Starting phenix.real_space_refine
on Sat May 10 06:51:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8enq_28276/05_2025/8enq_28276.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8enq_28276/05_2025/8enq_28276.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8enq_28276/05_2025/8enq_28276.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8enq_28276/05_2025/8enq_28276.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8enq_28276/05_2025/8enq_28276.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8enq_28276/05_2025/8enq_28276.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    3304      2.51       5
     N    1029      2.21       5
     O    1239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5593
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Link IDs: {'TRANS': 110}
    Chain: "B"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Link IDs: {'TRANS': 110}
    Chain: "C"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Link IDs: {'TRANS': 110}
    Chain: "D"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Link IDs: {'TRANS': 110}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Link IDs: {'TRANS': 110}
    Chain: "F"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Link IDs: {'TRANS': 110}
    Chain: "G"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Link IDs: {'TRANS': 110}
  Time building chain proxies: 3.80, per 1000 atoms: 0.68
  Number of scatterers: 5593
  At special positions: 0
  Unit cell: (51.3474, 51.3474, 184.142, 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      21     16.00
     O    1239      8.00
     N    1029      7.00
     C    3304      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 670.1 milliseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1302

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 66.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 142
      removed outlier: 6.405A  pdb=" N   ASP A  67 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   LEU A  92 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   THR A  69 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   GLN A  94 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   THR A  71 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   GLY A  96 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   HIS A  73 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   GLU A  44 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   ILE A  70 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ASN A  46 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   GLN A  72 " --> pdb=" O   ASN A  46 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   TYR A  48 " --> pdb=" O   GLN A  72 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY A  74 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   TYR A  50 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   SER B 134 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ASN B 136 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   THR B 138 " --> pdb=" O   ILE A  47 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN A  49 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   CYS B 140 " --> pdb=" O   GLN A  49 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLY A  51 " --> pdb=" O   CYS B 140 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   PHE B 142 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ASP B  67 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LEU B  92 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   THR B  69 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   GLN B  94 " --> pdb=" O   THR B  69 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   THR B  71 " --> pdb=" O   GLN B  94 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   GLY B  96 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   HIS B  73 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   GLU B  44 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   ILE B  70 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ASN B  46 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   GLN B  72 " --> pdb=" O   ASN B  46 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   TYR B  48 " --> pdb=" O   GLN B  72 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   GLY B  74 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   TYR B  50 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 60
      removed outlier: 6.630A  pdb=" N   SER A  55 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   VAL A  81 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   GLN A  83 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LEU A  59 " --> pdb=" O   GLN A  83 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   SER A  85 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN A 107 " --> pdb=" O   GLY A  84 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASP A  86 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   LYS A 109 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   GLY A 123 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   ALA A 148 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ALA A 125 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   GLN A 150 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ASP A 127 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 150
      removed outlier: 6.526A  pdb=" N   GLY B 123 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   ALA B 148 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ALA B 125 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   GLN B 150 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ASP B 127 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   SER B 100 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   VAL B 126 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   THR B 102 " --> pdb=" O   VAL B 126 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   GLN B 128 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ASP B 104 " --> pdb=" O   GLN B 128 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASN B 107 " --> pdb=" O   GLY B  84 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   ASP B  86 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LYS B 109 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   SER B  55 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 8.058A  pdb=" N   GLN B  83 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU B  59 " --> pdb=" O   GLN B  83 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   SER B  85 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA B  56 " --> pdb=" O   GLN C  49 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLN C  49 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA B  58 " --> pdb=" O   ILE C  47 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ILE C  47 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLN B  60 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU C  45 " --> pdb=" O   GLN B  60 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP C  67 " --> pdb=" O   ILE C  90 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   LEU C  92 " --> pdb=" O   ASP C  67 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR C  69 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   GLN C  94 " --> pdb=" O   THR C  69 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   THR C  71 " --> pdb=" O   GLN C  94 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   GLY C  96 " --> pdb=" O   THR C  71 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   HIS C  73 " --> pdb=" O   GLY C  96 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   SER C 134 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   ILE D  47 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   ASN C 136 " --> pdb=" O   ILE D  47 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   GLN D  49 " --> pdb=" O   ASN C 136 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   THR C 138 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   GLY D  51 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   CYS C 140 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ASP D  67 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   LEU D  92 " --> pdb=" O   ASP D  67 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR D  69 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   GLN D  94 " --> pdb=" O   THR D  69 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   THR D  71 " --> pdb=" O   GLN D  94 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   GLY D  96 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   HIS D  73 " --> pdb=" O   GLY D  96 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLY E 123 " --> pdb=" O   ALA E 146 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   ALA E 148 " --> pdb=" O   GLY E 123 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA E 125 " --> pdb=" O   ALA E 148 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   GLN E 150 " --> pdb=" O   ALA E 125 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASP E 127 " --> pdb=" O   GLN E 150 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER E 100 " --> pdb=" O   ALA E 124 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   VAL E 126 " --> pdb=" O   SER E 100 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   THR E 102 " --> pdb=" O   VAL E 126 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   GLN E 128 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASP E 104 " --> pdb=" O   GLN E 128 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASN E 107 " --> pdb=" O   GLY E  84 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ASP E  86 " --> pdb=" O   ASN E 107 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LYS E 109 " --> pdb=" O   ASP E  86 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER E  55 " --> pdb=" O   ALA E  79 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   VAL E  81 " --> pdb=" O   SER E  55 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU E  57 " --> pdb=" O   VAL E  81 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   GLN E  83 " --> pdb=" O   LEU E  57 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU E  59 " --> pdb=" O   GLN E  83 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   SER E  85 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 60
      removed outlier: 6.572A  pdb=" N   SER C  55 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      removed outlier: 8.238A  pdb=" N   VAL C  81 " --> pdb=" O   SER C  55 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU C  57 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   GLN C  83 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU C  59 " --> pdb=" O   GLN C  83 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   SER C  85 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN C 107 " --> pdb=" O   GLY C  84 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP C  86 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LYS C 109 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   SER C 100 " --> pdb=" O   ALA C 124 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   VAL C 126 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   THR C 102 " --> pdb=" O   VAL C 126 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN C 128 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ASP C 104 " --> pdb=" O   GLN C 128 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 55 through 60
      removed outlier: 6.638A  pdb=" N   SER D  55 " --> pdb=" O   ALA D  79 " (cutoff:3.500A)
      removed outlier: 8.251A  pdb=" N   VAL D  81 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   LEU D  57 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   GLN D  83 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LEU D  59 " --> pdb=" O   GLN D  83 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   SER D  85 " --> pdb=" O   LEU D  59 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASN D 107 " --> pdb=" O   GLY D  84 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   ASP D  86 " --> pdb=" O   ASN D 107 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   LYS D 109 " --> pdb=" O   ASP D  86 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER D 100 " --> pdb=" O   ALA D 124 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   VAL D 126 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   THR D 102 " --> pdb=" O   VAL D 126 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   GLN D 128 " --> pdb=" O   THR D 102 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ASP D 104 " --> pdb=" O   GLN D 128 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN D 145 " --> pdb=" O   THR E 138 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ASP E  67 " --> pdb=" O   ILE E  90 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   LEU E  92 " --> pdb=" O   ASP E  67 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR E  69 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   GLN E  94 " --> pdb=" O   THR E  69 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   THR E  71 " --> pdb=" O   GLN E  94 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   GLY E  96 " --> pdb=" O   THR E  71 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   HIS E  73 " --> pdb=" O   GLY E  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 44 through 52
      removed outlier: 6.426A  pdb=" N   ASP F  67 " --> pdb=" O   ILE F  90 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   LEU F  92 " --> pdb=" O   ASP F  67 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   THR F  69 " --> pdb=" O   LEU F  92 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLN F  94 " --> pdb=" O   THR F  69 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   THR F  71 " --> pdb=" O   GLN F  94 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   GLY F  96 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   HIS F  73 " --> pdb=" O   GLY F  96 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY G  51 " --> pdb=" O   CYS F 140 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE F 142 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   GLU G  44 " --> pdb=" O   LEU G  68 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ILE G  70 " --> pdb=" O   GLU G  44 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ASN G  46 " --> pdb=" O   ILE G  70 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLN G  72 " --> pdb=" O   ASN G  46 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   TYR G  48 " --> pdb=" O   GLN G  72 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   GLY G  74 " --> pdb=" O   TYR G  48 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  74 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASP G  67 " --> pdb=" O   ILE G  90 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   LEU G  92 " --> pdb=" O   ASP G  67 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   THR G  69 " --> pdb=" O   LEU G  92 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   GLN G  94 " --> pdb=" O   THR G  69 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   THR G  71 " --> pdb=" O   GLN G  94 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   GLY G  96 " --> pdb=" O   THR G  71 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   HIS G  73 " --> pdb=" O   GLY G  96 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   SER G  89 " --> pdb=" O   MET G 113 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   VAL G 115 " --> pdb=" O   SER G  89 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ASP G  91 " --> pdb=" O   VAL G 115 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   GLN G 117 " --> pdb=" O   ASP G  91 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   THR G  93 " --> pdb=" O   GLN G 117 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   GLY G 119 " --> pdb=" O   THR G  93 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   ARG G  95 " --> pdb=" O   GLY G 119 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLU G 112 " --> pdb=" O   VAL G 135 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   VAL G 137 " --> pdb=" O   GLU G 112 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   THR G 114 " --> pdb=" O   VAL G 137 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   GLN G 139 " --> pdb=" O   THR G 114 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LYS G 116 " --> pdb=" O   GLN G 139 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   GLY G 141 " --> pdb=" O   LYS G 116 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   PHE G 118 " --> pdb=" O   GLY G 141 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 55 through 60
      removed outlier: 6.664A  pdb=" N   SER F  55 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   VAL F  81 " --> pdb=" O   SER F  55 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU F  57 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLN F  83 " --> pdb=" O   LEU F  57 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LEU F  59 " --> pdb=" O   GLN F  83 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   SER F  85 " --> pdb=" O   LEU F  59 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   GLY F  78 " --> pdb=" O   ALA F 101 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   LEU F 103 " --> pdb=" O   GLY F  78 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASP F  80 " --> pdb=" O   LEU F 103 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   GLN F 105 " --> pdb=" O   ASP F  80 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   GLY F  82 " --> pdb=" O   GLN F 105 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   ASN F 107 " --> pdb=" O   GLY F  82 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   GLY F  84 " --> pdb=" O   ASN F 107 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LYS F 109 " --> pdb=" O   GLY F  84 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ASP F  86 " --> pdb=" O   LYS F 109 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   SER F 100 " --> pdb=" O   ALA F 124 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   VAL F 126 " --> pdb=" O   SER F 100 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR F 102 " --> pdb=" O   VAL F 126 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   GLN F 128 " --> pdb=" O   THR F 102 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ASP F 104 " --> pdb=" O   GLN F 128 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLY F 123 " --> pdb=" O   ALA F 146 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ALA F 148 " --> pdb=" O   GLY F 123 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   ALA F 125 " --> pdb=" O   ALA F 148 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   GLN F 150 " --> pdb=" O   ALA F 125 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASP F 127 " --> pdb=" O   GLN F 150 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   ASN F 145 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ALA G  58 " --> pdb=" O   ASN F 145 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   THR F 147 " --> pdb=" O   ALA G  58 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   GLN G  60 " --> pdb=" O   THR F 147 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   HIS F 149 " --> pdb=" O   GLN G  60 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   SER G  55 " --> pdb=" O   ALA G  79 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   VAL G  81 " --> pdb=" O   SER G  55 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU G  57 " --> pdb=" O   VAL G  81 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLN G  83 " --> pdb=" O   LEU G  57 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LEU G  59 " --> pdb=" O   GLN G  83 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   SER G  85 " --> pdb=" O   LEU G  59 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   THR G  61 " --> pdb=" O   SER G  85 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   GLY G  78 " --> pdb=" O   ALA G 101 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   LEU G 103 " --> pdb=" O   GLY G  78 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ASP G  80 " --> pdb=" O   LEU G 103 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   GLN G 105 " --> pdb=" O   ASP G  80 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLY G  82 " --> pdb=" O   GLN G 105 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   ASN G 107 " --> pdb=" O   GLY G  82 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   GLY G  84 " --> pdb=" O   ASN G 107 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   LYS G 109 " --> pdb=" O   GLY G  84 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ASP G  86 " --> pdb=" O   LYS G 109 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   SER G 100 " --> pdb=" O   ALA G 124 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   VAL G 126 " --> pdb=" O   SER G 100 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   THR G 102 " --> pdb=" O   VAL G 126 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   GLN G 128 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ASP G 104 " --> pdb=" O   GLN G 128 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLY G 123 " --> pdb=" O   ALA G 146 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   ALA G 148 " --> pdb=" O   GLY G 123 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ALA G 125 " --> pdb=" O   ALA G 148 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   GLN G 150 " --> pdb=" O   ALA G 125 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ASP G 127 " --> pdb=" O   GLN G 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    199 hydrogen bonds defined for protein.
    579 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2058
        1.34 -     1.45: 734
        1.45 -     1.57: 2843
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 5663
  Sorted by residual:
  bond pdb=" CA  GLY F  82 "
       pdb=" C   GLY F  82 "
    ideal  model  delta    sigma   weight residual
    1.516  1.529 -0.013 8.10e-03 1.52e+04 2.67e+00
  bond pdb=" CA  ASN F 110 "
       pdb=" CB  ASN F 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.554 -0.023 1.48e-02 4.57e+03 2.49e+00
  bond pdb=" CB  PRO E  41 "
       pdb=" CG  PRO E  41 "
    ideal  model  delta    sigma   weight residual
    1.492  1.562 -0.070 5.00e-02 4.00e+02 1.96e+00
  bond pdb=" CB  GLU F  44 "
       pdb=" CG  GLU F  44 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.82e+00
  bond pdb=" CB  ASN C 145 "
       pdb=" CG  ASN C 145 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 2.50e-02 1.60e+03 1.63e+00
  ... (remaining 5658 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 7302
        1.57 -     3.15: 289
        3.15 -     4.72: 47
        4.72 -     6.30: 11
        6.30 -     7.87: 9
  Bond angle restraints: 7658
  Sorted by residual:
  angle pdb=" N   GLY A 119 "
        pdb=" CA  GLY A 119 "
        pdb=" C   GLY A 119 "
      ideal   model   delta    sigma   weight residual
     111.21  115.53   -4.32 1.04e+00 9.25e-01 1.72e+01
  angle pdb=" N   GLY C  75 "
        pdb=" CA  GLY C  75 "
        pdb=" C   GLY C  75 "
      ideal   model   delta    sigma   weight residual
     110.80  117.67   -6.87 1.71e+00 3.42e-01 1.61e+01
  angle pdb=" N   GLY D 119 "
        pdb=" CA  GLY D 119 "
        pdb=" C   GLY D 119 "
      ideal   model   delta    sigma   weight residual
     111.21  115.17   -3.96 1.04e+00 9.25e-01 1.45e+01
  angle pdb=" N   GLY A  75 "
        pdb=" CA  GLY A  75 "
        pdb=" C   GLY A  75 "
      ideal   model   delta    sigma   weight residual
     110.80  117.28   -6.48 1.71e+00 3.42e-01 1.43e+01
  angle pdb=" N   GLY C  52 "
        pdb=" CA  GLY C  52 "
        pdb=" C   GLY C  52 "
      ideal   model   delta    sigma   weight residual
     110.80  117.10   -6.30 1.71e+00 3.42e-01 1.36e+01
  ... (remaining 7653 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.07: 2908
       14.07 -    28.14: 218
       28.14 -    42.21: 77
       42.21 -    56.27: 28
       56.27 -    70.34: 17
  Dihedral angle restraints: 3248
    sinusoidal: 1155
      harmonic: 2093
  Sorted by residual:
  dihedral pdb=" CA  ASP D  62 "
           pdb=" C   ASP D  62 "
           pdb=" N   CYS D  63 "
           pdb=" CA  CYS D  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.49  -17.51     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  ASP C  62 "
           pdb=" C   ASP C  62 "
           pdb=" N   CYS C  63 "
           pdb=" CA  CYS C  63 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.62  -17.38     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  ASP F  62 "
           pdb=" C   ASP F  62 "
           pdb=" N   CYS F  63 "
           pdb=" CA  CYS F  63 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.30  -16.70     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 3245 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 503
       0.035 -    0.071: 219
       0.071 -    0.106: 61
       0.106 -    0.142: 19
       0.142 -    0.177: 10
  Chirality restraints: 812
  Sorted by residual:
  chirality pdb=" CA  TYR F  48 "
            pdb=" N   TYR F  48 "
            pdb=" C   TYR F  48 "
            pdb=" CB  TYR F  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.86e-01
  chirality pdb=" CA  TYR C  48 "
            pdb=" N   TYR C  48 "
            pdb=" C   TYR C  48 "
            pdb=" CB  TYR C  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" CA  ILE E  70 "
            pdb=" N   ILE E  70 "
            pdb=" C   ILE E  70 "
            pdb=" CB  ILE E  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.90e-01
  ... (remaining 809 not shown)

  Planarity restraints: 1078
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F  42 "    0.014 2.00e-02 2.50e+03   2.85e-02 8.15e+00
        pdb=" C   ASN F  42 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ASN F  42 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER F  43 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN G 105 "   -0.009 2.00e-02 2.50e+03   1.90e-02 3.63e+00
        pdb=" CD  GLN G 105 "    0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLN G 105 "   -0.012 2.00e-02 2.50e+03
        pdb=" NE2 GLN G 105 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN F  49 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.95e+00
        pdb=" CD  GLN F  49 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLN F  49 "    0.011 2.00e-02 2.50e+03
        pdb=" NE2 GLN F  49 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1075 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 861
        2.79 -     3.31: 5002
        3.31 -     3.84: 10502
        3.84 -     4.37: 12241
        4.37 -     4.90: 21351
  Nonbonded interactions: 49957
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 122 "
            pdb=" ND2 ASN D 144 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NE2 GLN B  49 "
            pdb=" OE1 GLN B  72 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" NE2 GLN E 128 "
            pdb=" OG  SER E 133 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OG  SER C  43 "
            pdb=" O   CYS C  63 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OG  SER G  43 "
            pdb=" O   CYS G  63 "
     model   vdw
     2.312 3.040
  ... (remaining 49952 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'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     16.180
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2978
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      :  0.004   0.070   5663  Z= 0.185
  Angle     :  0.768   7.871   7658  Z= 0.429
  Chirality :  0.046   0.177    812
  Planarity :  0.004   0.050   1078
  Dihedral  : 13.928  70.342   1946
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.27), residues: 763
  helix:  None (None), residues: 0
  sheet:  1.69 (0.19), residues: 609
  loop : -2.39 (0.31), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP G 106 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.013   0.002   PHE A 118 
 TYR   0.011   0.001   TYR A  50 
 ARG   0.005   0.001   ARG A  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12176 (  199)
  hydrogen bonds       : angle       7.06102 (  579)
  covalent geometry    : bond        0.00384 ( 5663)
  covalent geometry    : angle       0.76797 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   47 ILE cc_start: 0.5250 (mp) cc_final: 0.4805 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1804
  time to fit residues: 9.2224
Evaluate side-chains
  30 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.0980
   chunk 58 optimal weight:    9.9990
   chunk 32 optimal weight:    0.3980
   chunk 19 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 105 GLN
B  73 HIS
** E  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  46 ASN
F 132 ASN
G  46 ASN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6631 r_free = 0.6631 target = 0.491653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.7136 r_free = 0.7136 target = 0.438061 restraints weight = 5423.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.7166 r_free = 0.7166 target = 0.443379 restraints weight = 3132.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.7177 r_free = 0.7177 target = 0.446611 restraints weight = 1955.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.6613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3641
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5663  Z= 0.186
  Angle     :  0.679   8.103   7658  Z= 0.374
  Chirality :  0.045   0.149    812
  Planarity :  0.003   0.029   1078
  Dihedral  :  5.394  16.798    805
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  4.25 %
    Favored  : 93.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.30), residues: 763
  helix:  None (None), residues: 0
  sheet:  1.15 (0.20), residues: 595
  loop : -0.92 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 106 
 HIS   0.005   0.002   HIS E 149 
 PHE   0.014   0.002   PHE D 142 
 TYR   0.012   0.002   TYR C 151 
 ARG   0.012   0.001   ARG B  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (  199)
  hydrogen bonds       : angle       6.07459 (  579)
  covalent geometry    : bond        0.00379 ( 5663)
  covalent geometry    : angle       0.67930 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 34
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  128 GLN cc_start: 0.3509 (OUTLIER) cc_final: 0.3245 (tp40)
REVERT: G  113 MET cc_start: 0.5511 (tmm) cc_final: 0.5195 (ttt)
  outliers start: 14
  outliers final: 5
  residues processed: 44
  average time/residue: 0.1559
  time to fit residues: 9.7738
Evaluate side-chains
  29 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  100 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 26 optimal weight:   30.0000
   chunk 59 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  73 HIS
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN
** B  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  60 GLN
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  73 HIS
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  46 ASN
F  73 HIS
** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 136 ASN
** G  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 117 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6407 r_free = 0.6407 target = 0.452778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.7026 r_free = 0.7026 target = 0.372553 restraints weight = 5996.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.7050 r_free = 0.7050 target = 0.375373 restraints weight = 4464.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.7060 r_free = 0.7060 target = 0.377275 restraints weight = 3482.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.5775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4599
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.147   5663  Z= 0.415
  Angle     :  1.109  11.861   7658  Z= 0.619
  Chirality :  0.057   0.209    812
  Planarity :  0.007   0.042   1078
  Dihedral  :  8.216  26.964    805
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 30.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.24 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  7.31 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.29), residues: 763
  helix:  None (None), residues: 0
  sheet: -0.86 (0.20), residues: 582
  loop : -1.56 (0.45), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP D 106 
 HIS   0.010   0.003   HIS B  73 
 PHE   0.028   0.004   PHE D 142 
 TYR   0.021   0.003   TYR B  48 
 ARG   0.007   0.001   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06460 (  199)
  hydrogen bonds       : angle       7.82814 (  579)
  covalent geometry    : bond        0.00878 ( 5663)
  covalent geometry    : angle       1.10894 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.5860 (mt)
REVERT: D   95 ARG cc_start: 0.5129 (OUTLIER) cc_final: 0.4139 (tpt170)
REVERT: D  113 MET cc_start: 0.4813 (tpt) cc_final: 0.4154 (tpt)
REVERT: F  118 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.4703 (m-80)
  outliers start: 19
  outliers final: 10
  residues processed: 64
  average time/residue: 0.1606
  time to fit residues: 13.8484
Evaluate side-chains
  50 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 37
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  149 HIS
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   95 ARG
Chi-restraints excluded: chain E residue   72 GLN
Chi-restraints excluded: chain F residue   48 TYR
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  118 PHE
Chi-restraints excluded: chain G residue   66 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 76 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  73 HIS
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 117 GLN
** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  42 ASN
E 139 GLN
E 150 GLN
** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 139 GLN
** G  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  49 GLN
** G  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 105 GLN
G 139 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6411 r_free = 0.6411 target = 0.455278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.7015 r_free = 0.7015 target = 0.374828 restraints weight = 6165.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.7054 r_free = 0.7054 target = 0.378087 restraints weight = 4650.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.7081 r_free = 0.7081 target = 0.380255 restraints weight = 3657.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.6374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4748
moved from start:          0.6541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5663  Z= 0.242
  Angle     :  0.807   9.351   7658  Z= 0.445
  Chirality :  0.047   0.163    812
  Planarity :  0.004   0.019   1078
  Dihedral  :  7.069  22.468    805
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 23.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.88 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.29), residues: 763
  helix:  None (None), residues: 0
  sheet: -1.26 (0.21), residues: 582
  loop : -1.84 (0.41), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 106 
 HIS   0.011   0.003   HIS B 149 
 PHE   0.016   0.003   PHE E 118 
 TYR   0.015   0.002   TYR B  50 
 ARG   0.005   0.001   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04321 (  199)
  hydrogen bonds       : angle       7.11178 (  579)
  covalent geometry    : bond        0.00498 ( 5663)
  covalent geometry    : angle       0.80655 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 12
  residues processed: 54
  average time/residue: 0.1570
  time to fit residues: 11.7729
Evaluate side-chains
  48 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASN
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain B residue   50 TYR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  100 SER
Chi-restraints excluded: chain G residue  117 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    0.0970
   chunk 36 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 139 GLN
C 144 ASN
** D  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 117 GLN
** G  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6411 r_free = 0.6411 target = 0.456264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.7043 r_free = 0.7043 target = 0.370243 restraints weight = 6046.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.7050 r_free = 0.7050 target = 0.373941 restraints weight = 4288.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.7113 r_free = 0.7113 target = 0.377280 restraints weight = 3312.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.6369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4782
moved from start:          0.7088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5663  Z= 0.195
  Angle     :  0.730   8.532   7658  Z= 0.401
  Chirality :  0.045   0.167    812
  Planarity :  0.003   0.018   1078
  Dihedral  :  6.527  20.524    805
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 20.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 13.27 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.29), residues: 763
  helix:  None (None), residues: 0
  sheet: -1.39 (0.21), residues: 572
  loop : -1.95 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 106 
 HIS   0.009   0.002   HIS B 149 
 PHE   0.017   0.002   PHE A  97 
 TYR   0.012   0.001   TYR B  50 
 ARG   0.004   0.001   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  199)
  hydrogen bonds       : angle       6.93917 (  579)
  covalent geometry    : bond        0.00395 ( 5663)
  covalent geometry    : angle       0.72968 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  113 MET cc_start: 0.1788 (ttm) cc_final: 0.1103 (ttm)
REVERT: C  113 MET cc_start: 0.6091 (mmm) cc_final: 0.5855 (tpt)
REVERT: E  113 MET cc_start: 0.4009 (ptm) cc_final: 0.3750 (ptm)
REVERT: E  128 GLN cc_start: 0.5252 (OUTLIER) cc_final: 0.4623 (tp40)
REVERT: F  100 SER cc_start: 0.7542 (OUTLIER) cc_final: 0.6399 (t)
REVERT: F  118 PHE cc_start: 0.5302 (OUTLIER) cc_final: 0.4729 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 53
  average time/residue: 0.1552
  time to fit residues: 11.4611
Evaluate side-chains
  53 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain B residue   50 TYR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain E residue   72 GLN
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain F residue  100 SER
Chi-restraints excluded: chain F residue  118 PHE
Chi-restraints excluded: chain G residue  117 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 GLN
** D  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 150 GLN
** G  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6425 r_free = 0.6425 target = 0.460186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.7061 r_free = 0.7061 target = 0.375982 restraints weight = 6017.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.7095 r_free = 0.7095 target = 0.380447 restraints weight = 4153.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.7128 r_free = 0.7128 target = 0.383382 restraints weight = 3078.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.6384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4677
moved from start:          0.7287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5663  Z= 0.143
  Angle     :  0.635   8.164   7658  Z= 0.345
  Chirality :  0.043   0.144    812
  Planarity :  0.002   0.016   1078
  Dihedral  :  5.671  20.115    805
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.27 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.30), residues: 763
  helix:  None (None), residues: 0
  sheet: -1.34 (0.21), residues: 583
  loop : -1.71 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 106 
 HIS   0.004   0.001   HIS F  73 
 PHE   0.015   0.002   PHE C 118 
 TYR   0.013   0.001   TYR B  50 
 ARG   0.002   0.000   ARG A  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02892 (  199)
  hydrogen bonds       : angle       6.50827 (  579)
  covalent geometry    : bond        0.00291 ( 5663)
  covalent geometry    : angle       0.63490 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: B  113 MET cc_start: 0.1768 (ttm) cc_final: 0.1138 (ttm)
REVERT: B  127 ASP cc_start: 0.5520 (m-30) cc_final: 0.5284 (m-30)
REVERT: C  113 MET cc_start: 0.6147 (mmm) cc_final: 0.5912 (tpt)
REVERT: E  113 MET cc_start: 0.4091 (ptm) cc_final: 0.3843 (ptm)
REVERT: E  128 GLN cc_start: 0.4977 (OUTLIER) cc_final: 0.2979 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 52
  average time/residue: 0.1620
  time to fit residues: 11.7140
Evaluate side-chains
  51 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   46 ASN
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain F residue   48 TYR
Chi-restraints excluded: chain G residue  117 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 ASN
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 150 GLN
** G  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  94 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 = 0.6417 r_free = 0.6417 target = 0.460171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.7046 r_free = 0.7046 target = 0.374908 restraints weight = 6069.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.7094 r_free = 0.7094 target = 0.379449 restraints weight = 4231.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.7120 r_free = 0.7120 target = 0.382391 restraints weight = 3147.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.6373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4693
moved from start:          0.7564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5663  Z= 0.144
  Angle     :  0.638   8.478   7658  Z= 0.347
  Chirality :  0.043   0.151    812
  Planarity :  0.002   0.015   1078
  Dihedral  :  5.586  20.125    805
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.24 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.30), residues: 763
  helix:  None (None), residues: 0
  sheet: -1.33 (0.22), residues: 565
  loop : -1.63 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 106 
 HIS   0.004   0.001   HIS B 149 
 PHE   0.013   0.002   PHE G 118 
 TYR   0.011   0.001   TYR E  48 
 ARG   0.003   0.000   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02848 (  199)
  hydrogen bonds       : angle       6.57686 (  579)
  covalent geometry    : bond        0.00300 ( 5663)
  covalent geometry    : angle       0.63785 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
REVERT: B  113 MET cc_start: 0.1887 (ttm) cc_final: 0.1159 (ttm)
REVERT: B  127 ASP cc_start: 0.5791 (m-30) cc_final: 0.5537 (m-30)
REVERT: E  128 GLN cc_start: 0.4858 (OUTLIER) cc_final: 0.2935 (tm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 51
  average time/residue: 0.1656
  time to fit residues: 11.7075
Evaluate side-chains
  49 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   46 ASN
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain G residue  117 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 71 optimal weight:    0.8980
   chunk 45 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 ASN
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 HIS
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 150 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6336 r_free = 0.6336 target = 0.446093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 99)----------------|
| r_work = 0.6983 r_free = 0.6983 target = 0.350994 restraints weight = 6019.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.7013 r_free = 0.7013 target = 0.354246 restraints weight = 4617.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.7048 r_free = 0.7048 target = 0.356671 restraints weight = 3755.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.6280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5035
moved from start:          0.8453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5663  Z= 0.260
  Angle     :  0.860   9.651   7658  Z= 0.479
  Chirality :  0.048   0.197    812
  Planarity :  0.004   0.022   1078
  Dihedral  :  7.125  22.624    805
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 23.72
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 13.50 %
    Favored  : 86.37 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.76 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.28), residues: 763
  helix:  None (None), residues: 0
  sheet: -1.96 (0.21), residues: 541
  loop : -2.61 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP C 106 
 HIS   0.006   0.002   HIS F  73 
 PHE   0.017   0.003   PHE E 118 
 TYR   0.022   0.002   TYR F  48 
 ARG   0.006   0.001   ARG D  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04629 (  199)
  hydrogen bonds       : angle       7.39548 (  579)
  covalent geometry    : bond        0.00541 ( 5663)
  covalent geometry    : angle       0.86018 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 TYR cc_start: 0.3733 (OUTLIER) cc_final: 0.3010 (m-10)
REVERT: B  113 MET cc_start: 0.2407 (ttm) cc_final: 0.2035 (ttm)
REVERT: B  127 ASP cc_start: 0.5736 (m-30) cc_final: 0.5410 (m-30)
REVERT: C   66 SER cc_start: 0.6300 (OUTLIER) cc_final: 0.5989 (t)
REVERT: D  113 MET cc_start: 0.5478 (tmm) cc_final: 0.4426 (tpt)
REVERT: E  113 MET cc_start: 0.3733 (ptm) cc_final: 0.3462 (ptt)
REVERT: E  128 GLN cc_start: 0.5447 (OUTLIER) cc_final: 0.3592 (tm-30)
REVERT: F  118 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4430 (m-80)
REVERT: G  113 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5790 (tmm)
REVERT: G  127 ASP cc_start: 0.5972 (m-30) cc_final: 0.5683 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 60
  average time/residue: 0.1731
  time to fit residues: 14.0113
Evaluate side-chains
  57 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   99 ASN
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain B residue   50 TYR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain E residue   72 GLN
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue   48 TYR
Chi-restraints excluded: chain F residue  118 PHE
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  117 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 71 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 29 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
** B  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 GLN
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  73 HIS
** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  46 ASN
G  54 ASN
G  94 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6529 r_free = 0.6529 target = 0.599323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 171)---------------|
| r_work = 0.7409 r_free = 0.7409 target = 0.472922 restraints weight = 8511.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.7541 r_free = 0.7541 target = 0.474044 restraints weight = 9378.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.7543 r_free = 0.7543 target = 0.475135 restraints weight = 7423.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.6364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4718
moved from start:          0.8417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5663  Z= 0.139
  Angle     :  0.651   9.105   7658  Z= 0.353
  Chirality :  0.044   0.139    812
  Planarity :  0.002   0.012   1078
  Dihedral  :  5.731  20.688    805
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.80 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.28), residues: 763
  helix:  None (None), residues: 0
  sheet: -1.79 (0.21), residues: 553
  loop : -2.26 (0.35), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 106 
 HIS   0.004   0.001   HIS C  73 
 PHE   0.014   0.002   PHE F 118 
 TYR   0.016   0.002   TYR F  50 
 ARG   0.003   0.000   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02637 (  199)
  hydrogen bonds       : angle       6.76836 (  579)
  covalent geometry    : bond        0.00282 ( 5663)
  covalent geometry    : angle       0.65140 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: C   66 SER cc_start: 0.6158 (OUTLIER) cc_final: 0.5888 (t)
REVERT: C  113 MET cc_start: 0.5303 (tpt) cc_final: 0.5029 (tpt)
REVERT: D  113 MET cc_start: 0.5217 (tmm) cc_final: 0.4338 (tpt)
REVERT: E  113 MET cc_start: 0.3391 (ptm) cc_final: 0.2989 (ptt)
REVERT: E  128 GLN cc_start: 0.5054 (OUTLIER) cc_final: 0.3247 (tm-30)
REVERT: G  127 ASP cc_start: 0.6213 (m-30) cc_final: 0.5791 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 53
  average time/residue: 0.1641
  time to fit residues: 12.0423
Evaluate side-chains
  50 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue  127 ASP
Chi-restraints excluded: chain E residue  128 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 64 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   chunk 72 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 132 ASN
A 144 ASN
** B  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 144 ASN
** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6300 r_free = 0.6300 target = 0.437910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.6940 r_free = 0.6940 target = 0.339429 restraints weight = 6223.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.6962 r_free = 0.6962 target = 0.342069 restraints weight = 5138.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.6990 r_free = 0.6990 target = 0.343856 restraints weight = 4383.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.5562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5013
moved from start:          0.9377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   5663  Z= 0.313
  Angle     :  0.964  11.904   7658  Z= 0.535
  Chirality :  0.051   0.173    812
  Planarity :  0.005   0.023   1078
  Dihedral  :  7.682  24.581    805
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 26.92
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 15.47 %
    Favored  : 84.14 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.46 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.28), residues: 763
  helix:  None (None), residues: 0
  sheet: -2.45 (0.20), residues: 583
  loop : -2.55 (0.35), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP C 106 
 HIS   0.010   0.002   HIS G  73 
 PHE   0.020   0.004   PHE F 142 
 TYR   0.022   0.003   TYR F  48 
 ARG   0.007   0.001   ARG D  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05228 (  199)
  hydrogen bonds       : angle       7.84350 (  579)
  covalent geometry    : bond        0.00663 ( 5663)
  covalent geometry    : angle       0.96442 ( 7658)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 GLN cc_start: 0.6949 (tt0) cc_final: 0.6730 (tm-30)
REVERT: C   66 SER cc_start: 0.6170 (OUTLIER) cc_final: 0.5966 (t)
REVERT: D  113 MET cc_start: 0.5805 (tmm) cc_final: 0.4648 (tpt)
REVERT: E  113 MET cc_start: 0.3449 (ptm) cc_final: 0.2875 (ptt)
REVERT: E  128 GLN cc_start: 0.6095 (OUTLIER) cc_final: 0.4918 (tp-100)
REVERT: F  100 SER cc_start: 0.7329 (OUTLIER) cc_final: 0.6831 (t)
REVERT: G  113 MET cc_start: 0.5866 (OUTLIER) cc_final: 0.5331 (tmm)
REVERT: G  127 ASP cc_start: 0.5748 (m-30) cc_final: 0.5371 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 62
  average time/residue: 0.1761
  time to fit residues: 14.8884
Evaluate side-chains
  58 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain E residue   72 GLN
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue   48 TYR
Chi-restraints excluded: chain F residue  100 SER
Chi-restraints excluded: chain F residue  139 GLN
Chi-restraints excluded: chain G residue  113 MET
Chi-restraints excluded: chain G residue  117 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.6495 r_free = 0.6495 target = 0.590462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 164)---------------|
| r_work = 0.7310 r_free = 0.7310 target = 0.457699 restraints weight = 8532.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.7420 r_free = 0.7420 target = 0.459155 restraints weight = 10129.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.7453 r_free = 0.7453 target = 0.459853 restraints weight = 7804.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.6296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5013
moved from start:          0.9379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5663  Z= 0.185
  Angle     :  0.765  10.431   7658  Z= 0.416
  Chirality :  0.046   0.162    812
  Planarity :  0.003   0.013   1078
  Dihedral  :  6.717  22.360    805
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 22.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.99 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.28), residues: 763
  helix:  None (None), residues: 0
  sheet: -2.31 (0.20), residues: 569
  loop : -2.62 (0.34), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 106 
 HIS   0.005   0.001   HIS C  73 
 PHE   0.013   0.002   PHE C 118 
 TYR   0.015   0.002   TYR F  50 
 ARG   0.003   0.001   ARG D  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  199)
  hydrogen bonds       : angle       7.40180 (  579)
  covalent geometry    : bond        0.00387 ( 5663)
  covalent geometry    : angle       0.76549 ( 7658)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1874.58 seconds
wall clock time: 33 minutes 46.45 seconds (2026.45 seconds total)