 354 through 356
      removed outlier: 3.931A  pdb=" N   ASN D 360 " --> pdb=" O   ASP D 356 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 93 through 95
      removed outlier: 3.577A  pdb=" N   TRP E  95 " --> pdb=" O   ASN E 101 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 151 through 152
    Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 264
      removed outlier: 4.078A  pdb=" N   VAL E 326 " --> pdb=" O   GLY E 260 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 354 through 356
      removed outlier: 3.932A  pdb=" N   ASN E 360 " --> pdb=" O   ASP E 356 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 93 through 95
      removed outlier: 3.578A  pdb=" N   TRP F  95 " --> pdb=" O   ASN F 101 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 151 through 152
    Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 264
      removed outlier: 4.078A  pdb=" N   VAL F 326 " --> pdb=" O   GLY F 260 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 354 through 356
      removed outlier: 3.931A  pdb=" N   ASN F 360 " --> pdb=" O   ASP F 356 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'G' and resid 93 through 95
      removed outlier: 3.577A  pdb=" N   TRP G  95 " --> pdb=" O   ASN G 101 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'G' and resid 151 through 152
    Processing sheet with id=AC9, first strand: chain 'G' and resid 260 through 264
      removed outlier: 4.079A  pdb=" N   VAL G 326 " --> pdb=" O   GLY G 260 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'G' and resid 354 through 356
      removed outlier: 3.931A  pdb=" N   ASN G 360 " --> pdb=" O   ASP G 356 " (cutoff:3.500A)

    252 hydrogen bonds defined for protein.
    504 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: 5.85

  Time building geometry restraints manager: 7.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 10137
        1.39 -     1.56: 13226
        1.56 -     1.73: 3
        1.73 -     1.90: 196
        1.90 -     2.06: 168
  Bond restraints: 23730
  Sorted by residual:
  bond pdb=" CB  CYS G 140 "
       pdb=" SG  CYS G 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.753  0.055 3.30e-02 9.18e+02 2.82e+00
  bond pdb=" CB  CYS E 140 "
       pdb=" SG  CYS E 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.753  0.055 3.30e-02 9.18e+02 2.81e+00
  bond pdb=" CB  CYS D 140 "
       pdb=" SG  CYS D 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.753  0.055 3.30e-02 9.18e+02 2.81e+00
  bond pdb=" CB  CYS C 140 "
       pdb=" SG  CYS C 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.753  0.055 3.30e-02 9.18e+02 2.80e+00
  bond pdb=" CB  CYS A 140 "
       pdb=" SG  CYS A 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.753  0.055 3.30e-02 9.18e+02 2.75e+00
  ... (remaining 23725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 31086
        2.49 -     4.97: 1327
        4.97 -     7.46: 242
        7.46 -     9.94: 175
        9.94 -    12.43: 63
  Bond angle restraints: 32893
  Sorted by residual:
  angle pdb=" N   ILE A 188 "
        pdb=" CA  ILE A 188 "
        pdb=" C   ILE A 188 "
      ideal   model   delta    sigma   weight residual
     109.34  120.83  -11.49 2.08e+00 2.31e-01 3.05e+01
  angle pdb=" N   ILE D 188 "
        pdb=" CA  ILE D 188 "
        pdb=" C   ILE D 188 "
      ideal   model   delta    sigma   weight residual
     109.34  120.83  -11.49 2.08e+00 2.31e-01 3.05e+01
  angle pdb=" N   ILE E 188 "
        pdb=" CA  ILE E 188 "
        pdb=" C   ILE E 188 "
      ideal   model   delta    sigma   weight residual
     109.34  120.82  -11.48 2.08e+00 2.31e-01 3.05e+01
  angle pdb=" N   ILE G 188 "
        pdb=" CA  ILE G 188 "
        pdb=" C   ILE G 188 "
      ideal   model   delta    sigma   weight residual
     109.34  120.82  -11.48 2.08e+00 2.31e-01 3.05e+01
  angle pdb=" N   ILE C 188 "
        pdb=" CA  ILE C 188 "
        pdb=" C   ILE C 188 "
      ideal   model   delta    sigma   weight residual
     109.34  120.82  -11.48 2.08e+00 2.31e-01 3.04e+01
  ... (remaining 32888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 12120
       17.44 -    34.88: 529
       34.88 -    52.32: 84
       52.32 -    69.76: 42
       69.76 -    87.20: 98
  Dihedral angle restraints: 12873
    sinusoidal: 4809
      harmonic: 8064
  Sorted by residual:
  dihedral pdb=" CA  ASN E 327 "
           pdb=" C   ASN E 327 "
           pdb=" N   CYS E 328 "
           pdb=" CA  CYS E 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.00   48.00     0      5.00e+00 4.00e-02 9.22e+01
  dihedral pdb=" CA  ASN D 327 "
           pdb=" C   ASN D 327 "
           pdb=" N   CYS D 328 "
           pdb=" CA  CYS D 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.01   47.99     0      5.00e+00 4.00e-02 9.21e+01
  dihedral pdb=" CA  ASN C 327 "
           pdb=" C   ASN C 327 "
           pdb=" N   CYS C 328 "
           pdb=" CA  CYS C 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.02   47.98     0      5.00e+00 4.00e-02 9.21e+01
  ... (remaining 12870 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1917
       0.046 -    0.092: 890
       0.092 -    0.138: 266
       0.138 -    0.184: 63
       0.184 -    0.229: 21
  Chirality restraints: 3157
  Sorted by residual:
  chirality pdb=" CB  VAL E   6 "
            pdb=" CA  VAL E   6 "
            pdb=" CG1 VAL E   6 "
            pdb=" CG2 VAL E   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  VAL C   6 "
            pdb=" CA  VAL C   6 "
            pdb=" CG1 VAL C   6 "
            pdb=" CG2 VAL C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  VAL F   6 "
            pdb=" CA  VAL F   6 "
            pdb=" CG1 VAL F   6 "
            pdb=" CG2 VAL F   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 3154 not shown)

  Planarity restraints: 4179
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC C 504 "   -0.011 2.00e-02 2.50e+03   5.68e-02 7.25e+01
        pdb=" C2C HEC C 504 "    0.153 2.00e-02 2.50e+03
        pdb=" C3C HEC C 504 "   -0.037 2.00e-02 2.50e+03
        pdb=" C4C HEC C 504 "   -0.007 2.00e-02 2.50e+03
        pdb=" CAC HEC C 504 "   -0.013 2.00e-02 2.50e+03
        pdb=" CHC HEC C 504 "   -0.020 2.00e-02 2.50e+03
        pdb=" CHD HEC C 504 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC C 504 "   -0.057 2.00e-02 2.50e+03
        pdb=" NC  HEC C 504 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC D 504 "    0.011 2.00e-02 2.50e+03   5.68e-02 7.25e+01
        pdb=" C2C HEC D 504 "   -0.153 2.00e-02 2.50e+03
        pdb=" C3C HEC D 504 "    0.037 2.00e-02 2.50e+03
        pdb=" C4C HEC D 504 "    0.006 2.00e-02 2.50e+03
        pdb=" CAC HEC D 504 "    0.013 2.00e-02 2.50e+03
        pdb=" CHC HEC D 504 "    0.020 2.00e-02 2.50e+03
        pdb=" CHD HEC D 504 "    0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC D 504 "    0.057 2.00e-02 2.50e+03
        pdb=" NC  HEC D 504 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC A 504 "   -0.011 2.00e-02 2.50e+03   5.68e-02 7.25e+01
        pdb=" C2C HEC A 504 "    0.153 2.00e-02 2.50e+03
        pdb=" C3C HEC A 504 "   -0.037 2.00e-02 2.50e+03
        pdb=" C4C HEC A 504 "   -0.006 2.00e-02 2.50e+03
        pdb=" CAC HEC A 504 "   -0.013 2.00e-02 2.50e+03
        pdb=" CHC HEC A 504 "   -0.020 2.00e-02 2.50e+03
        pdb=" CHD HEC A 504 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC A 504 "   -0.057 2.00e-02 2.50e+03
        pdb=" NC  HEC A 504 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 4176 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 332
        2.60 -     3.17: 19531
        3.17 -     3.75: 37987
        3.75 -     4.32: 56439
        4.32 -     4.90: 89022
  Nonbonded interactions: 203311
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A 332 "
            pdb="FE   HEC A 501 "
     model   vdw
     2.023 3.080
  nonbonded pdb=" NE2 HIS D 335 "
            pdb="FE   HEC D 504 "
     model   vdw
     2.044 3.080
  nonbonded pdb=" NE2 HIS E 335 "
            pdb="FE   HEC E 504 "
     model   vdw
     2.044 3.080
  nonbonded pdb=" NE2 HIS G 335 "
            pdb="FE   HEC G 504 "
     model   vdw
     2.044 3.080
  nonbonded pdb=" NE2 HIS C 335 "
            pdb="FE   HEC C 504 "
     model   vdw
     2.044 3.080
  ... (remaining 203306 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: 0.20
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

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:             0.160
  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:             0.020
  Extract box with map and model:          0.910
  Check model and map are aligned:         0.170
  Set scattering table:                    0.210
  Process input model:                     46.870
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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      :  0.014   0.297  23849  Z= 1.206
  Angle     :  1.377  12.428  32893  Z= 0.631
  Chirality :  0.059   0.229   3157
  Planarity :  0.009   0.071   4179
  Dihedral  : 14.341  87.197   7805
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  : 11.36 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.03 (0.12), residues: 2835
  helix: -3.87 (0.14), residues: 294
  sheet:  None (None), residues: 0
  loop : -2.84 (0.10), residues: 2541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP D 238 
 HIS   0.009   0.003   HIS D 335 
 PHE   0.021   0.003   PHE B 345 
 TYR   0.018   0.002   TYR B 150 
 ARG   0.008   0.001   ARG D 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24731 (  252)
  hydrogen bonds       : angle       8.22699 (  504)
  covalent geometry    : bond        0.00693 (23730)
  covalent geometry    : angle       1.37704 (32893)
  Misc. bond           : bond        0.18045 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 397
  time to evaluate  : 2.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ASP cc_start: 0.7961 (m-30) cc_final: 0.7589 (t0)
REVERT: C  107 ARG cc_start: 0.8402 (mmp80) cc_final: 0.7649 (mmp80)
REVERT: C  111 ASN cc_start: 0.8048 (m-40) cc_final: 0.7843 (m-40)
REVERT: D  221 THR cc_start: 0.8498 (t) cc_final: 0.8192 (p)
REVERT: D  377 VAL cc_start: 0.9263 (m) cc_final: 0.9060 (t)
REVERT: E  235 MET cc_start: 0.8587 (tpt) cc_final: 0.8223 (tpt)
REVERT: E  274 ASN cc_start: 0.8392 (m-40) cc_final: 0.8187 (m-40)
REVERT: F   10 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8039 (mm-30)
REVERT: F  107 ARG cc_start: 0.8468 (mmp80) cc_final: 0.7964 (mmp80)
REVERT: F  235 MET cc_start: 0.8427 (tpt) cc_final: 0.8079 (tpt)
REVERT: G   10 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8030 (mm-30)
REVERT: G  111 ASN cc_start: 0.8372 (m-40) cc_final: 0.8085 (m-40)
REVERT: G  377 VAL cc_start: 0.9260 (m) cc_final: 0.9043 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 397
  average time/residue: 0.3400
  time to fit residues: 212.3783
Evaluate side-chains
  182 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 2.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 236 optimal weight:   20.0000
   chunk 212 optimal weight:    9.9990
   chunk 117 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 143 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 219 optimal weight:    0.0770
   chunk 84 optimal weight:    6.9990
   chunk 133 optimal weight:    7.9990
   chunk 163 optimal weight:    0.7980
   chunk 254 optimal weight:   30.0000
   overall best weight:    2.9744

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

Flipped N/Q/H residues before XYZ refinement:
A  63 HIS
A 111 ASN
A 139 HIS
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 396 GLN
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS
B 111 ASN
B 139 HIS
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  51 HIS
C  63 HIS
C 111 ASN
C 139 HIS
C 327 ASN
C 373 GLN
** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  51 HIS
D  63 HIS
D 110 HIS
D 111 ASN
D 139 HIS
** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 373 GLN
** D 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  51 HIS
E  63 HIS
E 110 HIS
E 111 ASN
E 139 HIS
** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 373 GLN
** E 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  51 HIS
F  63 HIS
F 111 ASN
F 139 HIS
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 373 GLN
** F 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  51 HIS
G  63 HIS
G 111 ASN
G 139 HIS
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 373 GLN
** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 36

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.081678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.075155 restraints weight = 50815.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.077407 restraints weight = 20862.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.078774 restraints weight = 10673.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.267  23849  Z= 0.159
  Angle     :  0.805  12.647  32893  Z= 0.363
  Chirality :  0.044   0.155   3157
  Planarity :  0.005   0.074   4179
  Dihedral  : 15.513  89.601   3430
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.50 %
    Favored  : 88.25 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.62 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.55 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.14), residues: 2835
  helix: -1.82 (0.24), residues: 336
  sheet:  None (None), residues: 0
  loop : -2.31 (0.12), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 238 
 HIS   0.010   0.001   HIS F 332 
 PHE   0.016   0.002   PHE A 351 
 TYR   0.018   0.001   TYR B 150 
 ARG   0.004   0.001   ARG B 344 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03199 (  252)
  hydrogen bonds       : angle       4.74367 (  504)
  covalent geometry    : bond        0.00436 (23730)
  covalent geometry    : angle       0.80529 (32893)
  Misc. bond           : bond        0.09325 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 218
  time to evaluate  : 2.948 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LEU cc_start: 0.8575 (mt) cc_final: 0.8222 (mt)
REVERT: A  311 LYS cc_start: 0.8314 (mttp) cc_final: 0.7996 (mtpp)
REVERT: A  340 ASP cc_start: 0.7941 (m-30) cc_final: 0.7672 (t0)
REVERT: A  377 VAL cc_start: 0.9254 (m) cc_final: 0.9038 (t)
REVERT: B  118 ASN cc_start: 0.8347 (m-40) cc_final: 0.7949 (p0)
REVERT: D   36 MET cc_start: 0.8887 (mmt) cc_final: 0.8573 (mmm)
REVERT: D  111 ASN cc_start: 0.8377 (m110) cc_final: 0.7693 (t0)
REVERT: D  221 THR cc_start: 0.8533 (t) cc_final: 0.8043 (p)
REVERT: D  377 VAL cc_start: 0.9332 (m) cc_final: 0.9102 (t)
REVERT: E  377 VAL cc_start: 0.9292 (m) cc_final: 0.9034 (t)
REVERT: G  111 ASN cc_start: 0.8362 (m110) cc_final: 0.7982 (m-40)
REVERT: G  118 ASN cc_start: 0.8371 (m-40) cc_final: 0.8097 (p0)
REVERT: G  252 PRO cc_start: 0.7646 (Cg_exo) cc_final: 0.7425 (Cg_endo)
  outliers start: 46
  outliers final: 21
  residues processed: 249
  average time/residue: 0.3359
  time to fit residues: 143.4672
Evaluate side-chains
  187 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 2.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  351 PHE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  351 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 203 optimal weight:    8.9990
   chunk 1 optimal weight:   30.0000
   chunk 139 optimal weight:    8.9990
   chunk 240 optimal weight:    0.9990
   chunk 136 optimal weight:   30.0000
   chunk 42 optimal weight:   30.0000
   chunk 38 optimal weight:   20.0000
   chunk 144 optimal weight:    0.4980
   chunk 135 optimal weight:    6.9990
   chunk 271 optimal weight:   20.0000
   chunk 251 optimal weight:    6.9990
   overall best weight:    4.8988

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 ASN
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  52 GLN
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 404 HIS
C  25 ASN
C  52 GLN
C 233 GLN
C 404 HIS
D  52 GLN
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 404 HIS
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  52 GLN
E 274 ASN
** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 404 HIS
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  52 GLN
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  52 GLN
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 404 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.077733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.071233 restraints weight = 50480.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.073438 restraints weight = 20960.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.074773 restraints weight = 10832.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.309  23849  Z= 0.196
  Angle     :  0.869  17.986  32893  Z= 0.361
  Chirality :  0.045   0.212   3157
  Planarity :  0.005   0.056   4179
  Dihedral  : 15.307  89.334   3430
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.20 %
    Favored  : 87.55 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 10.30 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.15), residues: 2835
  helix: -0.76 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -2.01 (0.12), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP F 238 
 HIS   0.009   0.002   HIS A 332 
 PHE   0.016   0.002   PHE E  31 
 TYR   0.019   0.002   TYR E 186 
 ARG   0.003   0.000   ARG D 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03007 (  252)
  hydrogen bonds       : angle       4.54249 (  504)
  covalent geometry    : bond        0.00528 (23730)
  covalent geometry    : angle       0.86858 (32893)
  Misc. bond           : bond        0.11180 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 182
  time to evaluate  : 3.314 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8396 (mttp) cc_final: 0.8050 (mtpp)
REVERT: A  340 ASP cc_start: 0.7954 (m-30) cc_final: 0.7734 (t0)
REVERT: B   85 ASP cc_start: 0.7904 (m-30) cc_final: 0.7561 (m-30)
REVERT: B  118 ASN cc_start: 0.8286 (m-40) cc_final: 0.7938 (p0)
REVERT: C  165 ILE cc_start: 0.8737 (mt) cc_final: 0.8532 (mt)
REVERT: C  354 ILE cc_start: 0.9151 (mm) cc_final: 0.8923 (mt)
REVERT: D   36 MET cc_start: 0.8870 (mmt) cc_final: 0.8608 (mmm)
REVERT: D  221 THR cc_start: 0.8658 (t) cc_final: 0.8209 (p)
REVERT: D  340 ASP cc_start: 0.8273 (t0) cc_final: 0.7907 (t0)
REVERT: E  274 ASN cc_start: 0.8218 (m-40) cc_final: 0.7955 (m-40)
REVERT: F  118 ASN cc_start: 0.8276 (m-40) cc_final: 0.7977 (p0)
REVERT: F  274 ASN cc_start: 0.8514 (m-40) cc_final: 0.8305 (m-40)
  outliers start: 65
  outliers final: 38
  residues processed: 222
  average time/residue: 0.4043
  time to fit residues: 157.7933
Evaluate side-chains
  184 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 3.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  351 PHE
Chi-restraints excluded: chain B residue  403 CYS
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  403 CYS
Chi-restraints excluded: chain D residue  186 TYR
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  253 THR
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  403 CYS
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  362 ILE
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Chi-restraints excluded: chain G residue  351 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 262 optimal weight:    9.9990
   chunk 43 optimal weight:   20.0000
   chunk 169 optimal weight:   20.0000
   chunk 62 optimal weight:    5.9990
   chunk 197 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 204 optimal weight:    5.9990
   chunk 144 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   chunk 160 optimal weight:    2.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 ASN
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  51 HIS
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 404 HIS
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.079250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.072795 restraints weight = 51045.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.074999 restraints weight = 21269.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.076317 restraints weight = 10970.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.208  23849  Z= 0.154
  Angle     :  0.784  15.542  32893  Z= 0.332
  Chirality :  0.044   0.168   3157
  Planarity :  0.004   0.047   4179
  Dihedral  : 14.960  89.328   3430
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.51 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 11.58 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.16), residues: 2835
  helix: -0.33 (0.30), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.84 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  95 
 HIS   0.007   0.001   HIS G 332 
 PHE   0.013   0.002   PHE A 351 
 TYR   0.014   0.001   TYR F 150 
 ARG   0.004   0.000   ARG D 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02692 (  252)
  hydrogen bonds       : angle       4.33463 (  504)
  covalent geometry    : bond        0.00436 (23730)
  covalent geometry    : angle       0.78435 (32893)
  Misc. bond           : bond        0.08496 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 180
  time to evaluate  : 2.582 
Fit side-chains
REVERT: A  160 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8465 (t)
REVERT: A  189 LEU cc_start: 0.8715 (mt) cc_final: 0.8337 (mt)
REVERT: A  311 LYS cc_start: 0.8382 (mttp) cc_final: 0.8075 (mtpp)
REVERT: B   85 ASP cc_start: 0.8097 (m-30) cc_final: 0.7572 (m-30)
REVERT: B  340 ASP cc_start: 0.8360 (t0) cc_final: 0.8008 (t0)
REVERT: B  354 ILE cc_start: 0.9177 (mm) cc_final: 0.8834 (mt)
REVERT: C   71 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6784 (ptp)
REVERT: C  380 MET cc_start: 0.8831 (tpp) cc_final: 0.8580 (tpp)
REVERT: D   36 MET cc_start: 0.8895 (mmt) cc_final: 0.8619 (mmm)
REVERT: D  221 THR cc_start: 0.8566 (t) cc_final: 0.8245 (p)
REVERT: D  340 ASP cc_start: 0.8322 (t0) cc_final: 0.7954 (t0)
REVERT: G  111 ASN cc_start: 0.8480 (m110) cc_final: 0.8060 (m-40)
REVERT: G  149 LYS cc_start: 0.8295 (mttt) cc_final: 0.7778 (mmtt)
  outliers start: 81
  outliers final: 50
  residues processed: 238
  average time/residue: 0.3650
  time to fit residues: 152.1304
Evaluate side-chains
  208 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 156
  time to evaluate  : 2.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 CYS
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue    9 CYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  351 PHE
Chi-restraints excluded: chain B residue  403 CYS
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   71 MET
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  325 ASN
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue  186 TYR
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  253 THR
Chi-restraints excluded: chain D residue  331 CYS
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  403 CYS
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  124 THR
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  337 SER
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  325 ASN
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 199 optimal weight:   20.0000
   chunk 84 optimal weight:   20.0000
   chunk 218 optimal weight:    8.9990
   chunk 257 optimal weight:    4.9990
   chunk 166 optimal weight:   20.0000
   chunk 91 optimal weight:   10.0000
   chunk 164 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 156 optimal weight:   20.0000
   chunk 265 optimal weight:    0.0070
   overall best weight:    6.0006

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 ASN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 286 GLN
E 373 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.076312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.069803 restraints weight = 51407.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.072014 restraints weight = 21366.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.073337 restraints weight = 11052.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.297  23849  Z= 0.218
  Angle     :  0.868  18.132  32893  Z= 0.355
  Chirality :  0.045   0.169   3157
  Planarity :  0.004   0.045   4179
  Dihedral  : 15.242  89.228   3430
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.80 %
    Favored  : 86.95 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 12.45 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.16), residues: 2835
  helix: -0.34 (0.30), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.79 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G 238 
 HIS   0.008   0.002   HIS A 332 
 PHE   0.017   0.002   PHE E  31 
 TYR   0.016   0.001   TYR D 150 
 ARG   0.003   0.000   ARG B 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02798 (  252)
  hydrogen bonds       : angle       4.57619 (  504)
  covalent geometry    : bond        0.00588 (23730)
  covalent geometry    : angle       0.86842 (32893)
  Misc. bond           : bond        0.11596 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 157
  time to evaluate  : 2.240 
Fit side-chains
REVERT: A  107 ARG cc_start: 0.8472 (mmp80) cc_final: 0.8250 (mmp80)
REVERT: A  160 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8459 (t)
REVERT: A  189 LEU cc_start: 0.8718 (mt) cc_final: 0.8353 (mt)
REVERT: A  311 LYS cc_start: 0.8424 (mttp) cc_final: 0.8122 (mtpp)
REVERT: B   85 ASP cc_start: 0.7999 (m-30) cc_final: 0.7730 (m-30)
REVERT: B  354 ILE cc_start: 0.9161 (mm) cc_final: 0.8819 (mt)
REVERT: C   71 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6731 (ptp)
REVERT: C   85 ASP cc_start: 0.8117 (m-30) cc_final: 0.7558 (m-30)
REVERT: D   36 MET cc_start: 0.8886 (mmt) cc_final: 0.8635 (mmm)
REVERT: D  221 THR cc_start: 0.8643 (t) cc_final: 0.8329 (p)
REVERT: D  274 ASN cc_start: 0.8176 (m-40) cc_final: 0.7741 (m-40)
REVERT: D  340 ASP cc_start: 0.8520 (t0) cc_final: 0.8114 (t0)
REVERT: F  160 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8298 (t)
REVERT: F  342 MET cc_start: 0.8843 (tpp) cc_final: 0.8456 (tpp)
  outliers start: 84
  outliers final: 56
  residues processed: 217
  average time/residue: 0.2683
  time to fit residues: 100.6694
Evaluate side-chains
  203 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 144
  time to evaluate  : 2.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 CYS
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue    9 CYS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  351 PHE
Chi-restraints excluded: chain C residue    9 CYS
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   71 MET
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  325 ASN
Chi-restraints excluded: chain C residue  331 CYS
Chi-restraints excluded: chain C residue  351 PHE
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue  186 TYR
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  331 CYS
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  403 CYS
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   24 MET
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  124 THR
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  337 SER
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain F residue    6 VAL
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  331 CYS
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  362 ILE
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 135 optimal weight:   20.0000
   chunk 248 optimal weight:    8.9990
   chunk 159 optimal weight:    0.8980
   chunk 68 optimal weight:   20.0000
   chunk 53 optimal weight:   20.0000
   chunk 276 optimal weight:   20.0000
   chunk 165 optimal weight:    9.9990
   chunk 261 optimal weight:    0.9990
   chunk 145 optimal weight:   30.0000
   chunk 257 optimal weight:    0.8980
   chunk 143 optimal weight:    9.9990
   overall best weight:    4.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN
** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  25 ASN
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.077769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.071274 restraints weight = 50960.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.073498 restraints weight = 21185.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.074850 restraints weight = 10915.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.242  23849  Z= 0.173
  Angle     :  0.811  16.327  32893  Z= 0.336
  Chirality :  0.044   0.167   3157
  Planarity :  0.004   0.045   4179
  Dihedral  : 15.088  89.990   3430
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.36 %
    Favored  : 88.40 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 12.73 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.16), residues: 2835
  helix: -0.25 (0.30), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.74 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP F 238 
 HIS   0.007   0.001   HIS A 332 
 PHE   0.014   0.002   PHE F  86 
 TYR   0.014   0.001   TYR B 150 
 ARG   0.003   0.000   ARG D 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02667 (  252)
  hydrogen bonds       : angle       4.50433 (  504)
  covalent geometry    : bond        0.00484 (23730)
  covalent geometry    : angle       0.81133 (32893)
  Misc. bond           : bond        0.09393 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 162
  time to evaluate  : 3.370 
Fit side-chains
REVERT: A  107 ARG cc_start: 0.8501 (mmp80) cc_final: 0.8298 (mmp80)
REVERT: A  160 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8366 (t)
REVERT: A  311 LYS cc_start: 0.8578 (mttp) cc_final: 0.8251 (mtpp)
REVERT: A  342 MET cc_start: 0.8918 (tpp) cc_final: 0.8339 (ttm)
REVERT: B   85 ASP cc_start: 0.7905 (m-30) cc_final: 0.7583 (m-30)
REVERT: B  247 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8034 (p-80)
REVERT: B  340 ASP cc_start: 0.8431 (t0) cc_final: 0.8208 (t0)
REVERT: B  354 ILE cc_start: 0.9145 (mm) cc_final: 0.8804 (mt)
REVERT: C   71 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6566 (ptp)
REVERT: D   36 MET cc_start: 0.8883 (mmt) cc_final: 0.8613 (mmm)
REVERT: D  221 THR cc_start: 0.8656 (t) cc_final: 0.8354 (p)
REVERT: D  274 ASN cc_start: 0.8055 (m-40) cc_final: 0.7691 (m-40)
REVERT: D  340 ASP cc_start: 0.8527 (t0) cc_final: 0.8060 (t0)
REVERT: F  160 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8277 (t)
REVERT: F  235 MET cc_start: 0.7808 (tpt) cc_final: 0.7492 (tpt)
REVERT: G  149 LYS cc_start: 0.8313 (mttt) cc_final: 0.7788 (mmtt)
  outliers start: 82
  outliers final: 62
  residues processed: 218
  average time/residue: 0.2721
  time to fit residues: 103.1928
Evaluate side-chains
  215 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 149
  time to evaluate  : 2.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 CYS
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue    9 CYS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  247 HIS
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  351 PHE
Chi-restraints excluded: chain C residue    9 CYS
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   71 MET
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  325 ASN
Chi-restraints excluded: chain C residue  331 CYS
Chi-restraints excluded: chain C residue  403 CYS
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue  186 TYR
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  253 THR
Chi-restraints excluded: chain D residue  331 CYS
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain D residue  403 CYS
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  124 THR
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain E residue  403 CYS
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  245 ASP
Chi-restraints excluded: chain F residue  331 CYS
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  362 ILE
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Chi-restraints excluded: chain G residue  331 CYS
Chi-restraints excluded: chain G residue  351 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 207 optimal weight:    0.4980
   chunk 1 optimal weight:    0.2980
   chunk 252 optimal weight:    8.9990
   chunk 31 optimal weight:   20.0000
   chunk 248 optimal weight:    9.9990
   chunk 96 optimal weight:   20.0000
   chunk 49 optimal weight:   20.0000
   chunk 216 optimal weight:    7.9990
   chunk 132 optimal weight:   10.0000
   chunk 174 optimal weight:   50.0000
   chunk 137 optimal weight:    4.9990
   overall best weight:    4.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN
** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 274 ASN ** 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 = 0.2978 r_free = 0.2978 target = 0.077427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.070936 restraints weight = 50899.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.073148 restraints weight = 21190.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.074494 restraints weight = 10963.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.242  23849  Z= 0.179
  Angle     :  0.818  17.234  32893  Z= 0.337
  Chirality :  0.044   0.169   3157
  Planarity :  0.004   0.046   4179
  Dihedral  : 15.074  89.294   3430
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.24 %
    Favored  : 87.51 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 13.28 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.16), residues: 2835
  helix: -0.25 (0.30), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.71 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 238 
 HIS   0.008   0.001   HIS A 332 
 PHE   0.015   0.002   PHE F  86 
 TYR   0.014   0.001   TYR D 150 
 ARG   0.003   0.000   ARG C 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02689 (  252)
  hydrogen bonds       : angle       4.53467 (  504)
  covalent geometry    : bond        0.00501 (23730)
  covalent geometry    : angle       0.81758 (32893)
  Misc. bond           : bond        0.09809 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 162
  time to evaluate  : 2.484 
Fit side-chains
REVERT: A  160 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8382 (t)
REVERT: A  311 LYS cc_start: 0.8590 (mttp) cc_final: 0.8269 (mtpp)
REVERT: B   85 ASP cc_start: 0.7944 (m-30) cc_final: 0.7593 (m-30)
REVERT: B  247 HIS cc_start: 0.8813 (OUTLIER) cc_final: 0.8069 (p-80)
REVERT: B  354 ILE cc_start: 0.9121 (mm) cc_final: 0.8778 (mt)
REVERT: C   71 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6557 (ptp)
REVERT: C  327 ASN cc_start: 0.8033 (t0) cc_final: 0.7561 (t0)
REVERT: D   36 MET cc_start: 0.8863 (mmt) cc_final: 0.8575 (mmm)
REVERT: D  221 THR cc_start: 0.8720 (t) cc_final: 0.8413 (p)
REVERT: D  274 ASN cc_start: 0.8107 (m-40) cc_final: 0.7744 (m-40)
REVERT: D  340 ASP cc_start: 0.8544 (t0) cc_final: 0.8172 (t0)
REVERT: F  160 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8275 (t)
REVERT: F  235 MET cc_start: 0.7843 (tpt) cc_final: 0.7586 (tpt)
  outliers start: 91
  outliers final: 69
  residues processed: 231
  average time/residue: 0.2743
  time to fit residues: 110.7074
Evaluate side-chains
  227 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 154
  time to evaluate  : 2.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 CYS
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue    9 CYS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  247 HIS
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  351 PHE
Chi-restraints excluded: chain C residue    9 CYS
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   71 MET
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  325 ASN
Chi-restraints excluded: chain C residue  331 CYS
Chi-restraints excluded: chain C residue  403 CYS
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue  186 TYR
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  253 THR
Chi-restraints excluded: chain D residue  331 CYS
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain D residue  403 CYS
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  124 THR
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  186 TYR
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  331 CYS
Chi-restraints excluded: chain E residue  337 SER
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain E residue  403 CYS
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  245 ASP
Chi-restraints excluded: chain F residue  312 ILE
Chi-restraints excluded: chain F residue  331 CYS
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  362 ILE
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Chi-restraints excluded: chain G residue  331 CYS
Chi-restraints excluded: chain G residue  351 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 103 optimal weight:   20.0000
   chunk 172 optimal weight:   20.0000
   chunk 86 optimal weight:   30.0000
   chunk 120 optimal weight:   20.0000
   chunk 223 optimal weight:   30.0000
   chunk 216 optimal weight:   10.0000
   chunk 270 optimal weight:    6.9990
   chunk 144 optimal weight:    5.9990
   chunk 197 optimal weight:   20.0000
   chunk 90 optimal weight:   20.0000
   chunk 241 optimal weight:    8.9990
   overall best weight:   10.3994

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

Flipped N/Q/H residues before XYZ refinement:
A  25 ASN
A 274 ASN
A 286 GLN
** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  51 HIS
** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  51 HIS
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  51 HIS
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 325 ASN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  51 HIS
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  51 HIS
** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.072461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.066007 restraints weight = 52015.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.068164 restraints weight = 21647.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.069473 restraints weight = 11231.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.015   0.486  23849  Z= 0.339
  Angle     :  1.026  20.410  32893  Z= 0.420
  Chirality :  0.050   0.184   3157
  Planarity :  0.005   0.061   4179
  Dihedral  : 15.735  89.825   3430
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.93 %
    Favored  : 85.82 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 13.64 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.16), residues: 2835
  helix: -0.69 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.86 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 238 
 HIS   0.010   0.002   HIS A 332 
 PHE   0.026   0.003   PHE B  86 
 TYR   0.020   0.002   TYR D 150 
 ARG   0.006   0.001   ARG C 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03293 (  252)
  hydrogen bonds       : angle       5.13259 (  504)
  covalent geometry    : bond        0.00879 (23730)
  covalent geometry    : angle       1.02557 (32893)
  Misc. bond           : bond        0.17065 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 157
  time to evaluate  : 2.325 
Fit side-chains
REVERT: A  160 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8422 (t)
REVERT: A  314 ASP cc_start: 0.7875 (m-30) cc_final: 0.7569 (p0)
REVERT: A  342 MET cc_start: 0.8929 (tpp) cc_final: 0.8419 (ttm)
REVERT: B   85 ASP cc_start: 0.8141 (m-30) cc_final: 0.7624 (m-30)
REVERT: B  247 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.7933 (p-80)
REVERT: C   71 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7086 (mtm)
REVERT: C   85 ASP cc_start: 0.8219 (m-30) cc_final: 0.7600 (m-30)
REVERT: D   36 MET cc_start: 0.8928 (mmt) cc_final: 0.8669 (mmm)
REVERT: D   85 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7722 (m-30)
REVERT: D  138 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7282 (tt)
REVERT: D  221 THR cc_start: 0.8676 (t) cc_final: 0.8233 (p)
REVERT: D  340 ASP cc_start: 0.8727 (t0) cc_final: 0.8398 (t0)
REVERT: E  138 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7375 (tp)
REVERT: F  160 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8274 (t)
  outliers start: 98
  outliers final: 73
  residues processed: 233
  average time/residue: 0.2826
  time to fit residues: 115.9688
Evaluate side-chains
  225 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 145
  time to evaluate  : 2.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 CYS
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  247 HIS
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue    9 CYS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  247 HIS
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  351 PHE
Chi-restraints excluded: chain C residue    9 CYS
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   71 MET
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  245 ASP
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  331 CYS
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   85 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  253 THR
Chi-restraints excluded: chain D residue  331 CYS
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain D residue  390 ASP
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  124 THR
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  186 TYR
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  245 ASP
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  331 CYS
Chi-restraints excluded: chain E residue  337 SER
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  245 ASP
Chi-restraints excluded: chain F residue  331 CYS
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  377 VAL
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Chi-restraints excluded: chain G residue  331 CYS
Chi-restraints excluded: chain G residue  351 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 200 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 251 optimal weight:    5.9990
   chunk 216 optimal weight:    4.9990
   chunk 212 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 188 optimal weight:    7.9990
   chunk 194 optimal weight:   10.0000
   chunk 209 optimal weight:    0.2980
   chunk 276 optimal weight:   30.0000
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  25 ASN
** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  51 HIS
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  51 HIS
D  51 HIS
E  51 HIS
E 373 GLN
F  51 HIS
G 110 HIS
G 373 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.078785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.072277 restraints weight = 50986.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.074514 restraints weight = 21185.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.075857 restraints weight = 10930.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.208  23849  Z= 0.133
  Angle     :  0.769  14.625  32893  Z= 0.328
  Chirality :  0.043   0.168   3157
  Planarity :  0.004   0.048   4179
  Dihedral  : 15.154  89.825   3430
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.12 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.20 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.16), residues: 2835
  helix: -0.29 (0.30), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.69 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  95 
 HIS   0.006   0.001   HIS F 332 
 PHE   0.011   0.001   PHE E  86 
 TYR   0.012   0.001   TYR F 150 
 ARG   0.004   0.000   ARG F 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02682 (  252)
  hydrogen bonds       : angle       4.57050 (  504)
  covalent geometry    : bond        0.00393 (23730)
  covalent geometry    : angle       0.76898 (32893)
  Misc. bond           : bond        0.07390 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 188
  time to evaluate  : 4.415 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.7829 (m-30) cc_final: 0.7493 (p0)
REVERT: A  342 MET cc_start: 0.8933 (tpp) cc_final: 0.8321 (ttm)
REVERT: B  340 ASP cc_start: 0.8335 (t0) cc_final: 0.8057 (t0)
REVERT: B  354 ILE cc_start: 0.9070 (mm) cc_final: 0.8811 (mt)
REVERT: D   36 MET cc_start: 0.8908 (mmt) cc_final: 0.8617 (mmm)
REVERT: D  221 THR cc_start: 0.8610 (t) cc_final: 0.8332 (p)
REVERT: D  340 ASP cc_start: 0.8451 (t0) cc_final: 0.8192 (t0)
REVERT: E  138 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7294 (tp)
REVERT: E  189 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8051 (mt)
REVERT: F  160 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8411 (t)
REVERT: F  235 MET cc_start: 0.7966 (tpt) cc_final: 0.7501 (tpt)
REVERT: F  340 ASP cc_start: 0.8490 (t0) cc_final: 0.8227 (t0)
REVERT: G  149 LYS cc_start: 0.8219 (mttt) cc_final: 0.7743 (mmtt)
  outliers start: 71
  outliers final: 56
  residues processed: 241
  average time/residue: 0.3738
  time to fit residues: 158.6807
Evaluate side-chains
  220 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 161
  time to evaluate  : 2.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 CYS
Chi-restraints excluded: chain A residue   25 ASN
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue    9 CYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain C residue    9 CYS
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  331 CYS
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  253 THR
Chi-restraints excluded: chain D residue  331 CYS
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain D residue  390 ASP
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  124 THR
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  186 TYR
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  325 ASN
Chi-restraints excluded: chain E residue  331 CYS
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  331 CYS
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  362 ILE
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Chi-restraints excluded: chain G residue  331 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 243 optimal weight:    6.9990
   chunk 96 optimal weight:   20.0000
   chunk 134 optimal weight:    3.9990
   chunk 151 optimal weight:   20.0000
   chunk 174 optimal weight:    5.9990
   chunk 193 optimal weight:   30.0000
   chunk 91 optimal weight:   10.0000
   chunk 234 optimal weight:    9.9990
   chunk 175 optimal weight:    8.9990
   chunk 231 optimal weight:   30.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  25 ASN
** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 274 ASN
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.074884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.068382 restraints weight = 51735.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.070574 restraints weight = 21500.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.071904 restraints weight = 11153.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.301  23849  Z= 0.232
  Angle     :  0.892  17.839  32893  Z= 0.367
  Chirality :  0.046   0.179   3157
  Planarity :  0.005   0.050   4179
  Dihedral  : 15.400  89.465   3430
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 13.23 %
    Favored  : 86.53 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.57 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.16), residues: 2835
  helix: -0.42 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.71 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP G 238 
 HIS   0.009   0.001   HIS A 332 
 PHE   0.019   0.002   PHE B  86 
 TYR   0.016   0.001   TYR D 150 
 ARG   0.004   0.000   ARG D 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02938 (  252)
  hydrogen bonds       : angle       4.81878 (  504)
  covalent geometry    : bond        0.00635 (23730)
  covalent geometry    : angle       0.89157 (32893)
  Misc. bond           : bond        0.11928 (  119)

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

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

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5670 Ramachandran restraints generated.
    2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 162
  time to evaluate  : 2.482 
Fit side-chains
REVERT: A  314 ASP cc_start: 0.7856 (m-30) cc_final: 0.7463 (p0)
REVERT: A  342 MET cc_start: 0.8923 (tpp) cc_final: 0.8395 (ttm)
REVERT: B   85 ASP cc_start: 0.7978 (m-30) cc_final: 0.7666 (m-30)
REVERT: B  354 ILE cc_start: 0.9075 (mm) cc_final: 0.8815 (mt)
REVERT: C   85 ASP cc_start: 0.8123 (m-30) cc_final: 0.7518 (m-30)
REVERT: D   36 MET cc_start: 0.8813 (mmt) cc_final: 0.8595 (mmm)
REVERT: D  138 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7210 (tt)
REVERT: D  221 THR cc_start: 0.8728 (t) cc_final: 0.8296 (p)
REVERT: D  340 ASP cc_start: 0.8544 (t0) cc_final: 0.8309 (t0)
REVERT: E  138 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7365 (tp)
REVERT: F  118 ASN cc_start: 0.8278 (m-40) cc_final: 0.8034 (p0)
REVERT: F  160 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8316 (t)
REVERT: F  235 MET cc_start: 0.7824 (tpt) cc_final: 0.7452 (tpt)
  outliers start: 65
  outliers final: 59
  residues processed: 208
  average time/residue: 0.2731
  time to fit residues: 100.6683
Evaluate side-chains
  217 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 155
  time to evaluate  : 2.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 CYS
Chi-restraints excluded: chain A residue   25 ASN
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  331 CYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain B residue    9 CYS
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain C residue    9 CYS
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  331 CYS
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  247 HIS
Chi-restraints excluded: chain D residue  253 THR
Chi-restraints excluded: chain D residue  331 CYS
Chi-restraints excluded: chain D residue  351 PHE
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain D residue  390 ASP
Chi-restraints excluded: chain E residue    9 CYS
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  124 THR
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  186 TYR
Chi-restraints excluded: chain E residue  189 LEU
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  312 ILE
Chi-restraints excluded: chain E residue  325 ASN
Chi-restraints excluded: chain E residue  331 CYS
Chi-restraints excluded: chain E residue  351 PHE
Chi-restraints excluded: chain F residue    9 CYS
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  189 LEU
Chi-restraints excluded: chain F residue  274 ASN
Chi-restraints excluded: chain F residue  331 CYS
Chi-restraints excluded: chain F residue  351 PHE
Chi-restraints excluded: chain F residue  390 ASP
Chi-restraints excluded: chain G residue   24 MET
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  253 THR
Chi-restraints excluded: chain G residue  325 ASN
Chi-restraints excluded: chain G residue  331 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 280
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 89 optimal weight:    0.7980
   chunk 25 optimal weight:   30.0000
   chunk 74 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 145 optimal weight:   30.0000
   chunk 174 optimal weight:    0.0980
   chunk 71 optimal weight:    7.9990
   chunk 247 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    3.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  25 ASN
** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 GLN
** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 274 ASN
** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.078241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.071704 restraints weight = 51123.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.073933 restraints weight = 21347.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.075275 restraints weight = 11061.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.215  23849  Z= 0.147
  Angle     :  0.778  13.938  32893  Z= 0.331
  Chirality :  0.044   0.171   3157
  Planarity :  0.004   0.049   4179
  Dihedral  : 15.089  89.939   3430
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.93 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.52 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.16), residues: 2835
  helix: -0.26 (0.30), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.65 (0.13), residues: 2499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  95 
 HIS   0.005   0.001   HIS A 332 
 PHE   0.011   0.001   PHE F  86 
 TYR   0.013   0.001   TYR F 150 
 ARG   0.005   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02639 (  252)
  hydrogen bonds       : angle       4.55004 (  504)
  covalent geometry    : bond        0.00430 (23730)
  covalent geometry    : angle       0.77792 (32893)
  Misc. bond           : bond        0.08031 (  119)

===============================================================================
Job complete
usr+sys time: 6190.96 seconds
wall clock time: 114 minutes 27.57 seconds (6867.57 seconds total)