Starting phenix.real_space_refine
on Sat Jun  7 21:13:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wur_32839/06_2025/7wur_32839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wur_32839/06_2025/7wur_32839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wur_32839/06_2025/7wur_32839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wur_32839/06_2025/7wur_32839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wur_32839/06_2025/7wur_32839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wur_32839/06_2025/7wur_32839.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 336 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5636      2.51       5
     N    1528      2.21       5
     O    1706      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 94 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8922
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2725
          Classifications: {'peptide': 341}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2725
          Classifications: {'peptide': 341}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321}
    Chain: "E"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 915
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 821
          Classifications: {'peptide': 108}
          Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96}
    Chain: "G"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 915
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
    Chain: "H"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 821
          Classifications: {'peptide': 108}
          Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96}
  Time building chain proxies: 5.89, per 1000 atoms: 0.66
  Number of scatterers: 8922
  At special positions: 0
  Unit cell: (84.48, 109.56, 162.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1706      8.00
     N    1528      7.00
     C    5636      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.19
  Conformation dependent library (CDL) restraints added in 947.8 milliseconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2072

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 20 sheets defined
      12.8% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 53
      removed outlier: 3.759A  pdb=" N   LEU A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A  46 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLN A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 82
      removed outlier: 3.808A  pdb=" N   ASN A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU A  66 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   TRP A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      Proline residue:  A  73  - end of helix
      removed outlier: 3.637A  pdb=" N   HIS A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.592A  pdb=" N   HIS A 229 " --> pdb=" O   PRO A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.501A  pdb=" N   ASN A 255 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 53
      removed outlier: 3.675A  pdb=" N   LEU B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLN B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B  49 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 70
      removed outlier: 3.749A  pdb=" N   ASN B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU B  66 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 82
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 3.552A  pdb=" N   HIS B 229 " --> pdb=" O   PRO B 226 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 230 " --> pdb=" O   LYS B 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 226 through 230'
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.561A  pdb=" N   ASN B 255 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.665A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
      removed outlier: 3.716A  pdb=" N   LYS E  65 " --> pdb=" O   ASP E  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 62 through 65'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.670A  pdb=" N   THR E  91 " --> pdb=" O   ASP E  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 84
      removed outlier: 3.841A  pdb=" N   PHE F  84 " --> pdb=" O   PRO F  81 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 32
      removed outlier: 3.815A  pdb=" N   TYR G  32 " --> pdb=" O   PHE G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 65
      removed outlier: 3.822A  pdb=" N   LYS G  65 " --> pdb=" O   ASP G  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 62 through 65'
    Processing helix  chain 'H' and resid 80 through 84
      removed outlier: 3.899A  pdb=" N   PHE H  84 " --> pdb=" O   PRO H  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.598A  pdb=" N   GLY A  56 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89
      removed outlier: 3.642A  pdb=" N   MET A  89 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155
    Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331
      removed outlier: 4.366A  pdb=" N   PHE A 277 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 9.168A  pdb=" N   GLU A 213 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   ILE A 212 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ALA A 205 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER A 216 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ARG A 192 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ARG B 192 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER B 216 " --> pdb=" O   TRP B 201 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   ALA B 205 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   ILE B 212 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 9.118A  pdb=" N   GLU B 213 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   PHE B 277 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287
      removed outlier: 5.996A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   CYS A 313 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   VAL A 286 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 89
      removed outlier: 3.563A  pdb=" N   MET B  89 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLY B  56 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 155
    Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287
      removed outlier: 5.990A  pdb=" N   THR B 284 " --> pdb=" O   TRP B 311 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   CYS B 313 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL B 286 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.089A  pdb=" N   TYR E 107 " --> pdb=" O   SER E  98 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLY E 109 " --> pdb=" O   CYS E  96 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   CYS E  96 " --> pdb=" O   GLY E 109 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   GLY E 111 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   TYR E  94 " --> pdb=" O   GLY E 111 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   LEU E 113 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ALA E  92 " --> pdb=" O   LEU E 113 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 5 through 6
    Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12
    Processing sheet with id=AB6, first strand: chain 'F' and resid 19 through 20
      removed outlier: 3.601A  pdb=" N   ASP F  71 " --> pdb=" O   SER F  68 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 7
    Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 12
      removed outlier: 4.135A  pdb=" N   TYR G 107 " --> pdb=" O   SER G  98 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLY G 109 " --> pdb=" O   CYS G  96 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   CYS G  96 " --> pdb=" O   GLY G 109 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLY G 111 " --> pdb=" O   TYR G  94 " (cutoff:3.500A)
      removed outlier: 5.249A  pdb=" N   TYR G  94 " --> pdb=" O   GLY G 111 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   LEU G 113 " --> pdb=" O   ALA G  92 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   ALA G  92 " --> pdb=" O   LEU G 113 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER G  49 " --> pdb=" O   TRP G  36 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   ARG G  38 " --> pdb=" O   TRP G  47 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   TRP G  47 " --> pdb=" O   ARG G  38 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.680A  pdb=" N   PHE H  72 " --> pdb=" O   CYS H  23 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA H  19 " --> pdb=" O   ILE H  76 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 7
      removed outlier: 3.680A  pdb=" N   PHE H  72 " --> pdb=" O   CYS H  23 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP H  71 " --> pdb=" O   SER H  68 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.247A  pdb=" N   LEU H  11 " --> pdb=" O   GLU H 107 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TYR H  87 " --> pdb=" O   THR H 104 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    564 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2870
        1.34 -     1.46: 2341
        1.46 -     1.58: 3867
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 9150
  Sorted by residual:
  bond pdb=" N   GLN B 107 "
       pdb=" CA  GLN B 107 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.66e+00
  bond pdb=" N   GLN A 107 "
       pdb=" CA  GLN A 107 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.44e+00
  bond pdb=" CA  ILE B 243 "
       pdb=" CB  ILE B 243 "
    ideal  model  delta    sigma   weight residual
    1.540  1.522  0.018 1.23e-02 6.61e+03 2.11e+00
  bond pdb=" CB  GLN A  70 "
       pdb=" CG  GLN A  70 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.80e+00
  bond pdb=" C   PRO A 106 "
       pdb=" N   GLN A 107 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.71e+00
  ... (remaining 9145 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 12279
        2.65 -     5.30: 111
        5.30 -     7.95: 11
        7.95 -    10.60: 5
       10.60 -    13.25: 4
  Bond angle restraints: 12410
  Sorted by residual:
  angle pdb=" C   PRO B 106 "
        pdb=" N   GLN B 107 "
        pdb=" CA  GLN B 107 "
      ideal   model   delta    sigma   weight residual
     121.70  133.13  -11.43 1.80e+00 3.09e-01 4.03e+01
  angle pdb=" C   PRO A 106 "
        pdb=" N   GLN A 107 "
        pdb=" CA  GLN A 107 "
      ideal   model   delta    sigma   weight residual
     121.70  132.97  -11.27 1.80e+00 3.09e-01 3.92e+01
  angle pdb=" CB  MET E  34 "
        pdb=" CG  MET E  34 "
        pdb=" SD  MET E  34 "
      ideal   model   delta    sigma   weight residual
     112.70  125.95  -13.25 3.00e+00 1.11e-01 1.95e+01
  angle pdb=" CA  GLN A  70 "
        pdb=" CB  GLN A  70 "
        pdb=" CG  GLN A  70 "
      ideal   model   delta    sigma   weight residual
     114.10  122.69   -8.59 2.00e+00 2.50e-01 1.84e+01
  angle pdb=" CB  MET B 198 "
        pdb=" CG  MET B 198 "
        pdb=" SD  MET B 198 "
      ideal   model   delta    sigma   weight residual
     112.70  124.65  -11.95 3.00e+00 1.11e-01 1.59e+01
  ... (remaining 12405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 4831
       17.32 -    34.64: 478
       34.64 -    51.97: 97
       51.97 -    69.29: 6
       69.29 -    86.61: 14
  Dihedral angle restraints: 5426
    sinusoidal: 2178
      harmonic: 3248
  Sorted by residual:
  dihedral pdb=" CA  LYS A  33 "
           pdb=" C   LYS A  33 "
           pdb=" N   PHE A  34 "
           pdb=" CA  PHE A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.37  -23.63     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CB  CYS B  55 "
           pdb=" SG  CYS B  55 "
           pdb=" SG  CYS B 143 "
           pdb=" CB  CYS B 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.21   37.21     1      1.00e+01 1.00e-02 1.95e+01
  dihedral pdb=" CA  LYS A 189 "
           pdb=" C   LYS A 189 "
           pdb=" N   ASP A 190 "
           pdb=" CA  ASP A 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.90   22.10     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 5423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1080
       0.049 -    0.097: 177
       0.097 -    0.146: 71
       0.146 -    0.194: 0
       0.194 -    0.243: 2
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CA  GLN A 107 "
            pdb=" N   GLN A 107 "
            pdb=" C   GLN A 107 "
            pdb=" CB  GLN A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  GLN B 107 "
            pdb=" N   GLN B 107 "
            pdb=" C   GLN B 107 "
            pdb=" CB  GLN B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  GLN E 110 "
            pdb=" N   GLN E 110 "
            pdb=" C   GLN E 110 "
            pdb=" CB  GLN E 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.22e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  20 "   -0.010 2.00e-02 2.50e+03   1.30e-02 2.96e+00
        pdb=" CG  PHE B  20 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  20 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  20 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  20 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  20 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  20 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  70 "    0.009 2.00e-02 2.50e+03   1.70e-02 2.90e+00
        pdb=" C   GLN A  70 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLN A  70 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A  71 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  72 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO A  73 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A  73 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  73 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1575 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 925
        2.75 -     3.29: 8826
        3.29 -     3.82: 14527
        3.82 -     4.36: 17416
        4.36 -     4.90: 29740
  Nonbonded interactions: 71434
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 281 "
            pdb=" OG  SER E  52 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OE2 GLU B 281 "
            pdb=" OG  SER G  52 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG1 THR A 288 "
            pdb=" OD1 ASP A 290 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" N   GLU E  89 "
            pdb=" OE1 GLU E  89 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OG  SER B 103 "
            pdb=" OE1 GLN B 175 "
     model   vdw
     2.247 3.040
  ... (remaining 71429 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.270
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
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      :  0.003   0.040   9166  Z= 0.134
  Angle     :  0.680  13.252  12442  Z= 0.386
  Chirality :  0.043   0.243   1330
  Planarity :  0.003   0.035   1578
  Dihedral  : 14.344  86.610   3306
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  9.86 %
    Favored  : 89.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.26), residues: 1122
  helix: -1.02 (0.57), residues: 68
  sheet: -0.59 (0.29), residues: 360
  loop : -1.20 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 108 
 HIS   0.001   0.000   HIS B 229 
 PHE   0.030   0.001   PHE B  20 
 TYR   0.011   0.001   TYR B  32 
 ARG   0.003   0.000   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28486 (  219)
  hydrogen bonds       : angle       9.75418 (  564)
  SS BOND              : bond        0.00125 (   16)
  SS BOND              : angle       0.46009 (   32)
  covalent geometry    : bond        0.00267 ( 9150)
  covalent geometry    : angle       0.67998 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8624 (tpp) cc_final: 0.8311 (tpt)
REVERT: A  333 MET cc_start: 0.8411 (mmm) cc_final: 0.7856 (mtt)
REVERT: E  110 GLN cc_start: 0.8508 (mp10) cc_final: 0.7686 (pp30)
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 0.2484
  time to fit residues: 25.2002
Evaluate side-chains
  67 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain F residue    3 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 86 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.063373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.046489 restraints weight = 41494.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.047976 restraints weight = 19861.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.048998 restraints weight = 13078.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9166  Z= 0.124
  Angle     :  0.625  12.048  12442  Z= 0.330
  Chirality :  0.043   0.231   1330
  Planarity :  0.004   0.030   1578
  Dihedral  :  4.873  47.988   1237
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.86 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.26), residues: 1122
  helix: -0.33 (0.59), residues: 72
  sheet: -0.43 (0.29), residues: 348
  loop : -1.27 (0.24), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 108 
 HIS   0.002   0.000   HIS B 195 
 PHE   0.018   0.001   PHE B  34 
 TYR   0.010   0.001   TYR B  32 
 ARG   0.003   0.000   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04700 (  219)
  hydrogen bonds       : angle       6.42274 (  564)
  SS BOND              : bond        0.00171 (   16)
  SS BOND              : angle       0.54899 (   32)
  covalent geometry    : bond        0.00264 ( 9150)
  covalent geometry    : angle       0.62506 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 ARG cc_start: 0.8554 (ptp90) cc_final: 0.8097 (pmt-80)
REVERT: B  272 ARG cc_start: 0.8443 (mtt90) cc_final: 0.8180 (ttm110)
  outliers start: 8
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2163
  time to fit residues: 22.6830
Evaluate side-chains
  68 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain H residue    3 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** B  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 GLN ** 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 = 0.3318 r_free = 0.3318 target = 0.059829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.042868 restraints weight = 43239.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.044330 restraints weight = 20646.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.045256 restraints weight = 13573.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.068   9166  Z= 0.367
  Angle     :  0.766  12.192  12442  Z= 0.400
  Chirality :  0.045   0.235   1330
  Planarity :  0.004   0.039   1578
  Dihedral  :  5.629  54.059   1234
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.32 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.26), residues: 1122
  helix:  0.09 (0.60), residues: 72
  sheet: -0.82 (0.30), residues: 334
  loop : -1.25 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 168 
 HIS   0.007   0.001   HIS B 195 
 PHE   0.016   0.002   PHE A  34 
 TYR   0.020   0.002   TYR H  87 
 ARG   0.005   0.001   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04758 (  219)
  hydrogen bonds       : angle       5.98896 (  564)
  SS BOND              : bond        0.00420 (   16)
  SS BOND              : angle       0.78732 (   32)
  covalent geometry    : bond        0.00815 ( 9150)
  covalent geometry    : angle       0.76570 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.9067 (pm20) cc_final: 0.8683 (pm20)
REVERT: B   34 PHE cc_start: 0.6500 (m-80) cc_final: 0.6195 (m-80)
REVERT: E   59 ASP cc_start: 0.8920 (t0) cc_final: 0.8455 (t0)
REVERT: E  100 TYR cc_start: 0.8220 (t80) cc_final: 0.7854 (t80)
REVERT: F    1 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8333 (tp30)
REVERT: F   91 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8850 (tm-30)
REVERT: G    3 GLN cc_start: 0.8126 (mp10) cc_final: 0.7850 (mp10)
  outliers start: 13
  outliers final: 8
  residues processed: 73
  average time/residue: 0.2624
  time to fit residues: 28.6200
Evaluate side-chains
  70 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  139 GLU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain F residue   91 GLN
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 107 optimal weight:    0.4980
   chunk 106 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   chunk 90 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0770
   chunk 91 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
B 254 HIS
** H  91 GLN ** 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 = 0.3397 r_free = 0.3397 target = 0.062448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.045642 restraints weight = 41197.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.047142 restraints weight = 19346.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.048164 restraints weight = 12605.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9166  Z= 0.113
  Angle     :  0.626  11.883  12442  Z= 0.327
  Chirality :  0.043   0.239   1330
  Planarity :  0.003   0.032   1578
  Dihedral  :  4.944  50.837   1233
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 13.96 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.26), residues: 1122
  helix:  0.24 (0.59), residues: 72
  sheet: -0.46 (0.30), residues: 318
  loop : -1.31 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 108 
 HIS   0.002   0.001   HIS B 195 
 PHE   0.032   0.001   PHE A  34 
 TYR   0.009   0.001   TYR H  92 
 ARG   0.004   0.000   ARG B 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03524 (  219)
  hydrogen bonds       : angle       5.63943 (  564)
  SS BOND              : bond        0.00175 (   16)
  SS BOND              : angle       0.50412 (   32)
  covalent geometry    : bond        0.00249 ( 9150)
  covalent geometry    : angle       0.62607 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.9001 (pm20) cc_final: 0.8692 (pm20)
REVERT: A   67 MET cc_start: 0.8585 (tpp) cc_final: 0.8328 (tpp)
REVERT: A  184 MET cc_start: 0.8613 (tpp) cc_final: 0.8220 (ttt)
REVERT: B   67 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7703 (tpp)
REVERT: B  123 MET cc_start: 0.8338 (tpt) cc_final: 0.7341 (tpp)
REVERT: E   59 ASP cc_start: 0.8387 (t0) cc_final: 0.8033 (t0)
REVERT: E   76 LYS cc_start: 0.9508 (ptpp) cc_final: 0.9290 (ptpp)
REVERT: G    3 GLN cc_start: 0.8019 (mp10) cc_final: 0.7808 (mp10)
  outliers start: 7
  outliers final: 5
  residues processed: 71
  average time/residue: 0.2149
  time to fit residues: 22.2713
Evaluate side-chains
  70 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 58 optimal weight:    0.0060
   chunk 5 optimal weight:    0.5980
   chunk 16 optimal weight:    8.9990
   chunk 89 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0040
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.9212

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** H  91 GLN ** 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 = 0.3395 r_free = 0.3395 target = 0.062417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.045365 restraints weight = 41462.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.046880 restraints weight = 19667.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.047891 restraints weight = 12900.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9166  Z= 0.123
  Angle     :  0.622  11.837  12442  Z= 0.321
  Chirality :  0.043   0.236   1330
  Planarity :  0.003   0.036   1578
  Dihedral  :  4.740  45.840   1233
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.89 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.26), residues: 1122
  helix:  0.21 (0.58), residues: 72
  sheet: -0.51 (0.30), residues: 330
  loop : -1.16 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 108 
 HIS   0.002   0.001   HIS B 195 
 PHE   0.011   0.001   PHE A  34 
 TYR   0.012   0.001   TYR A  32 
 ARG   0.009   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03422 (  219)
  hydrogen bonds       : angle       5.47283 (  564)
  SS BOND              : bond        0.00161 (   16)
  SS BOND              : angle       0.50197 (   32)
  covalent geometry    : bond        0.00274 ( 9150)
  covalent geometry    : angle       0.62180 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 1.061 
Fit side-chains
REVERT: A   47 GLN cc_start: 0.8994 (pm20) cc_final: 0.8723 (pm20)
REVERT: A   67 MET cc_start: 0.8384 (tpp) cc_final: 0.8139 (tpp)
REVERT: A   97 MET cc_start: 0.8823 (mmt) cc_final: 0.8433 (tpp)
REVERT: A  184 MET cc_start: 0.8479 (tpp) cc_final: 0.8008 (ttt)
REVERT: B   67 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7583 (tpp)
REVERT: B  123 MET cc_start: 0.8186 (tpt) cc_final: 0.7161 (tpp)
REVERT: E   59 ASP cc_start: 0.8367 (t0) cc_final: 0.7997 (t0)
REVERT: E   76 LYS cc_start: 0.9503 (ptpp) cc_final: 0.9275 (ptpp)
REVERT: F   79 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8714 (mm)
REVERT: G   59 ASP cc_start: 0.8915 (t0) cc_final: 0.8440 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1978
  time to fit residues: 22.0854
Evaluate side-chains
  68 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0770
   chunk 49 optimal weight:    8.9990
   chunk 91 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    1.9742

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** H  91 GLN ** 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 = 0.3365 r_free = 0.3365 target = 0.061377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.044234 restraints weight = 41883.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.045723 restraints weight = 20151.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.046700 restraints weight = 13318.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9166  Z= 0.186
  Angle     :  0.657  11.888  12442  Z= 0.339
  Chirality :  0.043   0.237   1330
  Planarity :  0.003   0.033   1578
  Dihedral  :  4.906  43.751   1233
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.02 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.26), residues: 1122
  helix:  0.46 (0.60), residues: 72
  sheet: -0.51 (0.31), residues: 318
  loop : -1.17 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 108 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.027   0.001   PHE B  20 
 TYR   0.013   0.001   TYR A  32 
 ARG   0.003   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  219)
  hydrogen bonds       : angle       5.45141 (  564)
  SS BOND              : bond        0.00230 (   16)
  SS BOND              : angle       0.55652 (   32)
  covalent geometry    : bond        0.00418 ( 9150)
  covalent geometry    : angle       0.65767 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A   47 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8683 (pm20)
REVERT: A  184 MET cc_start: 0.8567 (tpp) cc_final: 0.8165 (ttt)
REVERT: B   47 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8138 (pm20)
REVERT: B   67 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7400 (tpp)
REVERT: B  123 MET cc_start: 0.8392 (tpt) cc_final: 0.7505 (tpp)
REVERT: E   59 ASP cc_start: 0.8606 (t0) cc_final: 0.8171 (t0)
REVERT: E  110 GLN cc_start: 0.8535 (mp10) cc_final: 0.7735 (pp30)
REVERT: F   79 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8836 (mm)
REVERT: G   59 ASP cc_start: 0.9031 (t0) cc_final: 0.8492 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 73
  average time/residue: 0.1941
  time to fit residues: 21.0539
Evaluate side-chains
  73 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:   40.0000
   chunk 1 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
B  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.059756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.042939 restraints weight = 42762.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.044381 restraints weight = 20379.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.045329 restraints weight = 13408.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   9166  Z= 0.320
  Angle     :  0.751  12.061  12442  Z= 0.387
  Chirality :  0.045   0.241   1330
  Planarity :  0.004   0.035   1578
  Dihedral  :  5.396  44.807   1233
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.32 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.26), residues: 1122
  helix:  0.46 (0.59), residues: 72
  sheet: -0.60 (0.30), residues: 322
  loop : -1.25 (0.24), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 168 
 HIS   0.006   0.001   HIS B 195 
 PHE   0.012   0.001   PHE B 247 
 TYR   0.019   0.002   TYR A 323 
 ARG   0.005   0.001   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  219)
  hydrogen bonds       : angle       5.59515 (  564)
  SS BOND              : bond        0.00364 (   16)
  SS BOND              : angle       0.66233 (   32)
  covalent geometry    : bond        0.00714 ( 9150)
  covalent geometry    : angle       0.75150 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A   47 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8686 (pm20)
REVERT: B   47 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8181 (pm20)
REVERT: B   67 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7416 (tpp)
REVERT: B  123 MET cc_start: 0.8621 (tpt) cc_final: 0.8056 (tpp)
REVERT: E   59 ASP cc_start: 0.9055 (t0) cc_final: 0.8506 (t0)
REVERT: E  100 TYR cc_start: 0.8208 (t80) cc_final: 0.7810 (t80)
REVERT: F    1 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8234 (tp30)
REVERT: F   79 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8849 (mm)
REVERT: F   91 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8748 (tm-30)
REVERT: G   59 ASP cc_start: 0.9107 (t0) cc_final: 0.8886 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1997
  time to fit residues: 21.6220
Evaluate side-chains
  75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain F residue   91 GLN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 13 optimal weight:   10.0000
   chunk 73 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 68 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** H  91 GLN ** 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 = 0.3377 r_free = 0.3377 target = 0.061896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.044826 restraints weight = 42392.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.046329 restraints weight = 20196.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.047338 restraints weight = 13279.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9166  Z= 0.127
  Angle     :  0.651  11.873  12442  Z= 0.334
  Chirality :  0.044   0.236   1330
  Planarity :  0.003   0.036   1578
  Dihedral  :  4.893  39.544   1233
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.74 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.26), residues: 1122
  helix:  0.65 (0.60), residues: 72
  sheet: -0.67 (0.30), residues: 330
  loop : -1.06 (0.25), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 108 
 HIS   0.003   0.001   HIS B 229 
 PHE   0.028   0.001   PHE B  20 
 TYR   0.012   0.001   TYR A  32 
 ARG   0.003   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03416 (  219)
  hydrogen bonds       : angle       5.41372 (  564)
  SS BOND              : bond        0.00171 (   16)
  SS BOND              : angle       0.50052 (   32)
  covalent geometry    : bond        0.00285 ( 9150)
  covalent geometry    : angle       0.65150 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A   47 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8635 (pm20)
REVERT: A  184 MET cc_start: 0.8511 (ttm) cc_final: 0.8146 (ttm)
REVERT: B   47 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8380 (pp30)
REVERT: B  123 MET cc_start: 0.8567 (tpt) cc_final: 0.7878 (tpp)
REVERT: E   59 ASP cc_start: 0.8601 (t0) cc_final: 0.8161 (t0)
REVERT: E   65 LYS cc_start: 0.9443 (mmmm) cc_final: 0.9172 (mmmm)
REVERT: E  110 GLN cc_start: 0.8707 (mp10) cc_final: 0.7845 (pp30)
REVERT: F   79 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8837 (mm)
REVERT: G   59 ASP cc_start: 0.9061 (t0) cc_final: 0.8528 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 75
  average time/residue: 0.2426
  time to fit residues: 26.3539
Evaluate side-chains
  72 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 94 optimal weight:    0.2980
   chunk 86 optimal weight:    9.9990
   chunk 99 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** H  91 GLN ** 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 = 0.3374 r_free = 0.3374 target = 0.061734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.044753 restraints weight = 41902.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.046248 restraints weight = 20091.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.047231 restraints weight = 13295.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9166  Z= 0.141
  Angle     :  0.674  15.297  12442  Z= 0.342
  Chirality :  0.043   0.237   1330
  Planarity :  0.003   0.035   1578
  Dihedral  :  4.621  25.027   1230
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 17.66 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.26), residues: 1122
  helix:  0.89 (0.62), residues: 68
  sheet: -0.67 (0.30), residues: 330
  loop : -0.96 (0.25), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 108 
 HIS   0.003   0.001   HIS B 195 
 PHE   0.019   0.001   PHE A  34 
 TYR   0.016   0.001   TYR A  32 
 ARG   0.009   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  219)
  hydrogen bonds       : angle       5.38789 (  564)
  SS BOND              : bond        0.00177 (   16)
  SS BOND              : angle       0.50435 (   32)
  covalent geometry    : bond        0.00318 ( 9150)
  covalent geometry    : angle       0.67450 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 1.265 
Fit side-chains
REVERT: A   47 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8641 (pm20)
REVERT: A  184 MET cc_start: 0.8466 (ttm) cc_final: 0.8065 (ttm)
REVERT: B   47 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8366 (pp30)
REVERT: B  123 MET cc_start: 0.8586 (tpt) cc_final: 0.7910 (tpp)
REVERT: E   59 ASP cc_start: 0.8720 (t0) cc_final: 0.8292 (t0)
REVERT: E   65 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9156 (mmmm)
REVERT: E  110 GLN cc_start: 0.8645 (mp10) cc_final: 0.7890 (pp30)
REVERT: F   79 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8830 (mm)
REVERT: G   59 ASP cc_start: 0.9073 (t0) cc_final: 0.8521 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2540
  time to fit residues: 26.4388
Evaluate side-chains
  73 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   chunk 28 optimal weight:    0.1980
   chunk 56 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.062812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.045844 restraints weight = 41726.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.047347 restraints weight = 20047.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.048359 restraints weight = 13245.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9166  Z= 0.115
  Angle     :  0.687  23.328  12442  Z= 0.341
  Chirality :  0.043   0.236   1330
  Planarity :  0.004   0.040   1578
  Dihedral  :  4.444  24.141   1230
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 17.66 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.26), residues: 1122
  helix:  0.74 (0.61), residues: 68
  sheet: -0.54 (0.29), residues: 350
  loop : -0.97 (0.25), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A  68 
 HIS   0.002   0.001   HIS A  26 
 PHE   0.020   0.001   PHE A  34 
 TYR   0.017   0.001   TYR A  32 
 ARG   0.010   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03247 (  219)
  hydrogen bonds       : angle       5.38212 (  564)
  SS BOND              : bond        0.00156 (   16)
  SS BOND              : angle       0.51720 (   32)
  covalent geometry    : bond        0.00259 ( 9150)
  covalent geometry    : angle       0.68692 (12410)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8626 (pm20)
REVERT: A  184 MET cc_start: 0.8413 (ttm) cc_final: 0.7996 (ttm)
REVERT: B   47 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8375 (pp30)
REVERT: B  123 MET cc_start: 0.8589 (tpt) cc_final: 0.7917 (tpp)
REVERT: B  174 ARG cc_start: 0.8532 (ptt-90) cc_final: 0.8300 (pmt170)
REVERT: E   59 ASP cc_start: 0.8580 (t0) cc_final: 0.8192 (t0)
REVERT: E   65 LYS cc_start: 0.9419 (mmmm) cc_final: 0.9144 (mmmm)
REVERT: E  110 GLN cc_start: 0.8586 (mp10) cc_final: 0.7871 (pp30)
REVERT: F   79 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8813 (mm)
REVERT: G   59 ASP cc_start: 0.9024 (t0) cc_final: 0.8511 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 79
  average time/residue: 0.2218
  time to fit residues: 25.1972
Evaluate side-chains
  73 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 GLN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain B residue   47 GLN
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 5 optimal weight:    0.3980
   chunk 17 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0170
   chunk 32 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 86 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 55 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.4824

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
** H  91 GLN ** 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 = 0.3380 r_free = 0.3380 target = 0.061850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.044803 restraints weight = 42123.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.046295 restraints weight = 20336.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.047210 restraints weight = 13466.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9166  Z= 0.156
  Angle     :  0.671  11.913  12442  Z= 0.343
  Chirality :  0.044   0.252   1330
  Planarity :  0.004   0.042   1578
  Dihedral  :  4.510  24.365   1230
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 18.17 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 1.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.26), residues: 1122
  helix:  0.69 (0.62), residues: 68
  sheet: -0.53 (0.30), residues: 326
  loop : -0.92 (0.25), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  68 
 HIS   0.003   0.001   HIS B 195 
 PHE   0.006   0.001   PHE A 217 
 TYR   0.010   0.001   TYR A 323 
 ARG   0.010   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  219)
  hydrogen bonds       : angle       5.31223 (  564)
  SS BOND              : bond        0.00188 (   16)
  SS BOND              : angle       0.51788 (   32)
  covalent geometry    : bond        0.00353 ( 9150)
  covalent geometry    : angle       0.67156 (12410)

===============================================================================
Job complete
usr+sys time: 3163.15 seconds
wall clock time: 57 minutes 44.59 seconds (3464.59 seconds total)